@article {pmid38691215,
year = {2024},
author = {Tokash-Peters, AG and Niyonzima, JD and Kayirangwa, M and Muhayimana, S and Tokash, IW and Jabon, JD and Lopez, SG and Kearns, PJ and Woodhams, DC},
title = {Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {64},
pmid = {38691215},
issn = {1432-184X},
support = {DGE 1249946//Directorate for Biological Sciences/ ; 1950051//Directorate for Biological Sciences/ ; 1947684//National Science Foundation/ ; 1947684//National Science Foundation/ ; },
mesh = {Rwanda ; Animals ; *Microbiota ; *Culicidae/microbiology ; *Wolbachia/genetics/isolation & purification/classification ; *Bacteria/classification/genetics/isolation & purification ; Mosquito Vectors/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Serratia/genetics/isolation & purification/classification ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.},
}

Rwanda
Animals
*Microbiota
*Culicidae/microbiology
*Wolbachia/genetics/isolation & purification/classification
*Bacteria/classification/genetics/isolation & purification
Mosquito Vectors/microbiology
Female
Male
RNA, Ribosomal, 16S/genetics
Serratia/genetics/isolation & purification/classification
Electron Transport Complex IV/genetics
High-Throughput Nucleotide Sequencing

@article {pmid38691180,
year = {2024},
author = {Qiu, T and Fang, Q and Tian, X and Feng, Z and Cao, Y and Li, Y and Tu, Y and Bai, J and Liu, Y},
title = {Postnatal nighttime light exposure and infant temperament at age 12 months: mediating role of genus Akkermansia.},
journal = {European child & adolescent psychiatry},
volume = {},
number = {},
pages = {},
pmid = {38691180},
issn = {1435-165X},
abstract = {The gut microbiome has been reported to be associated with nighttime light (NTL) exposure and temperament. However, the specific role of infant gut microbiome plays in NTL exposure and temperament is unclear. This study investigated the potential mediating role of infants' gut microbiome in correlations between NTL exposure and temperament. Demographic information, stool samples, and temperament scores were collected from 40 infants. Temperament was evaluated using the Infants Behavior Questionnaire-Revised (IBQ-R). The gut microbiota was analyzed using 16S rRNA sequencing. Cumulative and lagged effects of NTL exposure were calculated based on residential address (NTLpoint) and a concentric 1 km radius buffer zone around the address (NTL1000m), respectively. Mediation models were utilized for assessing the mediating effects of the gut microbiome. The gut microbiome of infants with higher fear scores was characterized by a higher abundance of Akkermansia and Clostridium_sensu_stricto_1 and a lower abundance of Bacteroides. Mediation models indicated Akkermansia played a full mediating role in associations between NTLpoint, NTL1000m and fear in specific time periods. Genus Akkermansia explained 24.46% and 33.50% of associations between fear and cumulative exposure to NTLpoint and NTL1000m, respectively. This study provides evidence for the mediating role of Akkermansia between NTL exposure and fear. However, further experimental is required to elucidate the mechanisms through which the gut microbiome mediates between NTL exposure and temperament in infants.},
}

@article {pmid38691091,
year = {2024},
author = {Omar, WEW and Singh, G and McBain, AJ and Cruickshank, F and Radhakrishnan, H},
title = {Gut Microbiota Profiles in Myopes and Nonmyopes.},
journal = {Investigative ophthalmology & visual science},
volume = {65},
number = {5},
pages = {2},
doi = {10.1167/iovs.65.5.2},
pmid = {38691091},
issn = {1552-5783},
mesh = {Humans ; Male ; Adult ; Female ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Myopia/microbiology/physiopathology ; Bacteria/genetics/isolation & purification ; Young Adult ; Middle Aged ; DNA, Bacterial ; },
abstract = {PURPOSE: To identify compositional differences in the gut microbiome of nonmyopes (NM) and myopes using 16S ribosomal RNA sequencing and to investigate whether the microbiome may contribute to the onset or progression of the condition.

METHODS: Faecal samples were collected from 52 adult participants, of whom 23 were NM, 8 were progressive myopes (PM), and 21 were stable myopes (SM). The composition of the gut microbiota in each group was analysed using 16S ribosomal RNA gene sequencing.

RESULTS: There were no significant differences in alpha and beta diversity between the three groups (NM, PM, and SM). However, the distributions of Bifidobacterium, Bacteroides, Megamonas, Faecalibacterium, Coprococcus, Dorea, Roseburia, and Blautia were significantly higher in the myopes (SM and PM combined) when compared with emmetropes. The myopes exhibited significantly greater abundance of bacteria that are linked to the regulation of dopaminergic signalling, such as Clostridium, Ruminococcus, Bifidobacterium, and Bacteroides. Individuals with stable myopia were found to have a significantly higher proportion of Prevotella copri than those with progressive myopia. Bifidobacterium adolescentis, a gamma-aminobutyric acid (GABA)-producing bacterium, was significantly higher in all myopes than in NM and, in the comparison between SM and PM, it is significantly higher in SM. B. uniformis and B. fragilis, both GABA-producing Bacteroides, were present in relatively high abundance in all myopes and in SM compared with PM, respectively.

CONCLUSIONS: The presence of bacteria related to dopamine effect and GABA-producing bacteria in the gut microbiome of myopes may suggest a role of these microorganisms in the onset and progression of myopia.},
}

Humans
Male
Adult
Female
*Gastrointestinal Microbiome/physiology
*Feces/microbiology
*RNA, Ribosomal, 16S/genetics
Myopia/microbiology/physiopathology
Bacteria/genetics/isolation & purification
Young Adult
Middle Aged
DNA, Bacterial

@article {pmid38691018,
year = {2024},
author = {Brickman, CE and Agnello, M and Imam, N and Camejo, P and Pino, R and Carroll, LN and Chein, A and Palefsky, JM},
title = {Distinct anal microbiome is correlated with anal cancer precursors in men who have sex with men living with HIV.},
journal = {AIDS (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAD.0000000000003920},
pmid = {38691018},
issn = {1473-5571},
abstract = {OBJECTIVES: Anal cancer risk is elevated in men who have sex with men living with HIV (MSMLWH). Anal high-risk human papillomavirus (hr-HPV) infection is necessary but insufficient to develop high-grade squamous intraepithelial lesion (HSIL), the anal cancer precursor, suggesting additional factors. We sought to determine whether the microbiome of the anal canal is distinct by comparing it with the microbiome of stool. We also sought to determine whether changes in the anal microbiome are associated with HSIL among MSMLWH.

DESIGN: Cross-sectional comparison of the microbiome of the anal canal with the microbiome of stool in MSMLWH and cross-sectional comparison of the anal microbiome of MSMLWH with anal HSIL with the anal microbiome of MSMLWH without anal HSIL.

METHODS: Sterile swabs were used to sample the anus of MSMLWH for microbiome and HPV testing, followed by high-resolution anoscopy. Stool samples were mailed from home. 16S sequencing was used for bacterial identification. Measures of alpha diversity, beta diversity and differential abundance analysis were used to compare samples.

RESULTS: 166 anal samples and 103 matching stool samples were sequenced. Beta diversity showed clustering of stool and anal samples. Of hr-HPV-positive MSMLWH, 31 had HSIL and 13 had no SIL. Comparison of the microbiome between these revealed 28 different species. The highest-fold enrichment among MSMLWH/hr-HPV/HSIL included pro-inflammatory and carcinogenic Prevotella, Parasuterella, Hungatella, Sneathia and Fusobacterium species. The anti-inflammatory Anaerostipes caccae showed the greatest reduction among MSMLWH/hr-HPV/HSIL.

CONCLUSIONS: The anal microbiome is distinct from stool. A pro-inflammatory and carcinogenic environment may be associated with anal HSIL.},
}

@article {pmid38690877,
year = {2024},
author = {Guo, J and Jia, P and Gu, Z and Tang, W and Wang, A and Sun, Y and Li, Z},
title = {Altered gut microbiota and metabolite profiles provide clues in understanding resistant hypertension.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000003716},
pmid = {38690877},
issn = {1473-5598},
abstract = {BACKGROUND: Resistant hypertension is a severe phenotype in hypertension that may be driven by interactions between genetic and environmental factors. Specific changes in gut microbiota and metabolites have been shown to influence cardiovascular disease progression. However, microbial and metabolomic changes associated with resistant hypertension remain elusive.

METHODS: In this study, the gut microbiome of 30 participants with resistant hypertension, 30 with controlled hypertension, and 30 nonhypertension was characterized using 16S rRNA amplicon sequencing. In addition, the serum metabolome of the same population was assessed by untargeted metabolomics.

RESULTS: The alpha diversity of microbiome in the resistant hypertension decreased, and changes were also observed in the composition of the gut microbiota. The resistant hypertension group was characterized by elevated levels of Actinobacteitia and Proteobacteria. Twenty-three genera were found to have significantly different abundances between resistant hypertension and controlled hypertension, as well as 55 genera with significantly different abundances between resistant hypertension and nonhypertension. Compared with the controlled hypertension group, the genera Rothia and Sharpea in resistant hypertension were more abundant. Compared with the nonhypertension group, the genera Escherichia-Shigella, Lactobacillus, Enterococcus were more abundant. Untargeted metabolomics provided distinctly different serum metabolic profiles for the three groups and identified a range of differential metabolites. These metabolites were mainly associated with the pathway of glycerophospholipid metabolism. Furthermore, correlation analysis provided evidence of new interactions between gut microbiota and metabolites in the resistant hypertension.

CONCLUSION: In conclusion, our study provides a comprehensive understanding of the resistant hypertension gut microbiota and metabolites, suggesting that treatment resistance in resistant hypertension patients may be related to the gut microbiota and serum metabolites.},
}

@article {pmid38690563,
year = {2024},
author = {Karaman, I and Pathak, A and Bayik, D and Watson, DC},
title = {Harnessing Bacterial Extracellular Vesicle Immune Effects for Cancer Therapy.},
journal = {Pathogens & immunity},
volume = {9},
number = {1},
pages = {56-90},
pmid = {38690563},
issn = {2469-2964},
abstract = {There are a growing number of studies linking the composition of the human microbiome to disease states and treatment responses, especially in the context of cancer. This has raised significant interest in developing microbes and microbial products as cancer immunotherapeutics that mimic or recapitulate the beneficial effects of host-microbe interactions. Bacterial extracellular vesicles (bEVs) are nano-sized, membrane-bound particles secreted by essentially all bacteria species and contain a diverse bioactive cargo of the producing cell. They have a fundamental role in facilitating interactions among cells of the same species, different microbial species, and even with multicellular host organisms in the context of colonization (microbiome) and infection. The interaction of bEVs with the immune system has been studied extensively in the context of infection and suggests that bEV effects depend largely on the producing species. They thus provide functional diversity, while also being nonreplicative, having inherent cell-targeting qualities, and potentially overcoming natural barriers. These characteristics make them highly appealing for development as cancer immunotherapeutics. Both natively secreted and engineered bEVs are now being investigated for their application as immunotherapeutics, vaccines, drug delivery vehicles, and combinations of the above, with promising early results. This suggests that both the intrinsic immunomodulatory properties of bEVs and their ability to be modified could be harnessed for the development of next-generation microbe-inspired therapies. Nonetheless, there remain major outstanding questions regarding how the observed preclinical effectiveness will translate from murine models to primates, and humans in particular. Moreover, research into the pharmacology, toxicology, and mass manufacturing of this potential novel therapeutic platform is still at early stages. In this review, we highlight the breadth of bEV interactions with host cells, focusing on immunologic effects as the main mechanism of action of bEVs currently in preclinical development. We review the literature on ongoing efforts to develop natively secreted and engineered bEVs from a variety of bacterial species for cancer therapy and finally discuss efforts to overcome outstanding challenges that remain for clinical translation.},
}

@article {pmid38690496,
year = {2024},
author = {Boyapati, R and Lanke, RB and Mudaliyar, MC and Gaddam, B and Babu Dasari, A and Dhulipalla, R},
title = {Exploring the Microbiome Landscape of Dental Plaque: A Cross-Sectional Analysis in Periodontal Health and Disease.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e57334},
pmid = {38690496},
issn = {2168-8184},
abstract = {OBJECTIVE: This study aimed to comprehensively analyze the microbiome of dental plaque in individuals with varying periodontal statuses, encompassing both periodontal health and disease. The primary objectives were to identify microbial markers associated with different clinical conditions, explore variations in microbial diversity, and investigate potential correlations between the oral microbiome and clinical parameters.

METHODS: A cross-sectional design was employed, involving 164 participants aged 18 to 65 years. Inclusion criteria comprised individuals with good oral and systemic health for the periodontal health group and those diagnosed with various stages of periodontal disease for the periodontal disease group. Dental plaque samples were meticulously collected from diverse tooth surfaces, and clinical examinations were conducted to assess periodontal health status. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene was utilized for microbiome analysis.

RESULTS: Demographic characteristics revealed a balanced distribution between the periodontal health and disease groups. Clinical parameters, including probing depth, clinical attachment loss, and bleeding on probing, exhibited significant differences between the two groups (p < 0.001). Microbial diversity indices indicated a higher diversity in the periodontal health group compared to the disease group (p < 0.001). Analysis of relative abundance of bacterial phyla identified significant variations, with Firmicutes, Bacteroidetes, and Actinobacteria showing differential prevalence between health and disease (p < 0.05). Differentially abundant taxa analysis highlighted specific species associated with each clinical condition, including Prevotella intermedia and Porphyromonas gingivalis. Network analysis revealed complex microbial interactions within the oral microbiome. Functional predictions indicated variations in metabolic capabilities between health and disease, with potential implications for virulence and antibiotic resistance.

CONCLUSION: This study provides a comprehensive analysis of the oral microbiome in periodontal health and disease, revealing significant associations between microbial composition and clinical parameters. The identification of microbial markers and functional insights enhances our understanding of the complex interplay within the oral ecosystem. These findings hold promise for advancing diagnostic and therapeutic approaches tailored to individual microbial profiles.},
}

@article {pmid38690424,
year = {2024},
author = {Gattlen, C and Frank, KR and Marie, DN and Trompette, A and Chriqui, LE and Hao, Y and Abdelnour, E and Gonzalez, M and Krueger, T and Dyson, PJ and Siankevich, S and von Garnier, C and Ubags, NDJ and Cavin, S and Perentes, JY},
title = {Use of a novel microbiome modulator improves anticancer immunity in a murine model of malignant pleural mesothelioma.},
journal = {JTCVS open},
volume = {18},
number = {},
pages = {324-344},
pmid = {38690424},
issn = {2666-2736},
abstract = {OBJECTIVE: Malignant pleural mesothelioma is a fatal disease and a clinical challenge, as few effective treatment modalities are available. Previous evidence links the gut microbiome to the host immunoreactivity to tumors. We thus evaluated the impact of a novel microbiome modulator compound (MMC) on the gut microbiota composition, tumor immune microenvironment, and cancer control in a model of malignant pleural mesothelioma.

METHODS: Age- and weight-matched immunocompetent (n = 23) or athymic BALB/c mice (n = 15) were randomly assigned to MMC or no treatment (control) groups. MMC (31 ppm) was administered through the drinking water 14 days before AB12 malignant mesothelioma cell inoculation into the pleural cavity. The impact of MMC on tumor growth, animal survival, tumor-infiltrating leucocytes, gut microbiome, and fecal metabolome was evaluated and compared with those of control animals.

RESULTS: The MMC delayed tumor growth and significantly prolonged the survival of immunocompetent animals (P = .0015) but not that of athymic mice. The improved tumor control in immunocompetent mice correlated with increased infiltration of CD3[+]CD8[+]GRZB[+] cytotoxic T lymphocytes in tumors. Gut microbiota analyses indicated an enrichment in producers of short chain fatty acids in MMC-treated animals. Finally, we observed a positive correlation between the level of fecal short chain fatty acids and abundance of tumor-infiltrating cytotoxic T cells in malignant pleural mesothelioma.

CONCLUSIONS: MMC administration boosts antitumor immunity, which correlates with a change in gut microbiome and metabolome. MMC may represent a valuable treatment option to combine with immunotherapy in patients with cancer.},
}

@article {pmid38690418,
year = {2024},
author = {},
title = {Discussion to: Use of a novel microbiome modulator improves anticancer immunity in a murine model of malignant pleural mesothelioma.},
journal = {JTCVS open},
volume = {18},
number = {},
pages = {345-346},
doi = {10.1016/j.xjon.2024.02.013},
pmid = {38690418},
issn = {2666-2736},
}

@article {pmid38690371,
year = {2024},
author = {Bowron, LA and Acosta, N and Thornton, CS and Carpentero, J and Waddell, BM and Bharadwaj, L and Ebbert, K and Castañeda-Mogollón, D and Conly, JM and Rabin, HR and Surette, MG and Parkins, MD},
title = {The airway microbiome of persons with cystic fibrosis correlates with acquisition and microbiological outcomes of incident Stenotrophomonas maltophilia infection.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1353145},
pmid = {38690371},
issn = {1664-302X},
abstract = {RATIONALE: Chronic infection with Stenotrophomonas maltophilia in persons with cystic fibrosis (pwCF) has been linked to an increased risk of pulmonary exacerbations and lung function decline. We sought to establish whether baseline sputum microbiome associates with risk of S. maltophilia incident infection and persistence in pwCF.

METHODS: pwCF experiencing incident S. maltophilia infections attending the Calgary Adult CF Clinic from 2010-2018 were compared with S. maltophilia-negative sex, age (+/-2 years), and birth-cohort-matched controls. Infection outcomes were classified as persistent (when the pathogen was recovered in ≥50% of cultures in the subsequent year) or transient. We assessed microbial communities from prospectively biobanked sputum using V3-V4 16S ribosomal RNA (rRNA) gene sequencing, in the year preceding (Pre) (n = 57), at (At) (n = 22), and after (Post) (n = 31) incident infection. We verified relative abundance data using S. maltophilia-specific qPCR and 16S rRNA-targeted qPCR to assess bioburden. Strains were typed using pulse-field gel electrophoresis.

RESULTS: Twenty-five pwCF with incident S. maltophilia (56% female, median 29 years, median FEV1 61%) with 33 total episodes were compared with 56 uninfected pwCF controls. Demographics and clinical characteristics were similar between cohorts. Among those with incident S. maltophilia infection, sputum communities did not cluster based on infection timeline (Pre, At, Post). Communities differed between the infection cohort and controls (n = 56) based on Shannon Diversity Index (SDI, p = 0.04) and clustered based on Aitchison distance (PERMANOVA, p = 0.01) prior to infection. At the time of incident S. maltophilia isolation, communities did not differ in SDI but clustered based on Aitchison distance (PERMANOVA, p = 0.03) in those that ultimately developed persistent infection versus those that were transient. S. maltophilia abundance within sputum was increased in samples from patients (Pre) relative to controls, measuring both relative (p = 0.004) and absolute (p = 0.001). Furthermore, S. maltophilia abundance was increased in sputum at incident infection in those who ultimately developed persistent infection relative to those with transient infection, measured relatively (p = 0.04) or absolute (p = 0.04), respectively.

CONCLUSION: Microbial community composition of CF sputum associates with S. maltophilia infection acquisition as well as infection outcome. Our study suggests sputum microbiome may serve as a surrogate for identifying infection risk and persistence risk.},
}

@article {pmid38690359,
year = {2024},
author = {Liu, Y and Azad, MAK and Zhao, X and Kong, X},
title = {Crude protein content in diets associated with intestinal microbiome and metabolome alteration in Huanjiang mini-pigs during different growth stages.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1398919},
pmid = {38690359},
issn = {1664-302X},
abstract = {INTRODUCTION: Adequate crude protein (CP) content in diets plays a crucial role in the intestinal health of the animal. This study investigated the impacts of CP content in diets on the intestinal microbiome and metabolome profiles in growing Huanjiang mini-pigs.

METHODS: A total of 360 pigs with similar body weight (BW) were allocated for three independent feeding trials based on three different BW stages, including (i) 5-10 kg BW, diets consisting of 14, 16, 18, 20, and 22% CP content; (ii) 10-20 kg BW, diets consisting of 12, 14, 16, 18, and 20% CP content; and (iii) 20-30 kg BW, diets consisting of 10, 12, 14, 16, and 18% CP content. These experiments lasted 28, 28, and 26 days, respectively.

RESULTS: The results showed that the Shannon and Simpson indices were decreased (p < 0.05) in the ileum of pigs in response to the 14-18% CP compared with the 20% CP content at 5-10 kg BW stage, while diets containing 12 and 14% CP had higher Chao1 (p < 0.05) and Shannon (p = 0.054) indices compared with 18% CP at 20-30 kg BW stage. Compared with the 20% CP, the diet containing 16% CP displayed an increasing trend (p = 0.089) of Firmicutes abundance but had decreased (p = 0.056) Actinobacteria abundance in the jejunum at 5-10 kg BW stage. In addition, a diet containing 16% CP had higher Lactobacillus abundance in the jejunum and ileum compared with the 18, 20, and 22% CP, while had lower Sphingomonas and Pelomonas abundances in the jejunum and Streptococcus abundance in the ileum compared with the diet containing 22% CP (p < 0.05). Diets containing lower CP content altered differential metabolites in the small intestine at the early stage, while higher CP content had less impact.

CONCLUSION: These findings suggest that a diet containing lower CP content (16% CP) may be an appropriate dietary CP content for 5-10 kg Huanjiang mini-pigs, as 16% CP content in diet has shown beneficial impacts on the intestinal microbiome and metabolome profiles at the early growth stage of pigs.},
}

@article {pmid38690357,
year = {2024},
author = {Rolland, C and Burzan, N and Leupin, OX and Boylan, AA and Frutschi, M and Wang, S and Jacquemin, N and Bernier-Latmani, R},
title = {Microbial hydrogen sinks in the sand-bentonite backfill material for the deep geological disposal of radioactive waste.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1359677},
pmid = {38690357},
issn = {1664-302X},
abstract = {The activity of subsurface microorganisms can be harnessed for engineering projects. For instance, the Swiss radioactive waste repository design can take advantage of indigenous microorganisms to tackle the issue of a hydrogen gas (H2) phase pressure build-up. After repository closure, it is expected that anoxic steel corrosion of waste canisters will lead to an H2 accumulation. This occurrence should be avoided to preclude damage to the structural integrity of the host rock. In the Swiss design, the repository access galleries will be back-filled, and the choice of this material provides an opportunity to select conditions for the microbially-mediated removal of excess gas. Here, we investigate the microbial sinks for H2. Four reactors containing an 80/20 (w/w) mixture of quartz sand and Wyoming bentonite were supplied with natural sulfate-rich Opalinus Clay rock porewater and with pure H2 gas for up to 108 days. Within 14 days, a decrease in the sulfate concentration was observed, indicating the activity of the sulfate-reducing bacteria detected in the reactor, e.g., from Desulfocurvibacter genus. Additionally, starting at day 28, methane was detected in the gas phase, suggesting the activity of methanogens present in the solid phase, such as the Methanosarcina genus. This work evidences the development, under in-situ relevant conditions, of a backfill microbiome capable of consuming H2 and demonstrates its potential to contribute positively to the long-term safety of a radioactive waste repository.},
}

@article {pmid38690316,
year = {2024},
author = {Rivera-Lopez, EO and Nieves-Morales, R and Melendez-Martinez, G and Paez-Diaz, JA and Rodriguez-Carrio, SM and Rodriguez-Ramos, J and Morales-Valle, L and Rios-Velazquez, C},
title = {Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110421},
pmid = {38690316},
issn = {2352-3409},
abstract = {The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.},
}

@article {pmid38690290,
year = {2024},
author = {Paudel, D and Nair, DVT and Joseph, G and Castro, R and Tiwari, AK and Singh, V},
title = {Gastrointestinal microbiota-directed nutritional and therapeutic interventions for inflammatory bowel disease: opportunities and challenges.},
journal = {Gastroenterology report},
volume = {12},
number = {},
pages = {goae033},
pmid = {38690290},
issn = {2052-0034},
abstract = {Evidence-based research has confirmed the role of gastrointestinal microbiota in regulating intestinal inflammation. These data have generated interest in developing microbiota-based therapies for the prevention and management of inflammatory bowel disease (IBD). Despite in-depth understanding of the etiology of IBD, it currently lacks a cure and requires ongoing management. Accumulating data suggest that an aberrant gastrointestinal microbiome, often referred to as dysbiosis, is a significant environmental instigator of IBD. Novel microbiome-targeted interventions including prebiotics, probiotics, fecal microbiota transplant, and small molecule microbiome modulators are being evaluated as therapeutic interventions to attenuate intestinal inflammation by restoring a healthy microbiota composition and function. In this review, the effectiveness and challenges of microbiome-centered interventions that have the potential to alleviate intestinal inflammation and improve clinical outcomes of IBD are explored.},
}

@article {pmid38689990,
year = {2024},
author = {Wei, J and Zhang, L and Xu, H and Luo, Q},
title = {Preterm birth, a consequence of immune deviation mediated hyperinflammation.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e28483},
pmid = {38689990},
issn = {2405-8440},
abstract = {Preterm birth represents a multifaceted syndrome with intricacies still present in our comprehension of its etiology. In the context of a semi-allograft, the prosperity from implantation to pregnancy to delivery hinges on the establishment of a favorable maternal-fetal immune microenvironment and a successful trilogy of immune activation, immune tolerance and then immune activation transitions. The occurrence of spontaneous preterm birth could be related to abnormalities within the immune trilogy, stemming from deviation in maternal and fetal immunity. These immune deviations, characterized by insufficient immune tolerance and early immune activation, ultimately culminated in an unsustainable pregnancy. In this review, we accentuated the role of both innate and adaptive immune reason in promoting spontaneous preterm birth, reviewed the risk of preterm birth from vaginal microbiome mediated by immune changes and the potential of vaginal microbiomes and metabolites as a new predictive marker, and discuss the changes in the role of progesterone and its interaction with immune cells in a preterm birth population. Our objective was to contribute to the growing body of knowledge in the field, shedding light on the immunologic reason of spontaneous preterm birth and effective biomarkers for early prediction, providing a roadmap for forthcoming investigations.},
}

@article {pmid38689534,
year = {2024},
author = {Walsh, M and Martindale, R},
title = {A review of perioperative immune-modulating and metabolic-modulating nutrition strategies for bowel resection surgery.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.2634},
pmid = {38689534},
issn = {1941-2444},
abstract = {Focused perioperative nutrition strategies have proven benefits on the outcomes for patients undergoing major abdominal surgery. In this brief article, we will review these strategies and the evidence to support them with a focus on gastrointestinal anastomotic healing. We will elaborate the risks and benefits of enteral feeds, immune- and metabolic-modulating formulas, prebiotics and probiotics, and prehabilitation in preparation for surgery. Additionally, we will discuss the role of fish oils (eicosapentaenoic acid and docosahexaenoic acid) in the surgical patient and new data on specialized proresolving mediators in inflammation resolution. Finally, this article will consider the harmful impact surgical trauma has on the microbiome and the potential for perioperative dietary modulation to attenuate these negative effects.},
}

@article {pmid38689488,
year = {2024},
author = {Salahi, A and Abd El-Ghany, WA},
title = {Beyond probiotics, uses of their next-generation for poultry and humans: A review.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.13972},
pmid = {38689488},
issn = {1439-0396},
abstract = {The production of healthy food is one of the basic requirements and challenges. Research efforts have been introduced in the human's food industry to reduce the microbial resistance and use safe and healthy alternatives with a high durability. However, the conducted work about these issues in the field of livestock animal production have been started since 2015. Inappropriate and extensive use of antibiotics has resulted in the increase of antimicrobial resistance, presence of drug residues in tissues, and destruction of the gut microbiome. Therefore, discovering and developing antibiotic substitutes were urgent demands. Probiotic compounds containing living micro-organisms are important antibiotic alternative that have been beneficially and extensively used in humans, animals, and poultry. However, some probiotics show some obstacles during production and applications. Accordingly, this review article proposes a comprehensive description of the next-generation of probiotics including postbiotics, proteobiotics, psychobiotics, immunobiotics and paraprobiotics and their effects on poultry production and human's therapy. These compounds proved great efficiency in terms of restoring gut health, improving performance and general health conditions, modulating the immune response and reducing the pathogenic micro-organisms. However, more future research work should be carried out regarding this issue.},
}

@article {pmid38689371,
year = {2024},
author = {Gooch, HCC and Labedan, M and Hall, LJ and Maxwell, A},
title = {Transplanting human infant gut microbiome species into Galleria mellonella.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {123},
pmid = {38689371},
issn = {1756-0500},
support = {NC/R001782/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; BB/P012523/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P012523/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P012523/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; *Moths/microbiology ; *Larva/microbiology ; Infant ; *Feces/microbiology ; Bifidobacterium/isolation & purification ; Enterococcus/isolation & purification ; },
abstract = {OBJECTIVE: Study of the human infant gut microbiome requires the use of surrogate mammalian species such as mice. We sought to investigate the usefulness of the greater wax moth larva, Galleria mellonella, as an alternative.

RESULTS: We have analysed the native gut microbiome of Galleria and developed methods for clearing the native microbiome and introducing species from human infant faecal samples. We find that some species, e.g. enterococci, are more successful at recolonisation, but that others, e.g. Bifidobacterium, are less so. The work paves the way for using Galleria rather than mice in this and similar work.},
}

Animals
*Gastrointestinal Microbiome/physiology
Humans
*Moths/microbiology
*Larva/microbiology
Infant
*Feces/microbiology
Bifidobacterium/isolation & purification
Enterococcus/isolation & purification

@article {pmid38689349,
year = {2024},
author = {Zhang, X and Zhang, F and Li, Y and Fan, N and Zhao, K and Zhang, A and Kang, J and Lin, Y and Xue, X and Jiang, X},
title = {Blockade of PI3K/AKT signaling pathway by Astragaloside IV attenuates ulcerative colitis via improving the intestinal epithelial barrier.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {406},
pmid = {38689349},
issn = {1479-5876},
support = {Grant No.: 82270563//National Natural Science Foundation of China/ ; Grant No.:82000522//National Natural Science Foundation of China/ ; Grant No.: GK202205010//Fundamental Research Funds for the Central Universities/ ; Grant No.: 2021-01-ZZ-017//Shaanxi Administration of Traditional Chinese Medicine/ ; },
mesh = {Animals ; Humans ; Male ; Mice ; Caco-2 Cells ; *Colitis, Ulcerative/drug therapy/pathology/metabolism ; *Intestinal Mucosa/drug effects/pathology/metabolism ; *Mice, Inbred C57BL ; *Phosphatidylinositol 3-Kinases/metabolism ; *Proto-Oncogene Proteins c-akt/metabolism ; *Saponins/pharmacology/therapeutic use ; *Signal Transduction/drug effects ; *Triterpenes/pharmacology/therapeutic use ; },
abstract = {BACKGROUND: The specific pathogenesis of UC is still unclear, but it has been clear that defects in intestinal barrier function play an important role in it. There is a temporary lack of specific drugs for clinical treatment. Astragaloside IV (AS-IV) is one of the main active ingredients extracted from Astragalus root and is a common Chinese herbal medicine for the treatment of gastrointestinal diseases. This study aimed to determine whether AS-IV has therapeutic value for DSS or LPS-induced intestinal epithelial barrier dysfunction in vivo and in vitro and its potential molecular mechanisms.

METHODS: The intestinal tissues from UC patients and colitis mice were collected, intestinal inflammation was observed by colonoscopy, and mucosal barrier function was measured by immunofluorescence staining. PI3K/AKT signaling pathway activator YS-49 and inhibitor LY-29 were administered to colitic mice to uncover the effect of this pathway on gut mucosal barrier modulation. Then, network pharmacology was used to screen Astragaloside IV (AS-IV), a core active component of the traditional Chinese medicine Astragalus membranaceus. The potential of AS-IV for intestinal barrier function repairment and UC treatment through blockade of the PI3K/AKT pathway was further confirmed by histopathological staining, FITC-dextran, transmission electron microscopy, ELISA, immunofluorescence, qRT-PCR, and western blotting. Finally, 16 S rRNA sequencing was performed to uncover whether AS-IV can ameliorate UC by regulating gut microbiota homeostasis.

RESULTS: Mucosal barrier function was significantly damaged in UC patients and murine colitis, and the activated PI3K/AKT signaling pathway was extensively involved. Both in vivo and vitro showed that the AS-IV-treated group significantly relieved inflammation and improved intestinal epithelial permeability by inhibiting the activation of the PI3K/AKT signaling pathway. In addition, microbiome data found that gut microbiota participates in AS-IV-mediated intestinal barrier recovery as well.

CONCLUSIONS: Our study highlights that AS-IV exerts a protective effect on the integrality of the mucosal barrier in UC based on the PI3K/AKT pathway, and AS-IV may serve as a novel AKT inhibitor to provide a potential therapy for UC.},
}

Animals
Humans
Male
Mice
Caco-2 Cells
*Colitis, Ulcerative/drug therapy/pathology/metabolism
*Intestinal Mucosa/drug effects/pathology/metabolism
*Mice, Inbred C57BL
*Phosphatidylinositol 3-Kinases/metabolism
*Proto-Oncogene Proteins c-akt/metabolism
*Saponins/pharmacology/therapeutic use
*Signal Transduction/drug effects
*Triterpenes/pharmacology/therapeutic use

@article {pmid38689099,
year = {2024},
author = {Agustinho, DP and Fu, Y and Menon, VK and Metcalf, GA and Treangen, TJ and Sedlazeck, FJ},
title = {Unveiling microbial diversity: harnessing long-read sequencing technology.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {38689099},
issn = {1548-7105},
support = {1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; III-2239114//National Science Foundation (NSF)/ ; EF-2126387//National Science Foundation (NSF)/ ; III-2239114//National Science Foundation (NSF)/ ; },
abstract = {Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.},
}

@article {pmid38689063,
year = {2024},
author = {Tito, RY and Verbandt, S and Aguirre Vazquez, M and Lahti, L and Verspecht, C and Lloréns-Rico, V and Vieira-Silva, S and Arts, J and Falony, G and Dekker, E and Reumers, J and Tejpar, S and Raes, J},
title = {Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {38689063},
issn = {1546-170X},
abstract = {Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80 years, mean 57.7 years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.},
}

@article {pmid38689061,
year = {2024},
author = {Jiao, N and Zhu, L and Zhu, R},
title = {The search for authentic microbiome-disease relationships.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {38689061},
issn = {1546-170X},
}

@article {pmid38688923,
year = {2024},
author = {Miyajima, Y and Karashima, S and Mizoguchi, R and Kawakami, M and Ogura, K and Ogai, K and Koshida, A and Ikagawa, Y and Ami, Y and Zhu, Q and Tsujiguchi, H and Hara, A and Kurihara, S and Arakawa, H and Nakamura, H and Tamai, I and Nambo, H and Okamoto, S},
title = {Prediction and causal inference of hyperuricemia using gut microbiota.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9901},
pmid = {38688923},
issn = {2045-2322},
support = {JP19K17956//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Hyperuricemia/microbiology/blood ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; *Machine Learning ; *Uric Acid/blood ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Middle Aged ; },
abstract = {Hyperuricemia (HUA) is a symptom of high blood uric acid (UA) levels, which causes disorders such as gout and renal urinary calculus. Prolonged HUA is often associated with hypertension, atherosclerosis, diabetes mellitus, and chronic kidney disease. Studies have shown that gut microbiota (GM) affect these chronic diseases. This study aimed to determine the relationship between HUA and GM. The microbiome of 224 men and 254 women aged 40 years was analyzed through next-generation sequencing and machine learning. We obtained GM data through 16S rRNA-based sequencing of the fecal samples, finding that alpha-diversity by Shannon index was significantly low in the HUA group. Linear discriminant effect size analysis detected a high abundance of the genera Collinsella and Faecalibacterium in the HUA and non-HUA groups. Based on light gradient boosting machine learning, we propose that HUA can be predicted with high AUC using four clinical characteristics and the relative abundance of nine bacterial genera, including Collinsella and Dorea. In addition, analysis of causal relationships using a direct linear non-Gaussian acyclic model indicated a positive effect of the relative abundance of the genus Collinsella on blood UA levels. Our results suggest abundant Collinsella in the gut can increase blood UA levels.},
}

Humans
*Gastrointestinal Microbiome
*Hyperuricemia/microbiology/blood
Male
Female
Adult
*RNA, Ribosomal, 16S/genetics
*Machine Learning
*Uric Acid/blood
Feces/microbiology
High-Throughput Nucleotide Sequencing
Middle Aged

@article {pmid38687802,
year = {2024},
author = {Shen, X and Zhu, X and Liu, H and Yuan, R and Guo, Q and Zhao, P},
title = {Leveraging genomic signatures of oral microbiome-associated antibiotic resistance genes for diagnosing pancreatic cancer.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302361},
pmid = {38687802},
issn = {1932-6203},
mesh = {Humans ; *Pancreatic Neoplasms/genetics/microbiology/diagnosis ; *Microbiota/genetics ; *Carcinoma, Pancreatic Ductal/genetics/microbiology/diagnosis ; Female ; Male ; Mouth/microbiology ; Middle Aged ; Drug Resistance, Microbial/genetics ; Aged ; Genomics/methods ; },
abstract = {Growing evidence has increasingly suggested a potential linkage between the oral microbiome and various diseases, including pancreatic ductal adenocarcinoma (PDAC). However, the utilization of gene-level information derived from the oral microbiome for diagnosing PDAC remains unexplored. In this study, we sought to investigate the novel potential of leveraging genomic signatures associated with antibiotic resistance genes (ARGs) within the oral microbiome for the diagnosis of PDAC. By conducting an analysis of oral microbiome samples obtained from PDAC patients, we successfully identified specific ARGs that displayed distinct sequence abundance profiles correlated with the presence of PDAC. In the healthy group, three ARGs were found to be enriched, whereas 21 ARGs were enriched in PDAC patients. Remarkably, these ARGs from oral microbiome exhibited promising diagnostic capabilities for PDAC (AUROC = 0.79), providing a non-invasive and early detection method. Our findings not only provide novel modal data for diagnosing PDAC but also shed light on the intricate interplay between the oral microbiome and PDAC.},
}

Humans
*Pancreatic Neoplasms/genetics/microbiology/diagnosis
*Microbiota/genetics
*Carcinoma, Pancreatic Ductal/genetics/microbiology/diagnosis
Female
Male
Mouth/microbiology
Middle Aged
Drug Resistance, Microbial/genetics
Aged
Genomics/methods

@article {pmid38687451,
year = {2024},
author = {Hidalgo-Martinez, K and Giachini, AJ and Schneider, M and Soriano, A and Baessa, MP and Martins, LF and de Oliveira, VM},
title = {Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38687451},
issn = {1614-7499},
support = {860/2020//Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS)/ ; },
abstract = {The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.},
}

@article {pmid38687183,
year = {2024},
author = {Yan, Y and Zhao, QH and Xu, C and Wei, RQ and Jiang, H and Liu, SJ},
title = {Anaerolentibacter hominis gen. nov. sp. nov., Diplocloster hominis sp. nov. and Pilosibacter fragilis gen. nov. sp. nov., isolated from human faeces.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {4},
pages = {},
doi = {10.1099/ijsem.0.006359},
pmid = {38687183},
issn = {1466-5034},
mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Base Composition ; *DNA, Bacterial/genetics ; Humans ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; Fatty Acids/analysis ; Genome, Bacterial ; Whole Genome Sequencing ; },
abstract = {Three Gram-positive, obligately anaerobic bacterial strains, namely CSJ-1[T], CSJ-3[T], and CSJ-4[T], were isolated from faeces of healthy persons. They were characterized through a combination of whole-genome sequencing, phenotypic traits, and metabolomic analysis. The genome sizes of CSJ-1[T], CSJ-4[T], and CSJ-3[T] were 3.3, 3.8, and 6.1 Mbp, with DNA G+C contents of 47.2, 48.3, and 48.8 mol%, respectively. Strain CSJ-3[T] was identified as representing a novel species, Diplocloster hominis (type strain CSJ-3[T]=CGMCC 1.18033[T]=JCM 36512[T]) of the genus Diplocloster. The 16S rRNA gene sequence similarity and whole genome average nucleotide identity (gANI) of CSJ-4[T] to its closest related species, Diplocloster modestus ASD 4241[T], were 98.3 and 91.4 %, respectively. Comparative analysis of 16S rRNA gene sequences showed 91.6 % similarity between CSJ-1[T] and its closest phylogenetic neighbour, Catenibacillus scindens DSM 106146[T], and 93.3 % similarity between CSJ-4[T] and its closest relative strain, Clostridium fessum SNUG30386[T]. Based on the polyphasic taxonomic results, we proposed two novel genera and three novel species. Strain CSJ-1[T] was identified as representing a novel species of novel genus, Anaerolentibacter hominis gen. nov. sp. nov. (type strain CSJ-1[T]=CGMCC 1.18046[T]=JCM 36511[T]) of the family Lachnospiraceae, and strain CSJ-4[T] was identified as representing a novel species of novel genus Pilosibacter fragilis gen. nov. sp. nov. (type strain CSJ-4[T]=CGMCC 1.18026[T]= JCM 36513[T]) of the family Clostridiaceae.},
}

*Phylogeny
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Base Composition
*DNA, Bacterial/genetics
Humans
*Bacterial Typing Techniques
*Sequence Analysis, DNA
Fatty Acids/analysis
Genome, Bacterial
Whole Genome Sequencing

@article {pmid38687072,
year = {2024},
author = {Nagpal, S and Mande, SS and Hooda, H and Dutta, U and Taneja, B},
title = {EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0415023},
doi = {10.1128/spectrum.04150-23},
pmid = {38687072},
issn = {2165-0497},
abstract = {UNLABELLED: Bacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon-based microbiome studies have generally paid skewed attention, that too at a rather shallow genus level resolution, to the highly abundant bacteriome, with interest now forking toward the other microorganisms, particularly fungi. Given the generally sparse abundance of other microbes in the total microbiome, simultaneous sequencing of amplicons targeting multiple microbial kingdoms could be possible even with full multiplexing. Guiding studies are currently needed for performing and monitoring multi-kingdom-amplicon sequencing and data capture at scale. Aiming to address these gaps, amplification of full-length bacterial 16S rRNA gene and entire fungal internal-transcribed spacer (ITS) region was performed for human saliva samples (n = 96, including negative and positive controls). Combined amplicon DNA libraries were prepared for nanopore sequencing using a major fraction of 16S molecules and a minor fraction of ITS amplicons. Sequencing was performed in a single run of an R10.4.1 flow cell employing the latest V14 chemistry. An approach for real-time monitoring of the species saturation using dynamic rarefaction was designed as a guiding determinant of optimal run time. Real-time saturation monitoring for both bacterial and fungal species enabled the completion of sequencing within 30 hours, utilizing less than 60% of the total nanopores. Approximately 5 million high quality (HQ) taxonomically assigned reads were generated (~4.2 million bacterial and 0.7 million fungal), providing a wider (beyond bacteriome) snapshot of human oral microbiota at species-level resolution. Among the more than 400 bacterial and 240 fungal species identified in the studied samples, the species of Streptococcus (e.g., Streptococcus mitis and Streptococcus oralis) and Candida (e.g., Candida albicans and Candida tropicalis) were observed to be the dominating microbes in the oral cavity, respectively. This conformed well with the previous reports of the human oral microbiota. EnsembleSeq provides a proof-of-concept toward the identification of both fungal and bacterial species simultaneously in a single fully multiplexed nanopore sequencing run in a time- and resource-effective manner. Details of this workflow, along with the associated codebase, are provided to enable large-scale application for a holistic species-level microbiome study.

IMPORTANCE: Human microbiome is a sum total of a variety of microbial genomes (including bacteria, fungi, protists, viruses, etc.) present in and on the human body. Yet, a majority of amplicon-based microbiome studies have largely remained skewed toward bacteriome as an assumed proxy of the total microbiome, primarily at a shallow genus level. Cost, time, effort, data quality/management, and importantly lack of guiding studies often limit progress in the direction of moving beyond bacteriome. Here, EnsembleSeq presents a proof-of-concept toward concomitantly capturing multiple-kingdoms of microorganisms (bacteriome and mycobiome) in a fully multiplexed (96-sample) single run of long-read amplicon sequencing. In addition, the workflow captures dynamic tracking of species-level saturation in a time- and resource-effective manner.},
}

@article {pmid38686626,
year = {2024},
author = {Shin, DS and Basak, S and Veena, MS and Comin-Anduix, B and Bhattacharya, A and Dong, TS and Ko, A and Han, P and Jacobs, J and Moatamed, NA and Avila, L and Pellegrini, M and Wang, M and Srivatsan, ES},
title = {Enhanced CTLA-4 blockade anti-tumor immunity with APG-157 combination in a murine head and neck cancer.},
journal = {Cancer medicine},
volume = {13},
number = {9},
pages = {e7212},
pmid = {38686626},
issn = {2045-7634},
support = {I01 BX005588/BX/BLRD VA/United States ; },
mesh = {Animals ; Mice ; *CTLA-4 Antigen/antagonists & inhibitors ; *Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Cell Line, Tumor ; *Tumor Microenvironment/immunology/drug effects ; *Head and Neck Neoplasms/immunology/drug therapy/pathology ; Humans ; Female ; Antineoplastic Combined Chemotherapy Protocols/pharmacology/therapeutic use ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Disease Models, Animal ; },
abstract = {BACKGROUND: A phase I clinical study for patients with locally advanced H&N cancer with a new class of botanical drug APG-157 provided hints of potential synergy with immunotherapy. We sought to evaluate the efficacy of the combination of APG-157 and immune checkpoint inhibitors.

METHODS: CCL23, UM-SCC1 (human), and SCCVII (HPV-), MEER (HPV+) (murine) H&N cancer cell lines were utilized for in vitro and in vivo studies. We measured tumor growth by treating the mice with APG-157, anti-PD-1, and anti-CTLA-4 antibody combinations (8 groups). The tumor microenvironments were assessed by multi-color flow cytometry, immunohistochemistry, and RNA-seq analysis. Fecal microbiome was analyzed by 16S rRNA sequence.

RESULTS: Among the eight treatment groups, APG-157 + anti-CTLA-4 demonstrated the best tumor growth suppression (p = 0.0065 compared to the control), followed by anti-PD-1 + anti-CTLA-4 treatment group (p = 0.48 compared to the control). Immunophenotype showed over 30% of CD8+ T cells in APG-157 + anti-CTLA-4 group compared to 4%-5% of CD8+ T cells for the control group. Differential gene expression analysis revealed that APG-157 + anti-CTLA-4 group showed an enriched set of genes for inflammatory response and apoptotic signaling pathways. The fecal microbiome analysis showed a substantial difference of lactobacillus genus among groups, highest for APG-157 + anti-CTLA-4 treatment group. We were unable to perform correlative studies for MEER model as there was tumor growth suppression with all treatment conditions, except for the untreated control group.

CONCLUSIONS: The results indicate that APG-157 and immune checkpoint inhibitor combination treatment could potentially lead to improved tumor control.},
}

Animals
Mice
*CTLA-4 Antigen/antagonists & inhibitors
*Immune Checkpoint Inhibitors/pharmacology/therapeutic use
Cell Line, Tumor
*Tumor Microenvironment/immunology/drug effects
*Head and Neck Neoplasms/immunology/drug therapy/pathology
Humans
Female
Antineoplastic Combined Chemotherapy Protocols/pharmacology/therapeutic use
Programmed Cell Death 1 Receptor/antagonists & inhibitors
Disease Models, Animal

@article {pmid38686499,
year = {2024},
author = {Schwarz, A and Hernandez, L and Arefin, S and Sartirana, E and Witasp, A and Wernerson, A and Stenvinkel, P and Kublickiene, K},
title = {Sweet, bloody consumption - what we eat and how it affects vascular ageing, the BBB and kidney health in CKD.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2341449},
pmid = {38686499},
issn = {1949-0984},
mesh = {Humans ; *Renal Insufficiency, Chronic/etiology/metabolism/microbiology/physiopathology ; *Gastrointestinal Microbiome ; *Blood-Brain Barrier/metabolism ; *Kidney/physiopathology/metabolism ; Animals ; Uremic Toxins/metabolism ; Diet, Western/adverse effects ; },
abstract = {In today's industrialized society food consumption has changed immensely toward heightened red meat intake and use of artificial sweeteners instead of grains and vegetables or sugar, respectively. These dietary changes affect public health in general through an increased incidence of metabolic diseases like diabetes and obesity, with a further elevated risk for cardiorenal complications. Research shows that high red meat intake and artificial sweeteners ingestion can alter the microbial composition and further intestinal wall barrier permeability allowing increased transmission of uremic toxins like p-cresyl sulfate, indoxyl sulfate, trimethylamine n-oxide and phenylacetylglutamine into the blood stream causing an array of pathophysiological effects especially as a strain on the kidneys, since they are responsible for clearing out the toxins. In this review, we address how the burden of the Western diet affects the gut microbiome in altering the microbial composition and increasing the gut permeability for uremic toxins and the detrimental effects thereof on early vascular aging, the kidney per se and the blood-brain barrier, in addition to the potential implications for dietary changes/interventions to preserve the health issues related to chronic diseases in future.},
}

Humans
*Renal Insufficiency, Chronic/etiology/metabolism/microbiology/physiopathology
*Gastrointestinal Microbiome
*Blood-Brain Barrier/metabolism
*Kidney/physiopathology/metabolism
Animals
Uremic Toxins/metabolism
Diet, Western/adverse effects

@article {pmid38686450,
year = {2024},
author = {Marchi, E and Hinks, TSC and Richardson, M and Khalfaoui, L and Symon, FA and Rajasekar, P and Clifford, R and Hargadon, B and Austin, CD and MacIsaac, JL and Kobor, MS and Siddiqui, S and Mar, JS and Arron, JR and Choy, DF and Bradding, P},
title = {The effects of inhaled corticosteroids on healthy airways.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16146},
pmid = {38686450},
issn = {1398-9995},
support = {211050/Z/18/z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: The effects of inhaled corticosteroids (ICS) on healthy airways are poorly defined.

OBJECTIVES: To delineate the effects of ICS on gene expression in healthy airways, without confounding caused by changes in disease-related genes and disease-related alterations in ICS responsiveness.

METHODS: Randomized open-label bronchoscopy study of high-dose ICS therapy in 30 healthy adult volunteers randomized 2:1 to (i) fluticasone propionate 500 mcg bd daily or (ii) no treatment, for 4 weeks. Laboratory staff were blinded to allocation. Biopsies and brushings were analysed by immunohistochemistry, bulk RNA sequencing, DNA methylation array and metagenomics.

RESULTS: ICS induced small between-group differences in blood and lamina propria eosinophil numbers, but not in other immunopathological features, blood neutrophils, FeNO, FEV1, microbiome or DNA methylation. ICS treatment upregulated 72 genes in brushings and 53 genes in biopsies, and downregulated 82 genes in brushings and 416 genes in biopsies. The most downregulated genes in both tissues were canonical markers of type-2 inflammation (FCER1A, CPA3, IL33, CLEC10A, SERPINB10 and CCR5), T cell-mediated adaptive immunity (TARP, TRBC1, TRBC2, PTPN22, TRAC, CD2, CD8A, HLA-DQB2, CD96, PTPN7), B-cell immunity (CD20, immunoglobulin heavy and light chains) and innate immunity, including CD48, Hobit, RANTES, Langerin and GFI1. An IL-17-dependent gene signature was not upregulated by ICS.

CONCLUSIONS: In healthy airways, 4-week ICS exposure reduces gene expression related to both innate and adaptive immunity, and reduces markers of type-2 inflammation. This implies that homeostasis in health involves tonic type-2 signalling in the airway mucosa, which is exquisitely sensitive to ICS.},
}

@article {pmid38686335,
year = {2024},
author = {Le, SH and Nguyen Ngoc Minh, C and de Sessions, PF and Jie, S and Tran Thi Hong, C and Thwaites, GE and Baker, S and Pham, DT and Chung The, H},
title = {The impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea.},
journal = {npj antimicrobials and resistance},
volume = {2},
number = {1},
pages = {12},
pmid = {38686335},
issn = {2731-8745},
abstract = {Infectious diarrhoeal diseases remain a substantial health burden in young children in low- and middle-income countries. The disease and its variable treatment options significantly alter the gut microbiome, which may affect clinical outcomes and overall gut health. Antibiotics are often prescribed, but their impact on the gut microbiome during recovery is unclear. Here, we used 16S rRNA sequencing to investigate changes in the gut microbiota in Vietnamese children with acute watery diarrhoea, and highlight the impact of antibiotic treatment on these changes. Our analyses identified that, regardless of treatment, recovery was characterised by reductions in Streptococcus and Rothia species and expansion of Bacteroides/Phocaeicola, Lachnospiraceae and Ruminococcacae taxa. Antibiotic treatment significantly delayed the temporal increases in alpha- and beta-diversity within patients, resulting in distinctive patterns of taxonomic change. These changes included a pronounced, transient overabundance of Enterococcus species and depletion of Bifidobacterium pseudocatenulatum. Our findings demonstrate that antibiotic treatment slows gut microbiota recovery in children following watery diarrhoea.},
}

@article {pmid38686220,
year = {2024},
author = {Bruggeman, A and Vandendriessche, C and Hamerlinck, H and De Looze, D and Tate, DJ and Vuylsteke, M and De Commer, L and Devolder, L and Raes, J and Verhasselt, B and Laukens, D and Vandenbroucke, RE and Santens, P},
title = {Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson's disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial.},
journal = {EClinicalMedicine},
volume = {71},
number = {},
pages = {102563},
pmid = {38686220},
issn = {2589-5370},
abstract = {BACKGROUND: Dysregulation of the gut microbiome has been implicated in Parkinson's disease (PD). This study aimed to evaluate the clinical effects and safety of a single faecal microbiota transplantation (FMT) in patients with early-stage PD.

METHODS: The GUT-PARFECT trial, a single-centre randomised, double-blind, placebo-controlled trial was conducted at Ghent University Hospital between December 01, 2020 and December 12, 2022. Participants (aged 50-65 years, Hoehn and Yahr stage 2) were randomly assigned to receive nasojejunal FMT with either healthy donor stool or their own stool. Computer-generated randomisation was done in a 1:1 ratio through permutated-block scheduling. Treatment allocation was concealed for participants and investigators. The primary outcome measure at 12 months was the change in the Movement Disorders Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) motor score obtained during off-medication evaluations. Intention-to-treat analysis was performed using a mixed model for repeated measures analysis. This completed trial is registered on ClinicalTrials.gov (NCT03808389).

FINDINGS: Between December 2020 and December 2021, FMT procedures were conducted on 46 patients with PD: 22 in the healthy donor group and 24 in the placebo group. Clinical evaluations were performed at baseline, 3, 6, and 12 months post-FMT. Full data analysis was possible for 21 participants in the healthy donor group and 22 in the placebo group. After 12 months, the MDS-UPDRS motor score significantly improved by a mean of 5.8 points (95% CI -11.4 to -0.2) in the healthy donor group and by 2.7 points (-8.3 to 2.9) in the placebo group (p = 0.0235). Adverse events were limited to temporary abdominal discomfort.

INTERPRETATION: Our findings suggested a single FMT induced mild, but long-lasting beneficial effects on motor symptoms in patients with early-stage PD. These findings highlight the potential of modulating the gut microbiome as a therapeutic approach and warrant a further exploration of FMT in larger cohorts of patients with PD in various disease stages.

FUNDING: Flemish PD patient organizations (VPL and Parkili), Research Foundation Flanders (FWO), Biocodex Microbiota Foundation.},
}

@article {pmid38686186,
year = {2024},
author = {Chen, Q and Huang, X and Zhang, H and Jiang, X and Zeng, X and Li, W and Su, H and Chen, Y and Lin, F and Li, M and Gu, X and Jin, H and Wang, R and Diao, D and Wang, W and Li, J and Wei, S and Zhang, W and Liu, W and Huang, Z and Deng, Y and Luo, W and Liu, Z and Zhang, B},
title = {Characterization of tongue coating microbiome from patients with colorectal cancer.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2344278},
pmid = {38686186},
issn = {2000-2297},
abstract = {BACKGROUND: Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC).

METHODS: Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model.

RESULTS: We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as Atopobium rimae, Streptococcus sanguinis, and Prevotella oris aided differentiation of CRC patients from healthy participants.

CONCLUSION: These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.},
}

@article {pmid38686113,
year = {2024},
author = {Zhang, J and Zhou, X and Zhang, Y and Dai, Z and He, Z and Qiu, Y and Alharbi, SA and Wei, F and Wei, L and Ahmed, W and Ji, G},
title = {Pre-soil fumigation with ammonium bicarbonate and lime modulates the rhizosphere microbiome to mitigate clubroot disease in Chinese cabbage.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1376579},
pmid = {38686113},
issn = {1664-302X},
abstract = {BACKGROUND: Plasmodiophora brassicae is an ever-increasing threat to cruciferous crop production worldwide.

AIMS AND METHODS: This study investigated the impact of pre-soil fumigation with ammonium bicarbonate (N) and lime (NB) to manage clubroot disease in Chinese cabbage through 16S rRNA gene amplification sequencing.

RESULTS: We found that soil fumigation with N and NB suppressed disease incidence by reducing the soil acidity and population of P. brassicae in the rhizosphere. Minimum disease incidence and maximum relative control effect of about 74.68 and 66.28% were achieved in greenhouse and field experiments, respectively, under the combined application of ammonium bicarbonate and lime (LNB) as compared with N, NB, and control (GZ). Microbial diversity analysis through Miseq sequencing proved that pre-soil fumigation with N, NB, and LNB clearly manipulated rhizosphere microbial community composition and changed the diversity and structure of rhizosphere microbes compared with GZ. Bacterial phyla such as Proteobacteria, Bacteriodetes, and Acidobacteria and fungal phyla including Olpidiomycota and Ascomycota were most dominant in the rhizosphere of Chinese cabbage plants. Soil fumigation with N and NB significantly reduced the abundance of clubroot pathogen at genus (Plasmodiophora) level compared with GZ, while decreased further under combined application LNB. Microbial co-occurrence network analysis showed a highly connected and complex network and less competition for resources among microbes under combined application LNB.

CONCLUSION: We conclude that for environmentally friendly and sustainable agriculture, soil fumigation with combined ammonium bicarbonate and lime plays a crucial role in mitigating Chinese cabbage clubroot disease by alleviating soil pH, reducing pathogen population, and manipulating the rhizosphere microbiome.},
}

@article {pmid38685939,
year = {2024},
author = {Qin, X and Pu, H and Fang, X and Shang, Q and Li, J and Zhao, Q and Wang, X and Gu, W},
title = {Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17240},
pmid = {38685939},
issn = {2167-8359},
mesh = {*Schisandra/metabolism/chemistry ; Soil Microbiology ; Microbiota/genetics ; Oils, Volatile/metabolism ; Secondary Metabolism ; Plant Stems/microbiology/metabolism ; Sesquiterpenes/metabolism ; Bacteria/genetics/classification/metabolism ; },
abstract = {BACKGROUND: Schisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera?

METHODS: In this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed.

RESULTS: The major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new opportunity to further understand the effects of microorganisms on the active secondary metabolites and provided a basis for further research on the sustainable utilization of S. sphenanthera.},
}

*Schisandra/metabolism/chemistry
Soil Microbiology
Microbiota/genetics
Oils, Volatile/metabolism
Secondary Metabolism
Plant Stems/microbiology/metabolism
Sesquiterpenes/metabolism
Bacteria/genetics/classification/metabolism

@article {pmid38685821,
year = {2024},
author = {Williams, SC and Garcet, S and Hur, H and Miura, S and Gonzalez, J and Navrazhina, K and Yamamura-Murai, M and Yamamura, K and Li, X and Frew, J and Fischetti, VA and Sela, U and Krueger, JG},
title = {Gram-negative anaerobes elicit a robust keratinocytes immune response with potential insights into HS pathogenesis.},
journal = {Experimental dermatology},
volume = {33},
number = {5},
pages = {e15087},
doi = {10.1111/exd.15087},
pmid = {38685821},
issn = {1600-0625},
support = {/GM/NIGMS NIH HHS/United States ; },
mesh = {*Keratinocytes/immunology/microbiology/metabolism ; Humans ; Animals ; Mice ; *Hidradenitis Suppurativa/microbiology/immunology ; Staphylococcus aureus/immunology ; Staphylococcus epidermidis/immunology ; Fusobacterium nucleatum/immunology ; Transcriptome ; Cytokines/metabolism ; Bacteria, Anaerobic ; Interleukin-17/metabolism ; Microbiota ; Prevotella/immunology ; },
abstract = {Hidradenitis Suppurativa (HS) is a chronic autoinflammatory skin disease with activated keratinocytes, tunnel formation and a complex immune infiltrate in tissue. The HS microbiome is polymicrobial with an abundance of commensal gram-positive facultative (GPs) Staphylococcus species and gram-negative anaerobic (GNA) bacteria like Prevotella, Fusobacterium and Porphyromonas with increasing predominance of GNAs with disease severity. We sought to define the keratinocyte response to bacteria commonly isolated from HS lesions to probe pathogenic relationships between HS and the microbiome. Type strains of Prevotella nigrescens, Prevotella melaninogenica, Prevotella intermedia, Prevotella asaccharolytica, Fusobacterium nucleatum, as well as Staphylococcus aureus and the normal skin commensal Staphylococcus epidermidis were heat-killed and co-incubated with normal human keratinocytes. RNA was collected and analysed using RNAseq and RT-qPCR. The supernatant was collected from cell culture for protein quantification. Transcriptomic profiles between HS clinical samples and stimulated keratinocytes were compared. Co-staining of patient HS frozen sections was used to localize bacteria in lesions. A mouse intradermal injection model was used to investigate early immune recruitment. TLR4 and JAK inhibitors were used to investigate mechanistic avenues of bacterial response inhibition. GNAs, especially F. nucleatum, stimulated vastly higher CXCL8, IL17C, CCL20, IL6, TNF and IL36γ transcription in normal skin keratinocytes than the GPs S. epidermidis and S. aureus. Using RNAseq, we found that F. nucleatum (and Prevotella) strongly induced the IL-17 pathway in keratinocytes and overlapped with transcriptome profiles of HS patient clinical samples. Bacteria were juxtaposed to activated keratinocytes in vivo, and F. nucleatum strongly recruited murine neutrophil and macrophage migration. Both the TLR4 and pan-JAK inhibitors reduced cytokine production. Detailed transcriptomic profiling of healthy skin keratinocytes exposed to GNAs prevalent in HS revealed a potent, extensive inflammatory response vastly stronger than GPs. GNAs stimulated HS-relevant genes, including many genes in the IL-17 response pathway, and were significantly associated with HS tissue transcriptomes. The close association of activated keratinocytes with bacteria in HS lesions and innate infiltration in murine skin cemented GNA pathogenic potential. These novel mechanistic insights could drive future targeted therapies.},
}

*Keratinocytes/immunology/microbiology/metabolism
Humans
Animals
Mice
*Hidradenitis Suppurativa/microbiology/immunology
Staphylococcus aureus/immunology
Staphylococcus epidermidis/immunology
Fusobacterium nucleatum/immunology
Transcriptome
Cytokines/metabolism
Bacteria, Anaerobic
Interleukin-17/metabolism
Microbiota
Prevotella/immunology

@article {pmid38685799,
year = {2024},
author = {He, S and Tian, J and Zang, J and Long, L and Liu, P and Zhang, Y and Xiao, J},
title = {Implications of intestinal microecology and immune function alterations for immunotherapy outcomes in advanced unresectable lung adenocarcinoma.},
journal = {The clinical respiratory journal},
volume = {18},
number = {5},
pages = {e13762},
pmid = {38685799},
issn = {1752-699X},
support = {2012Z31//Shandong Provincial Key Program of Science and Technology of Traditional Chinese Medicine/ ; 20120Q75//Shandong Provincial Youth Program of Science and Technology of Traditional Chinese Medicine/ ; 2021-WJZD034//Qingdao Medical and Health Research Program/ ; 320.6750.2021-February 93//2021 Special Fund for Clinical Research of Wu Jieping Medical Foundation/ ; 2022-10//2022-2024 Qingdao Municipal Clinical Key Specialties-Climbing Peak Discipline Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; *Lung Neoplasms/immunology/pathology/therapy ; Middle Aged ; *Adenocarcinoma of Lung/immunology/pathology/therapy/drug therapy ; *Immunotherapy/methods ; Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; },
abstract = {OBJECTIVE: This investigation aims to explore alterations in intestinal microecology and immune function among patients with advanced, unresectable lung adenocarcinoma undergoing different outcomes from immunotherapy.

METHODS: A cohort of 30 patients diagnosed with advanced unresectable lung adenocarcinoma received sintilimab immunotherapy as a monotherapy. Post four treatment cycles, efficacy was assessed, leading to the segregation of patients into two distinct cohorts: those responsive to treatment and those nonresponsive. Analysis involved observing variations in the abundance, distribution, and composition of fecal intestinal microorganisms pretreatment and posttreatment via 16S rRNA gene sequencing.

RESULTS: In this study involving 30 advanced lung adenocarcinoma patients, significant observations were made regarding the impact of immunotherapy on immune function and the gut microbiome composition. Patients were divided into treatment and control groups, revealing that immunotherapy led to a significant increase in CD4+ T cells and a decrease in CD8+ T cells among the treatment-responsive individuals, indicating an enhanced immune response. Furthermore, an in-depth analysis of the gut microbiome showed an increase in diversity and abundance of beneficial bacteria such as Faecalibacterium and Subdoligranulum in the treatment group. These findings highlight the dual effect of immunotherapy on modulating immune function and altering gut microbiome diversity, suggesting its potential therapeutic benefits in improving the health status of patients with advanced lung adenocarcinoma.

CONCLUSION: The structuring of gut flora plays a pivotal role in augmenting the efficacy of anti-tumor immunotherapy, underscoring the interplay between intestinal microecology and immune response in cancer treatment outcomes.},
}

Humans
*Gastrointestinal Microbiome/immunology
Male
Female
*Lung Neoplasms/immunology/pathology/therapy
Middle Aged
*Adenocarcinoma of Lung/immunology/pathology/therapy/drug therapy
*Immunotherapy/methods
Aged
RNA, Ribosomal, 16S/genetics
Treatment Outcome

@article {pmid38685762,
year = {2024},
author = {Ishnaiwer, M and Le Bastard, Q and Naour, M and Zeman, M and Dailly, E and Montassier, E and Batard, E and Dion, M},
title = {Efficacy of an inulin-based treatment on intestinal colonization by multidrug-resistant E. coli: insight into the mechanism of action.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2347021},
pmid = {38685762},
issn = {1949-0984},
mesh = {Animals ; *Inulin/pharmacology/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Escherichia coli/drug effects/genetics ; *Feces/microbiology ; *Amoxicillin/pharmacology ; *Pantoprazole/pharmacology ; *Drug Resistance, Multiple, Bacterial ; beta-Lactamases/metabolism/genetics ; Dysbiosis/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/drug therapy/microbiology ; Female ; Prebiotics/administration & dosage ; },
abstract = {Inulin, an increasingly studied dietary fiber, alters intestinal microbiota. The aim of this study was to assess whether inulin decreases intestinal colonization by multidrug resistant E. coli and to investigate its potential mechanisms of action. Mice with amoxicillin-induced intestinal dysbiosis mice were inoculated with extended spectrum beta-lactamase producing E. coli (ESBL-E. coli). The combination of inulin and pantoprazole (IP) significantly reduced ESBL-E. coli fecal titers, whereas pantoprazole alone did not and inulin had a delayed and limited effect. Fecal microbiome was assessed using shotgun metagenomic sequencing and qPCR. The efficacy of IP was predicted by increased abundance of 74 taxa, including two species of Adlercreutzia. Preventive treatments with A. caecimuris or A. muris also reduced ESBL-E. coli fecal titers. Fecal microbiota of mice effectively treated by IP was enriched in genes involved in inulin catabolism, production of propionate and expression of beta-lactamases. They also had increased beta-lactamase activity and decreased amoxicillin concentration. These results suggest that IP act through production of propionate and degradation of amoxicillin by the microbiota. The combination of pantoprazole and inulin is a potential treatment of intestinal colonization by multidrug-resistant E. coli. The ability of prebiotics to promote propionate and/or beta-lactamase producing bacteria may be used as a screening tool to identify potential treatments of intestinal colonization by multidrug resistant Enterobacterales.},
}

Animals
*Inulin/pharmacology/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Escherichia coli/drug effects/genetics
*Feces/microbiology
*Amoxicillin/pharmacology
*Pantoprazole/pharmacology
*Drug Resistance, Multiple, Bacterial
beta-Lactamases/metabolism/genetics
Dysbiosis/microbiology/drug therapy
Anti-Bacterial Agents/pharmacology
Escherichia coli Infections/drug therapy/microbiology
Female
Prebiotics/administration & dosage

@article {pmid38685731,
year = {2024},
author = {Zhang, Z and Mocanu, V and Deehan, EC and Hotte, N and Zhu, Y and Wei, S and Kao, DH and Karmali, S and Birch, DW and Walter, J and Madsen, KL},
title = {Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2345134},
pmid = {38685731},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Metabolic Syndrome/therapy/microbiology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Feces/microbiology ; *Bile Acids and Salts/metabolism/blood ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Obesity/therapy/microbiology ; Dietary Fiber/administration & dosage/metabolism ; Insulin Resistance ; Treatment Outcome ; },
abstract = {Microbial-based therapeutics in clinical practice are of considerable interest, and a recent study demonstrated fecal microbial transplantation (FMT) followed by dietary fiber supplements improved glucose homeostasis. Previous evidence suggests that donor and recipient compatibility and FMT protocol are key determinants, but little is known about the involvement of specific recipient factors. Using data from our recent randomized placebo-control phase 2 clinical trial in adults with obesity and metabolic syndrome, we grouped participants that received FMT from one of 4 donors with either fiber supplement into HOMA-IR responders (n = 21) and HOMA-IR non-responders (n = 8). We further assessed plasma bile acids using targeted metabolomics and performed subgroup analyzes to evaluate the effects of recipient parameters and gastrointestinal factors on microbiota engraftment and homeostatic model assessment of insulin resistance (HOMA2-IR) response. The baseline fecal microbiota composition at genus level of recipients could predict the improvements in HOMA2-IR at week 6 (ROC-AUC = 0.70). Prevotella was identified as an important predictor, with responders having significantly lower relative abundance than non-responders (p = .02). In addition, recipients displayed a highly individualized degree of microbial engraftment from donors. Compared to the non-responders, the responders had significantly increased bacterial richness (Chao1) after FMT and a more consistent engraftment of donor-specific bacteria ASVs (amplicon sequence variants) such as Faecalibacillus intestinalis (ASV44), Roseburia spp. (ASV103), and Christensenellaceae spp. (ASV140) (p < .05). Microbiota engraftment was strongly associated with recipients' factors at baseline including initial gut microbial diversity, fiber and nutrient intakes, inflammatory markers, and bile acid derivative levels. This study identified that responders to FMT therapy had a higher engraftment rate in the transplantation of specific donor-specific microbes, which were strongly correlated with insulin sensitivity improvements. Further, the recipient baseline gut microbiota and related factors were identified as the determinants for responsiveness to FMT and fiber supplementation. The findings provide a basis for the development of precision microbial therapeutics for the treatment of metabolic syndrome.},
}

Humans
*Fecal Microbiota Transplantation
*Metabolic Syndrome/therapy/microbiology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
*Feces/microbiology
*Bile Acids and Salts/metabolism/blood
*Bacteria/classification/isolation & purification/genetics/metabolism
Obesity/therapy/microbiology
Dietary Fiber/administration & dosage/metabolism
Insulin Resistance
Treatment Outcome

@article {pmid38685730,
year = {2024},
author = {Yang, W and Fan, X and Li, W and Chen, Y},
title = {Causal influence of gut microbiota on small cell lung cancer: a Mendelian randomization study.},
journal = {The clinical respiratory journal},
volume = {18},
number = {5},
pages = {e13764},
pmid = {38685730},
issn = {1752-699X},
support = {2023RY020//Dalian City Outstanding Young Science and Technology Talent Program/ ; },
mesh = {Humans ; *Mendelian Randomization Analysis/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/microbiology/genetics ; *Small Cell Lung Carcinoma/microbiology/genetics ; Genome-Wide Association Study ; Male ; Female ; Case-Control Studies ; },
abstract = {BACKGROUND: Previous studies have hinted at a significant link between lung cancer and the gut microbiome, yet their causal relationship remains to be elucidated.

METHODS: GWAS data for small cell lung cancer (SCLC) was extracted from the FinnGen consortium, comprising 179 cases and 218 613 controls. Genetic variation data for 211 gut microbiota were obtained as instrumental variables from MiBioGen. Mendelian randomization (MR) was employed to determine the causal relationship between the two, with inverse variance weighting (IVW) being the primary method for causal analysis. The MR results were validated through several sensitivity analyses.

RESULTS: The study identified a protective effect against SCLC for the genus Eubacterium ruminantium group (OR = 0.413, 95% CI: 0.223-0.767, p = 0.00513), genus Barnesiella (OR = 0.208, 95% CI: 0.0640-0.678, p = 0.00919), family Lachnospiraceae (OR = 0.319, 95% CI: 0.107-0.948, p = 0.03979), and genus Butyricimonas (OR = 0.376, 95% CI: 0.144-0.984, p = 0.04634). Conversely, genus Intestinibacter (OR = 3.214, 95% CI: 1.303-7.926, p = 0.01125), genus Eubacterium oxidoreducens group (OR = 3.391, 95% CI: 1.215-9.467, p = 0.01973), genus Bilophila (OR = 3.547, 95% CI: 1.106-11.371, p = 0.03315), and order Bacillales (OR = 1.860, 95% CI: 1.034-3.347, p = 0.03842) were found to potentially promote the onset of SCLC.

CONCLUSION: We identified potential causal relationships between certain gut microbiota and SCLC, offering new insights into microbiome-mediated mechanisms of SCLC pathogenesis, resistance, mutations, and more.},
}

Humans
*Mendelian Randomization Analysis/methods
*Gastrointestinal Microbiome/genetics
*Lung Neoplasms/microbiology/genetics
*Small Cell Lung Carcinoma/microbiology/genetics
Genome-Wide Association Study
Male
Female
Case-Control Studies

@article {pmid38685708,
year = {2024},
author = {Liu, J and Xu, W and Zhang, Q and Liao, W and Li, L and Chen, S and Yang, J and Wang, Z and Xu, F},
title = {OsPHR2-mediated recruitment of Pseudomondaceae enhances rice phosphorus uptake.},
journal = {Plant communications},
volume = {},
number = {},
pages = {100930},
doi = {10.1016/j.xplc.2024.100930},
pmid = {38685708},
issn = {2590-3462},
abstract = {Plant can shape their root microbiome for growth and nutrients uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome for phosphorus uptake is unclear. Here, we investigate the roles of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolites analysis. OsPHR2-overexpressing (OsPHR2 OE) rice exhibited 69.8% greater shoot P uptake in natural soil compared to sterilized soil under high phosphorus (HP) conditions; while there was only a 54.8% increase in wildtype (WT). Next, the abundance of the family Pseudomondaceae was significantly enriched in the OsPHR2 OE root, relative to WT rice. Compared to the WT, OsPHR2 OE had different root exudates (succinic acid and methylmalonic acid), which were associated with distinct changes in the root microbiome. After inoculation with Pseudomonas sp (P6), rice phosphorus uptake in WT and OsPHR2 OE rice was higher than that of uninoculated rice plants under low phosphorus (LP) conditions. Together, our results suggest that OsPHR2 can increase rice phosphorus use through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.},
}

@article {pmid38685365,
year = {2024},
author = {Wang, XH and Yang, YN and Li, YH and Cheng, JL and Yan, L and Liang, Y and Zeng, Q and Zhan, T and Wang, DW and Yu, RH and Wu, CM},
title = {Oral bacteriome and mycobiome of patients with idiopathic membranous nephropathy with different tongue coatings treated with a Chinese herbal formula.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118233},
doi = {10.1016/j.jep.2024.118233},
pmid = {38685365},
issn = {1872-7573},
abstract = {Moshen Fuyuan Formula (MSFY) is one of the representative Chinese medicine compound for Idiopathic membranous nephropathy (IMN), that originate from Fang Ji Huang Qi decoction in the Han dynasty. IMN is usually accompanied by different tongue coatings in traditional Chinese medicine (TCM), and tongue microorganisms are important factors affecting the formation of the tongue coating. Recently, oral microbiomes, including bacteria and fungi, have been identified as pivotal factors that contribute to disease development. However, the regulation of oral microbiomes by MSFY has not been defined.

AIM OF THE STUDY: In this work, we explore the characteristics of oral bacteria and fungi in IMN patients with different tongue coatings, and clarify the therapeutic effect of MSFY based on oral microbiome.

MATERIALS AND METHODS: We enrolled 24 patients with IMN, including 11 with white tongue (IMN-W) and 13 with yellow tongue (IMN-Y), and recruited an additional 10 healthy individuals. Patients with IMN were treated with the MSFY. The oral bacteriome and fungi before and after treatment were detected using full-length 16S rRNA and internal transcribed spacer gene sequencing.

RESULTS: The therapeutic effect of MSFY on patients with yellow tongue coating was more significant than that on patients with white tongue coating. In terms of oral bacteriome, Campylobacter bacteria were enriched in patients with yellow tongue and could be a promising biomarker for yellow coating. Enrichment of Veillonella parvula_A may partially account for the therapeutic effect of MSFY. As for oral fungi, Malassezia globosa was enhanced in patients with IMN-W and reduced in patients with IMN-Y. Notably, it was reduced by MSFY. We also found that mycobiome-bacteriome interactions were highly complex and dynamic in patients with IMN.

CONCLUSION: The regulation of the dynamic balance between oral fungi and bacteria by MSFY contributes to the treatment of IMN. This study determined the oral bacteriome and mycobiome of patients with IMN with different tongue coatings before and after MSFY treatment, which aids in promoting personalized treatment in clinical TCM and provides direction for investigating the mechanism of Chinese herbal medicines.},
}

@article {pmid38685289,
year = {2024},
author = {Stevanoska, M and Folz, J and Beekmann, K and Aichinger, G},
title = {Physiologically based kinetic (PBK) modeling as a new approach methodology (NAM) for predicting systemic levels of gut microbial metabolites.},
journal = {Toxicology letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.toxlet.2024.04.013},
pmid = {38685289},
issn = {1879-3169},
abstract = {There is a clear need to develop new approach methodologies (NAMs) that combine in vitro and in silico testing to reduce and replace animal use in chemical risk assessment. Physiologically based kinetic (PBK) models are gaining popularity as NAMs in toxico/pharmacokinetics, but their coverage of complex metabolic pathways occurring in the gut are incomplete. Chemical modification of xenobiotics by the gut microbiome plays a critical role in the host response, for example, by prolonging exposure to harmful metabolites, but there is not a comprehensive approach to quantify this impact on human health. There are examples of PBK models that have implemented gut microbial biotransformation of xenobiotics with the gut as a dedicated metabolic compartment. However, the integration of microbial metabolism and parameterization of PBK models is not standardized and has only been applied to a few chemical transformations. A challenge in this area is the measurement of microbial metabolic kinetics, for which different fermentation approaches are used. Without a standardized method to measure gut microbial metabolism ex vivo/in vitro, the kinetic constants obtained will lead to conflicting conclusions drawn from model predictions. Nevertheless, there are specific cases where PBK models accurately predict systemic concentrations of gut microbial metabolites, offering potential solutions to the challenges outlined above. This review focuses on models that integrate gut microbial bioconversions and use ex vivo/in vitro methods to quantify metabolic constants that accurately represent in vivo conditions.},
}

@article {pmid38685283,
year = {2024},
author = {Behrens, LMP and Gasparotto, J and Rampelotto, PH and Escalona, MAR and da Silva, LDS and Carazza-Kessler, FG and Barbosa, CP and Campos, MS and Dorn, M and Gelain, DP and Moreira, JCF},
title = {Sodium Propionate Oral Supplementation ameliorates Depressive-Like Behavior through Gut Microbiome and Histone 3 Epigenetic Regulation.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109660},
doi = {10.1016/j.jnutbio.2024.109660},
pmid = {38685283},
issn = {1873-4847},
abstract = {Major Depressive Disorder (MDD) is a global health concern, affecting over 250 million individuals worldwide. In recent years, the gut-brain axis has emerged as a promising field for understanding the pathophysiology of MDD. Microbial metabolites, such as Short-Chain Fatty Acids (SCFAs) - acetate, butyrate, and propionate -, have gained attention for their potential to influence epigenetic modifications within the host brain. However, the precise mechanisms through which these metabolites participate in MDD pathophysiology remain elusive. This study was designed to investigate the effects of oral SCFA supplementation in adult male Wistar rats subjected to Chronic Unpredictable Mild Stress (CUMS). A subset of control and CUMS-exposed rats received different supplementations: sodium acetate (NaOAc) at a concentration of 60 mM, sodium butyrate (NaB) at 40 mM, sodium propionate (NaP) at 50 mM, or a mixture of these SCFAs. The gut microbiome was assessed through 16S rRNA sequencing, and epigenetic profiling was performed using Western blot analysis. Results demonstrated that NaP supplementation significantly alleviated anhedonia in stressed animals, as evidenced by improved performance in the sucrose consumption test. This ameliorative effect was potentially associated with the modulation of gut bacterial communities, accompanied by the attenuation of the region-specific epigenetic dysregulation in the brain of the animals exposed to chronic stress. These findings suggest a potential association between gut dysbiosis and stress response, and NaP could be a promising target for future MDD interventions. However, further studies are needed to fully elucidate the underlying mechanisms of these effects.},
}

@article {pmid38685158,
year = {2024},
author = {Li, J and Jin, MK and Huang, L and Liu, ZF and Wang, T and Chang, RY and Op de Beeck, M and Lambers, H and Hui, D and Xiao, KQ and Chen, QL and Sardans, J and Peñuelas, J and Yang, XR and Zhu, YG},
title = {Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108688},
doi = {10.1016/j.envint.2024.108688},
pmid = {38685158},
issn = {1873-6750},
abstract = {The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.},
}

@article {pmid38685022,
year = {2024},
author = {Zhang, W and Yin, Y and Jiang, Y and Yang, Y and Wang, W and Wang, X and Ge, Y and Liu, B and Yao, L},
title = {Relationship between vaginal and oral microbiome in patients of human papillomavirus (HPV) infection and cervical cancer.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {396},
pmid = {38685022},
issn = {1479-5876},
support = {GSWSKY2021-026//Health Commission of Gansu Province/ ; 22JR5RA941//Natural Science Foundation of Gansu Province/ ; 22JR5RA998//Natural Science Foundation of Gansu Province/ ; ldyyyn2022-49//First Clinical Medical School, Lanzhou University/ ; ZX-62000002-2021-225//Project of the First Hospital of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Microbiota ; *Vagina/microbiology/virology ; *Uterine Cervical Neoplasms/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mouth/microbiology/virology ; Adult ; Middle Aged ; Papillomaviridae/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: The aim of this study was to assess the microbial variations and biomarkers in the vaginal and oral environments of patients with human papillomavirus (HPV) and cervical cancer (CC) and to develop novel prediction models.

MATERIALS AND METHODS: This study included 164 samples collected from both the vaginal tract and oral subgingival plaque of 82 women. The participants were divided into four distinct groups based on their vaginal and oral samples: the control group (Z/KZ, n = 22), abortion group (AB/KAB, n = 17), HPV-infected group (HP/KHP, n = 21), and cervical cancer group (CC/KCC, n = 22). Microbiota analysis was conducted using full-length 16S rDNA gene sequencing with the PacBio platform.

RESULTS: The vaginal bacterial community in the Z and AB groups exhibited a relatively simple structure predominantly dominated by Lactobacillus. However, CC group shows high abundances of anaerobic bacteria and alpha diversity. Biomarkers such as Bacteroides, Mycoplasma, Bacillus, Dialister, Porphyromonas, Anaerococcus, and Prevotella were identified as indicators of CC. Correlations were established between elevated blood C-reactive protein (CRP) levels and local/systemic inflammation, pregnancy, childbirth, and abortion, which contribute to unevenness in the vaginal microenvironment. The altered microbial diversity in the CC group was confirmed by amino acid metabolism. Oral microbial diversity exhibited an inverse pattern to that of the vaginal microbiome, indicating a unique relationship. The microbial diversity of the KCC group was significantly lower than that of the KZ group, indicating a link between oral health and cancer development. Several microbes, including Fusobacterium, Campylobacter, Capnocytophaga, Veillonella, Streptococcus, Lachnoanaerobaculum, Propionibacterium, Prevotella, Lactobacillus, and Neisseria, were identified as CC biomarkers. Moreover, periodontal pathogens were associated with blood CRP levels and oral hygiene conditions. Elevated oral microbial amino acid metabolism in the CC group was closely linked to the presence of pathogens. Positive correlations indicated a synergistic relationship between vaginal and oral bacteria.

CONCLUSION: HPV infection and CC impact both the vaginal and oral microenvironments, affecting systemic metabolism and the synergy between bacteria. This suggests that the use of oral flora markers is a potential screening tool for the diagnosis of CC.},
}

Humans
Female
*Microbiota
*Vagina/microbiology/virology
*Uterine Cervical Neoplasms/microbiology/virology
*Papillomavirus Infections/virology/microbiology
*Mouth/microbiology/virology
Adult
Middle Aged
Papillomaviridae/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics
Human Papillomavirus Viruses

@article {pmid38684791,
year = {2024},
author = {Forry, SP and Servetas, SL and Kralj, JG and Soh, K and Hadjithomas, M and Cano, R and Carlin, M and Amorim, MG and Auch, B and Bakker, MG and Bartelli, TF and Bustamante, JP and Cassol, I and Chalita, M and Dias-Neto, E and Duca, AD and Gohl, DM and Kazantseva, J and Haruna, MT and Menzel, P and Moda, BS and Neuberger-Castillo, L and Nunes, DN and Patel, IR and Peralta, RD and Saliou, A and Schwarzer, R and Sevilla, S and Takenaka, IKTM and Wang, JR and Knight, R and Gevers, D and Jackson, SA},
title = {Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9785},
pmid = {38684791},
issn = {2045-2322},
mesh = {Humans ; *Metagenomics/methods/standards ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbiota/genetics ; Bias ; Metagenome ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.},
}

Humans
*Metagenomics/methods/standards
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Microbiota/genetics
Bias
Metagenome
Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods

@article {pmid38684759,
year = {2024},
author = {Gupta, A and Chan, SY and Toh, R and Low, JM and Liu, IMZ and Lim, SL and Lee, LY and Swarup, S},
title = {Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9855},
pmid = {38684759},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Diabetes, Gestational/microbiology ; *Dysbiosis/microbiology ; Pilot Projects ; Adult ; Singapore/epidemiology ; Prospective Studies ; Asian People ; RNA, Ribosomal, 16S/genetics ; Diet ; Ethnicity ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Gut microbiome dysbiosis contributes to the pathophysiology of both gestational diabetes mellitus (GDM) and its associated adverse outcomes in the woman and offspring. Even though GDM prevalence, complications, and outcomes vary among different ethnic groups, limited information is available about the influence of ethnicity on gut microbiome dysbiosis in pregnancies complicated by GDM. This pilot prospective cohort study examined the impact of ethnicity on gut dysbiosis in GDM among three Asian ethnic groups (Chinese, Malay, Indian) living in Singapore, and investigated the potential modulatory roles of diet and lifestyle modifications on gut microbiome post-GDM diagnosis. Women with GDM (n = 53) and without GDM (n = 16) were recruited. Fecal samples were collected at 24-28- and 36-40-weeks' gestation and analyzed by targeted 16S rRNA gene-based amplicon sequencing. Permutational multivariate analysis of variance (PERMANOVA) analysis was performed to evaluate differences between groups. Differentially abundant taxa were identified by DeSeq2 based analysis. Functional prediction was performed using the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2). Among women with GDM, gut microbiome from different ethnicities harbored common microbial features. However, among those without GDM, there was contrasting microbiome composition between ethnic groups. Microbial members such as Collinsella, Blautia, Ruminococcus, Ruminococcus gnavus, Ruminococcus torques, and Eubacterium hallii groups were differentially enriched (p < 0.05) in women with GDM compared to those without. Among women with GDM, no differences in alpha- and beta- diversity were observed when comparing 24-28 weeks' samples with 36-40 weeks' samples, a period covering intense dietary and lifestyle modification, suggesting an inability to modulate gut microbiota through classic GDM management. Women with GDM have a distinct gut microbiome profile which harbours common features across different Asian ethnic groups, consistent with the notion that specific microbes are involved in the pathogenesis of insulin resistance, pro-inflammatory conditions, and other metabolic dysregulation known to be present in GDM.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
*Diabetes, Gestational/microbiology
*Dysbiosis/microbiology
Pilot Projects
Adult
Singapore/epidemiology
Prospective Studies
Asian People
RNA, Ribosomal, 16S/genetics
Diet
Ethnicity
Feces/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid38684664,
year = {2024},
author = {Ma, W and Wang, Y and Nguyen, LH and Mehta, RS and Ha, J and Bhosle, A and Mclver, LJ and Song, M and Clish, CB and Strate, LL and Huttenhower, C and Chan, AT},
title = {Gut microbiome composition and metabolic activity in women with diverticulitis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3612},
pmid = {38684664},
issn = {2041-1723},
support = {K23 DK125838/DK/NIDDK NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Diverticulitis/metabolism/microbiology ; *Feces/microbiology ; Aged ; Prospective Studies ; Bilophila/metabolism ; Metabolomics ; Case-Control Studies ; Clostridiales/metabolism/isolation & purification ; Bile Acids and Salts/metabolism ; Adult ; Dietary Fiber/metabolism ; Metabolome ; Metagenomics/methods ; },
abstract = {The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.},
}

Humans
Female
*Gastrointestinal Microbiome
Middle Aged
*Diverticulitis/metabolism/microbiology
*Feces/microbiology
Aged
Prospective Studies
Bilophila/metabolism
Metabolomics
Case-Control Studies
Clostridiales/metabolism/isolation & purification
Bile Acids and Salts/metabolism
Adult
Dietary Fiber/metabolism
Metabolome
Metagenomics/methods

@article {pmid38684545,
year = {2024},
author = {El-Kurdi, N and El-Shatoury, S and ElBaghdady, K and Hammad, S and Ghazy, M},
title = {Biodegradation of polystyrene nanoplastics by Achromobacter xylosoxidans M9 offers a mealworm gut-derived solution for plastic pollution.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {238},
pmid = {38684545},
issn = {1432-072X},
mesh = {Animals ; *Polystyrenes/metabolism ; *Biodegradation, Environmental ; *Achromobacter denitrificans/metabolism ; *Gastrointestinal Microbiome ; Plastics/metabolism/chemistry ; Larva/microbiology ; Microplastics/metabolism ; },
abstract = {Nanoplastics pose significant environmental problems due to their high mobility and increased toxicity. These particles can cause infertility and inflammation in aquatic organisms, disrupt microbial signaling and act as pollutants carrier. Despite extensive studies on their harmful impact on living organisms, the microbial degradation of nanoplastics is still under research. This study investigated the degradation of nanoplastics by isolating bacteria from the gut microbiome of Tenebrio molitor larvae fed various plastic diets. Five bacterial strains capable of degrading polystyrene were identified, with Achromobacter xylosoxidans M9 showing significant nanoplastic degradation abilities. Within 6 days, this strain reduced nanoplastic particle size by 92.3%, as confirmed by SEM and TEM analyses, and altered the chemical composition of the nanoplastics, indicating a potential for enhanced bioremediation strategies. The strain also caused a 7% weight loss in polystyrene film over 30 days, demonstrating its efficiency in degrading nanoplastics faster than polystyrene film. These findings might enhance plastic bioremediation strategies.},
}

Animals
*Polystyrenes/metabolism
*Biodegradation, Environmental
*Achromobacter denitrificans/metabolism
*Gastrointestinal Microbiome
Plastics/metabolism/chemistry
Larva/microbiology
Microplastics/metabolism

@article {pmid38683843,
year = {2024},
author = {Hernández, AM and Alcaraz, LD and Hernández-Álvarez, C and Romero, MF and Jara-Servín, A and Barajas, H and Ramírez, CM and Peimbert, M},
title = {Revealing the microbiome diversity and biocontrol potential of field Aedes ssp.: Implications for disease vector management.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302328},
pmid = {38683843},
issn = {1932-6203},
mesh = {*Aedes/microbiology ; Animals ; *Microbiota ; *Mosquito Vectors/microbiology ; *RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/physiology/isolation & purification ; Larva/microbiology ; Metagenomics/methods ; Mexico ; Mosquito Control/methods ; },
abstract = {The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages-eggs, larvae, and adults-gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.},
}

*Aedes/microbiology
Animals
*Microbiota
*Mosquito Vectors/microbiology
*RNA, Ribosomal, 16S/genetics
Wolbachia/genetics/physiology/isolation & purification
Larva/microbiology
Metagenomics/methods
Mexico
Mosquito Control/methods

@article {pmid38683402,
year = {2024},
author = {Suslov, AV and Panas, A and Sinelnikov, MY and Maslennikov, RV and Trishina, AS and Zharikova, TS and Zharova, NV and Kalinin, DV and Pontes-Silva, A and Zharikov, YO},
title = {Applied physiology: gut microbiota and antimicrobial therapy.},
journal = {European journal of applied physiology},
volume = {},
number = {},
pages = {},
pmid = {38683402},
issn = {1439-6327},
abstract = {The gut microbiota plays an important role in maintaining human health and in the pathogenesis of several diseases. Antibiotics are among the most commonly prescribed drugs and have a significant impact on the structure and function of the gut microbiota. The understanding that a healthy gut microbiota prevents the development of many diseases has also led to its consideration as a potential therapeutic target. At the same time, any factor that alters the gut microbiota becomes important in this approach. Exercise and antibacterial therapy have a direct effect on the microbiota. The review reflects the current state of publications on the mechanisms of intestinal bacterial involvement in the pathogenesis of cardiovascular, metabolic, and neurodegenerative diseases. The physiological mechanisms of the influence of physical activity on the composition of the gut microbiota are considered. The mechanisms of the common interface between exercise and antibacterial therapy will be considered using the example of several socially important diseases. The aim of the study is to show the physiological relationship between the effects of exercise and antibiotics on the gut microbiota.},
}

@article {pmid38683195,
year = {2024},
author = {Cook, R and Telatin, A and Hsieh, SY and Newberry, F and Tariq, MA and Baker, DJ and Carding, SR and Adriaenssens, EM},
title = {Nanopore and Illumina sequencing reveal different viral populations from human gut samples.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001236},
pmid = {38683195},
issn = {2057-5858},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Genome, Viral ; *Gastrointestinal Microbiome/genetics ; *Feces/virology/microbiology ; Nanopores ; Nanopore Sequencing/methods ; Viruses/genetics/classification/isolation & purification ; Virome/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Genome, Viral
*Gastrointestinal Microbiome/genetics
*Feces/virology/microbiology
Nanopores
Nanopore Sequencing/methods
Viruses/genetics/classification/isolation & purification
Virome/genetics
Sequence Analysis, DNA/methods

@article {pmid38683185,
year = {2024},
author = {Thedim, M and Vacas, S},
title = {Postoperative Delirium and the Older Adult: Untangling the Confusion.},
journal = {Journal of neurosurgical anesthesiology},
volume = {},
number = {},
pages = {},
pmid = {38683185},
issn = {1537-1921},
abstract = {Postoperative delirium is one of the most prevalent postoperative complications, affecting mostly older adults. Its incidence is expected to rise because of surgical advances, shifting demographics, and increased life expectancy. Although an acute alteration in brain function, postoperative delirium is associated with adverse outcomes, including progressive cognitive decline and dementia, that place significant burdens on patients' lives and healthcare systems. This has prompted efforts to understand the mechanisms of postoperative delirium to provide effective prevention and treatment. There are multiple mechanisms involved in the etiology of postoperative delirium that share similarities with the physiological changes associated with the aging brain. In addition, older patients often have multiple comorbidities including increased cognitive impairment that is also implicated in the genesis of delirium. These tangled connections pinpointed a shift toward creation of a holistic model of the pathophysiology of postoperative delirium. Scientific advancements integrating clinical risk factors, possible postoperative delirium biomarkers, genetic features, digital platforms, and other biotechnical and information technological innovations, will become available in the near future. Advances in artificial intelligence, for example, will aggregate cognitive testing platforms with patient-specific postoperative delirium risk stratification studies, panels of serum and cerebrospinal fluid molecules, electroencephalogram signatures, and gut microbiome features, along with the integration of novel polygenetic variants of sleep and cognition. These advances will allow for the enrollment of high-risk patients into prevention programs and help uncover new pharmacologic targets.},
}

@article {pmid38683098,
year = {2024},
author = {Romero-Sánchez, C and Ferrer-Santos, C and Abril, D and Acosta-Hernández, E and Ávila, J and Ramos-Casallas, A and Escobar, J and Bautista-Molano, W and Jaimes, D and Beltrán-Ostos, A and Bello-Gualtero, JM and Flórez-Sarmiento, C and Parra-Izquierdo, V and Calixto, OJ},
title = {[Faecal microbiota study reveals specific dysbiosis in spondyloarthritis according to subtype, disease activity and treatment].},
journal = {Revista alergia Mexico (Tecamachalco, Puebla, Mexico : 1993)},
volume = {71},
number = {1},
pages = {81},
doi = {10.29262/ram.v71i1.1305},
pmid = {38683098},
issn = {2448-9190},
mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Adult ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Middle Aged ; Prohibitins ; Spondylarthritis/microbiology/drug therapy ; Spondylitis, Ankylosing/drug therapy/microbiology ; Arthritis, Psoriatic/microbiology/drug therapy ; Arthritis, Reactive/microbiology/drug therapy ; },
abstract = {OBJECTIVE: To compare the diversity and composition of the gastrointestinal microbiome of patients with SpA.

METHODS: MiSeq sequencing of the V3-V4 region of the 16S ribosomal RNA gene was performed on DNA isolated from stool. Patients with concurrent SpA and IBD were excluded. Differences were assessed for richness and diversity indices by QIIME 2™. Differences between means >0,2% with a p-value<0,05 were assumed significant. Institutional Ethics Committee endorsement.

RESULTS: 69 individuals included, 49 with SpA (ankylosing spondylitis-AS 72,9%, psoriatic arthritis-PsA 18,8%, reactive arthritis-ReA 8,3%) 5 positive controls-dysbiosis and 15 controls-eubiosis. Conventional treatment in 42,9%, anti-IL-17 16,3% and anti-TNF 40,8%. By subtype, statistically significant differences in favour of AS were found for the diversity indices. AS vs PsA there was a difference in favour of AS for Clostridium clostridioforme (p=0,002), Gemmiger formicilis (p=0,009), Roseburia inulivorans (p=0,008) and Lachnospira pectinoschiza. AS vs ReA there was a difference in favour of AS for L. pectinoschiza (p=0,009), Ruminococcus callidus (p=0.006), Clostridium ruminantium (p=0.031); G. formicilis (p=0,034). Diversity and richness showed differences in patients with high activity for Simpson's and Pielou's indices. In high activity, lower enrichment of Bacteroides eggerthii (p= 0,0003), C. ruminantium (p= 0,026) and Alistipes putredinis (p=0,035) was found. The number of ASV was higher in the anti-IL-17 vs conventional group (p=0.025) and a trend between anti-IL-17 vs anti-TNF (p=0.09). In anti-TNF there was a lower proportion for C. clostridioforme (p=0.023), G. formicilis (p=0.030) and R. callidus (p= 0.003). In anti IL-17, Alistipes indistinctus (p= 0.012) was decreased.

CONCLUSIONS: There are differences in microbial diversity for SpA subtypes. The level of disease activity is plausible to influence the composition of the faecal microbiota. Anti-TNFα treatment may influence the microbiome environment favouring restoration of the gut microbiota, while anti-IL-17 may maintain an inflammatory environment.},
}

Humans
*Dysbiosis/microbiology
Male
Female
Adult
*Feces/microbiology
*Gastrointestinal Microbiome
Middle Aged
Prohibitins
Spondylarthritis/microbiology/drug therapy
Spondylitis, Ankylosing/drug therapy/microbiology
Arthritis, Psoriatic/microbiology/drug therapy
Arthritis, Reactive/microbiology/drug therapy

@article {pmid38682956,
year = {2024},
author = {Pol, S and Kallonen, T and Mäklin, T and Sar, P and Hopkins, J and Soeng, S and Miliya, T and Ling, CL and Bentley, SD and Corander, J and Turner, P},
title = {Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing.},
journal = {mBio},
volume = {},
number = {},
pages = {e0078424},
doi = {10.1128/mbio.00784-24},
pmid = {38682956},
issn = {2150-7511},
abstract = {UNLABELLED: The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data.

IMPORTANCE: The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.},
}

@article {pmid38682944,
year = {2024},
author = {Gemeinhardt, K and Park, H and Won, JI and Lee, JH and Hwang, ET and Angenent, LT and Jeon, BS},
title = {Draft genome sequence of Magnusiomyces sp. LA-1 isolated from a C6-C8 acid-producing bioreactor.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0093523},
doi = {10.1128/mra.00935-23},
pmid = {38682944},
issn = {2576-098X},
abstract = {Here, we report the draft genome of Magnusiomyces sp. LA-1, which was isolated from a C6-C8 carboxylic acid-producing bioreactor. The draft genome of Magnusiomyces sp. LA-1 is 19,829,165 bp in length, is divided into six contigs that comprise 6,557 CDS regions, and has a GC content of 34.5%.},
}

@article {pmid38682799,
year = {2024},
author = {Abraham, JO and Lin, B and Miller, AE and Henry, LP and Demmel, MY and Warungu, R and Mwangi, M and Lobura, PM and Pallares, LF and Ayroles, JF and Pringle, RM and Rubenstein, DI},
title = {Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17370},
doi = {10.1111/mec.17370},
pmid = {38682799},
issn = {1365-294X},
support = {//High Meadows Environmental Institute, Princeton University/ ; 2019256075//National Science Foundation/ ; DEB-2225088//National Science Foundation/ ; },
abstract = {The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analysed faecal DNA for both the trnL-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (E. quagga) and Grevy's zebra (E. grevyi). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.},
}

@article {pmid38682769,
year = {2024},
author = {Vighnesh, L and Jagadeeshwari, U and Sasikala, C and Venkata Ramana, C},
title = {Metagenome-assembled genome of Zalaria obscura strain JY119.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0078623},
doi = {10.1128/mra.00786-23},
pmid = {38682769},
issn = {2576-098X},
abstract = {Here, we report a 22.1-Mbp genome sequence of microcolonial fungi, Zalaria obscura, isolated from a pine tree bark. The microbiome of the new fungi is predicted to be largely associated with Acidobacteriota. The genome sequence of Zalaria obscura will help us in understanding the unusual relationship with Acidobacteriota member(s).},
}

@article {pmid38682201,
year = {2024},
author = {Ayabe, RI and White, MG},
title = {Metastasis and the Microbiome: The Impact of Bacteria in Disseminated Colorectal Cancer.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {29},
number = {4},
pages = {152},
doi = {10.31083/j.fbl2904152},
pmid = {38682201},
issn = {2768-6698},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/therapy ; *Gastrointestinal Microbiome/physiology ; *Neoplasm Metastasis ; Dysbiosis/microbiology ; Bacteria/classification/genetics ; Fecal Microbiota Transplantation ; },
abstract = {Metastasis remains a leading cause of mortality for patients with solid tumors. An expanding body of literature suggests interplay between the host, gut, and tumoral microbiomes may play a role in cancer initiation and distant dissemination. These associations have been particularly well-studied in colorectal cancer, where gut dysbiosis and an endotoxin-induced inflammatory milieu foster premalignant polyp formation, setting the stage for carcinogenesis. Subsequent violation of the gut vascular barrier enables dissemination of bacterial agents to sites such as the liver, where they contribute to establishment of pre-metastatic niches, which promote tumor cell extravasation and metastatic outgrowth. Intriguingly, breakdown of this vascular barrier has been shown to be aided by the presence of tumoral bacteria. The presence of similar species, including Fusobacterium nucleatum and Escherichia Coli, in both primary and metastatic colorectal tumors, supports this hypothesis and their presence is associated with chemotherapy resistance and an overall poor prognosis. Specific gut microbial populations are also associated with differential response to immunotherapy, which has a growing role in microsatellite unstable colorectal cancers. Recent work suggests that modulation of gut microbiome using dietary modification, targeted antibiotics, or fecal microbiota transplantation may improve response to immunotherapy and oncologic outcomes. Elucidation of the precise mechanistic links between the microbiome and cancer dissemination will open the doors to additional therapeutic possibilities.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/therapy
*Gastrointestinal Microbiome/physiology
*Neoplasm Metastasis
Dysbiosis/microbiology
Bacteria/classification/genetics
Fecal Microbiota Transplantation

@article {pmid38682010,
year = {2024},
author = {Yang, Y and Xu, Z and Guo, J and Xiong, Z and Hu, B},
title = {Exploring the gut microbiome-Postoperative Cognitive Dysfunction connection: Mechanisms, clinical implications, and future directions.},
journal = {Brain, behavior, & immunity - health},
volume = {38},
number = {},
pages = {100763},
pmid = {38682010},
issn = {2666-3546},
abstract = {Postoperative Cognitive Dysfunction (POCD) is a common yet poorly understood complication of surgery that can lead to long-term cognitive decline. The gut-brain axis, a bidirectional communication system between the central nervous system and the gut microbiota, plays a significant role in maintaining cognitive health. The potential for anesthetic agents and perioperative medications to modulate the gut microbiota and influence the trajectory of POCD suggests the need for a more integrated approach in perioperative care. Perioperative medications, including opioids and antibiotics, further compound these disruptions, leading to dysbiosis and consequent systemic and neuroinflammation implicated in cognitive impairment. Understanding how surgical interventions and associated treatments affect this relationship is crucial for developing strategies to reduce the incidence of POCD. Strategies to preserve and promote a healthy gut microbiome may mitigate the risk and severity of POCD. Future research should aim to clarify the mechanisms linking gut flora alterations to cognitive outcomes and explore targeted interventions, such as probiotic supplementation and microbiota-friendly prescription practices, to safeguard cognitive function postoperatively.},
}

@article {pmid38681959,
year = {2024},
author = {Wang, H and Kim, R and Wang, Y and Furtado, KL and Sims, CE and Tamayo, R and Allbritton, NL},
title = {In vitro co-culture of Clostridium scindens with primary human colonic epithelium protects the epithelium against Staphylococcus aureus.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1382389},
pmid = {38681959},
issn = {2296-4185},
abstract = {A complex and dynamic network of interactions exists between human gastrointestinal epithelium and intestinal microbiota. Therefore, comprehending intestinal microbe-epithelial cell interactions is critical for the understanding and treatment of intestinal diseases. Primary human colonic epithelial cells derived from a healthy human donor were co-cultured with Clostridium scindens (C. scindens), a probiotic obligate anaerobe; Staphylococcus aureus (S. aureus), a facultative anaerobe and intestinal pathogen; or both bacterial species in tandem. The co-culture hanging basket platform used for these experiments possessed walls of controlled oxygen (O2) permeability to support the formation of an O2 gradient across the intestinal epithelium using cellular O2 consumption, resulting in an anaerobic luminal and aerobic basal compartment. Both the colonic epithelial cells and C. scindens remained viable over 48 h during co-culture. In contrast, co-culture with S. aureus elicited significant damage to colonic epithelial cells within 24 h. To explore the influence of the intestinal pathogen on the epithelium in the presence of the probiotic bacteria, colonic epithelial cells were inoculated sequentially with the two bacterial species. Under these conditions, C. scindens was capable of repressing the production of S. aureus enterotoxin. Surprisingly, although C. scindens converted cholic acid to secondary bile acids in the luminal medium, the growth of S. aureus was not significantly inhibited. Nevertheless, this combination of probiotic and pathogenic bacteria was found to benefit the survival of the colonic epithelial cells compared with co-culture of the epithelial cells with S. aureus alone. This platform thus provides an easy-to-use and low-cost tool to study the interaction between intestinal bacteria and colonic cells in vitro to better understand the interplay of intestinal microbiota with human colonic epithelium.},
}

@article {pmid38681863,
year = {2024},
author = {Moeckli, B and Delaune, V and Gilbert, B and Peloso, A and Oldani, G and El Hajji, S and Slits, F and Ribeiro, JR and Mercier, R and Gleyzolle, A and Rubbia-Brandt, L and Gex, Q and Lacotte, S and Toso, C},
title = {Maternal obesity increases the risk of hepatocellular carcinoma through the transmission of an altered gut microbiome.},
journal = {JHEP reports : innovation in hepatology},
volume = {6},
number = {5},
pages = {101056},
pmid = {38681863},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Emerging evidence suggests that maternal obesity negatively impacts the health of offspring. Additionally, obesity is a risk factor for hepatocellular carcinoma (HCC). Our study aims to investigate the impact of maternal obesity on the risk for HCC development in offspring and elucidate the underlying transmission mechanisms.

METHODS: Female mice were fed either a high-fat diet (HFD) or a normal diet (ND). All offspring received a ND after weaning. We studied liver histology and tumor load in a N-diethylnitrosamine (DEN)-induced HCC mouse model.

RESULTS: Maternal obesity induced a distinguishable shift in gut microbial composition. At 40 weeks, female offspring of HFD-fed mothers (HFD offspring) were more likely to develop steatosis (9.43% vs. 3.09%, p = 0.0023) and fibrosis (3.75% vs. 2.70%, p = 0.039), as well as exhibiting an increased number of inflammatory infiltrates (4.8 vs. 1.0, p = 0.018) and higher expression of genes involved in fibrosis and inflammation, compared to offspring of ND-fed mothers (ND offspring). A higher proportion of HFD offspring developed liver tumors after DEN induction (79.8% vs. 37.5%, p = 0.0084) with a higher mean tumor volume (234 vs. 3 μm[3], p = 0.0041). HFD offspring had a significantly less diverse microbiota than ND offspring (Shannon index 2.56 vs. 2.92, p = 0.0089), which was rescued through co-housing. In the principal component analysis, the microbiota profile of co-housed animals clustered together, regardless of maternal diet. Co-housing of HFD offspring with ND offspring normalized their tumor load.

CONCLUSIONS: Maternal obesity increases female offspring's susceptibility to HCC. The transmission of an altered gut microbiome plays an important role in this predisposition.

IMPACT AND IMPLICATIONS: The worldwide incidence of obesity is constantly rising, with more and more children born to obese mothers. In this study, we investigate the impact of maternal diet on gut microbiome composition and its role in liver cancer development in offspring. We found that mice born to mothers with a high-fat diet inherited a less diverse gut microbiome, presented chronic liver injury and an increased risk of developing liver cancer. Co-housing offspring from normal diet- and high-fat diet-fed mothers restored the gut microbiome and, remarkably, normalized the risk of developing liver cancer. The implementation of microbial screening and restoration of microbial diversity holds promise in helping to identify and treat individuals at risk to prevent harm for future generations.},
}

@article {pmid38681527,
year = {2024},
author = {Chen, X and Moreno, LL and Tang, X and Gasaly, N and Schols, HA and de Vos, P},
title = {A novel "microbiota-host interaction model" to study the real-time effects of fermentation of non-digestible carbohydrate (NDCs) on gut barrier function.},
journal = {Current research in food science},
volume = {8},
number = {},
pages = {100736},
pmid = {38681527},
issn = {2665-9271},
abstract = {In this study, an in vitro co-culture model using an electric cell-substrate impedance sensing system (ECIS) for testing the impact of real-time fermentation of non-digestible carbohydrates (NDCs) by the intestinal microbiota on gut barrier function was established. We applied Lactobacillus plantarum WCFS1 as a model intestinal bacterium and alginate-pectin as immobilization polymers as well as a source of NDCs to determine the impact of pectin fermentation on the barrier function of T84 gut epithelial cells. In the first design, L. plantarum WCFS1 was encapsulated in an alginate capsule followed by embedding in an agar layer to mimic a firm mucus layer that might be present in the colon. In this experimental design, the presence of the agar layer interfered with the transepithelial electrical resistance (TEER) measurement of T84 cells. Subsequently, we removed the agar layer and used encapsulated bacteria in an alginate gel and found that the TEER measurement was adequate. The encapsulation of the L. plantarum WCFS1 does avoid direct contact with cells. Also, the encapsulation system allows higher amounts of packing densities of L. plantarum WCFS1 in a limited space which can limit the oxygen concentration within the capsule and therefore create anaerobic conditions. To test this design, T84 cells were co-incubated with L. plantarum alginate-capsules supplemented with graded loads of fermentable pectin (0, 4, and 8 mg/ml per capsule) to investigate the effect of pectin fermentation on gut barrier function. We observed that as the pectin content in the L. plantarum capsules increased, pectin showed a gradually stronger protective effect on the TEER of the gut epithelium. This could partly be explained by enhanced SCFA production as both lactate and acetate were enhanced in L. plantarum containing alginate capsules with 8 mg/ml pectin. Overall, this newly designed in vitro co-culture model allows for studying the impact of bacteria-derived fermentation products but also for studying the direct effects of NDCs on gut barrier function in a relatively high-throughput way.},
}

@article {pmid38681125,
year = {2024},
author = {Wu, QL and Fang, XT and Wan, XX and Ding, QY and Zhang, YJ and Ji, L and Lou, YL and Li, X},
title = {Fusobacterium nucleatum-induced imbalance in microbiome-derived butyric acid levels promotes the occurrence and development of colorectal cancer.},
journal = {World journal of gastroenterology},
volume = {30},
number = {14},
pages = {2018-2037},
pmid = {38681125},
issn = {2219-2840},
mesh = {*Fusobacterium nucleatum ; Animals ; *Colorectal Neoplasms/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Butyric Acid/pharmacology/metabolism ; Humans ; *Mice, Inbred BALB C ; Mice ; *Feces/microbiology ; *Cell Proliferation/drug effects ; HCT116 Cells ; Male ; Mitochondria/metabolism/drug effects ; Fusobacterium Infections/microbiology ; Disease Models, Animal ; Cell Line, Tumor ; Female ; Disease Progression ; Dysbiosis ; Membrane Potential, Mitochondrial/drug effects ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignant tumors globally. Recent reports suggest that Fusobacterium nucleatum (F. nucleatum) contributes to the initiation, progression, and prognosis of CRC. Butyrate, a short-chain fatty acid derived from the bacterial fermentation of soluble dietary fiber, is known to inhibit various cancers. This study is designed to explore whether F. nucleatum influences the onset and progression of CRC by impacting the intestinal metabolite butyric acid.

AIM: To investigate the mechanism by which F. nucleatum affects CRC occurrence and development.

METHODS: Alterations in the gut microbiota of BALB/c mice were observed following the oral administration of F. nucleatum. Additionally, DLD-1 and HCT116 cell lines were exposed to sodium butyrate (NaB) and F. nucleatum in vitro to examine the effects on proliferative proteins and mitochondrial function.

RESULTS: Our research indicates that the prevalence of F. nucleatum in fecal samples from CRC patients is significantly greater than in healthy counterparts, while the prevalence of butyrate-producing bacteria is notably lower. In mice colonized with F. nucleatum, the population of butyrate-producing bacteria decreased, resulting in altered levels of butyric acid, a key intestinal metabolite of butyrate. Exposure to NaB can impair mitochondrial morphology and diminish mitochondrial membrane potential in DLD-1 and HCT116 CRC cells. Consequently, this leads to modulated production of adenosine triphosphate and reactive oxygen species, thereby inhibiting cancer cell proliferation. Additionally, NaB triggers the adenosine monophosphate-activated protein kinase (AMPK) signaling pathway, blocks the cell cycle in HCT116 and DLD-1 cells, and curtails the proliferation of CRC cells. The combined presence of F. nucleatum and NaB attenuated the effects of the latter. By employing small interfering RNA to suppress AMPK, it was demonstrated that AMPK is essential for NaB's inhibition of CRC cell proliferation.

CONCLUSION: F. nucleatum can promote cancer progression through its inhibitory effect on butyric acid, via the AMPK signaling pathway.},
}

*Fusobacterium nucleatum
Animals
*Colorectal Neoplasms/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Butyric Acid/pharmacology/metabolism
Humans
*Mice, Inbred BALB C
Mice
*Feces/microbiology
*Cell Proliferation/drug effects
HCT116 Cells
Male
Mitochondria/metabolism/drug effects
Fusobacterium Infections/microbiology
Disease Models, Animal
Cell Line, Tumor
Female
Disease Progression
Dysbiosis
Membrane Potential, Mitochondrial/drug effects

@article {pmid38680954,
year = {2024},
author = {Hastings, MH and Castro, C and Freeman, R and Abdul Kadir, A and Lerchenmüller, C and Li, H and Rhee, J and Roh, JD and Roh, K and Singh, AP and Wu, C and Xia, P and Zhou, Q and Xiao, J and Rosenzweig, A},
title = {Intrinsic and Extrinsic Contributors to the Cardiac Benefits of Exercise.},
journal = {JACC. Basic to translational science},
volume = {9},
number = {4},
pages = {535-552},
pmid = {38680954},
issn = {2452-302X},
abstract = {Among its many cardiovascular benefits, exercise training improves heart function and protects the heart against age-related decline, pathological stress, and injury. Here, we focus on cardiac benefits with an emphasis on more recent updates to our understanding. While the cardiomyocyte continues to play a central role as both a target and effector of exercise's benefits, there is a growing recognition of the important roles of other, noncardiomyocyte lineages and pathways, including some that lie outside the heart itself. We review what is known about mediators of exercise's benefits-both those intrinsic to the heart (at the level of cardiomyocytes, fibroblasts, or vascular cells) and those that are systemic (including metabolism, inflammation, the microbiome, and aging)-highlighting what is known about the molecular mechanisms responsible.},
}

@article {pmid38680914,
year = {2024},
author = {Wang, J and Zhang, S and Kong, J and Chang, J},
title = {Pecan secondary metabolites influenced the population of Zeuzera coffeae by affecting the structure and function of the larval gut microbiota.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1379488},
pmid = {38680914},
issn = {1664-302X},
abstract = {BACKGROUND: The plant secondary metabolites (PSMs), as important plant resistance indicators, are important targets for screening plant insect resistance breeding. In this study, we aimed to investigate whether the population of Zeuzera coffeae (ZC) is affected by different varieties of Carya illinoinensis PSMs content. At the same time, the structure and function of the gut microbiome of ZC were also analyzed in relation to different pecan varieties.

METHODS: We counted the populations of ZC larvae in four pecan varieties and determined the content of four types of PSMs. The structure and function of the larval gut microbiota were studied in connection to the number of larvae and the content of PSMs. The relationships were investigated between larval number, larval gut microbiota, and PSM content.

RESULTS: We found that the tannins, total phenolics, and total saponins of 4 various pecans PSMs stifled the development of the ZC larval population. The PSMs can significantly affect the diversity and abundance of the larval gut microbiota. Enrichment of ASV46 (Pararhizobium sp.), ASV994 (Olivibacter sp.), ASV743 (Rhizobium sp.), ASV709 (Rhizobium sp.), ASV671 (Luteolibacter sp.), ASV599 (Agrobacterium sp.), ASV575 (Microbacterium sp.), and ASV27 (Rhizobium sp.) in the gut of larvae fed on high-resistance cultivars was positively associated with their tannin, total saponin, and total phenolic content. The results of the gut microbiome functional prediction for larvae fed highly resistant pecan varieties showed that the enriched pathways in the gut were related to the breakdown of hazardous chemicals.

CONCLUSION: Our findings provide further evidence that pecan PSMs influence the structure and function of the gut microbiota, which in turn affects the population stability of ZC. The study's findings can serve as a theoretical foundation for further work on selecting ZC-resistant cultivars and developing green management technology for ZC.},
}

@article {pmid38680911,
year = {2024},
author = {Chen See, JR and Leister, J and Wright, JR and Kruse, PI and Khedekar, MV and Besch, CE and Kumamoto, CA and Madden, GR and Stewart, DB and Lamendella, R},
title = {Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1398018},
pmid = {38680911},
issn = {1664-302X},
abstract = {Clostridioides difficile infection (CDI) is responsible for around 300,000 hospitalizations yearly in the United States, with the associated monetary cost being billions of dollars. Gut microbiome dysbiosis is known to be important to CDI. To the best of our knowledge, metatranscriptomics (MT) has only been used to characterize gut microbiome composition and function in one prior study involving CDI patients. Therefore, we utilized MT to investigate differences in active community diversity and composition between CDI+ (n = 20) and CDI- (n = 19) samples with respect to microbial taxa and expressed genes. No significant (Kruskal-Wallis, p > 0.05) differences were detected for richness or evenness based on CDI status. However, clustering based on CDI status was significant for both active microbial taxa and expressed genes datasets (PERMANOVA, p ≤ 0.05). Furthermore, differential feature analysis revealed greater expression of the opportunistic pathogens Enterocloster bolteae and Ruminococcus gnavus in CDI+ compared to CDI- samples. When only fungal sequences were considered, the family Saccharomycetaceae expressed more genes in CDI-, while 31 other fungal taxa were identified as significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) associated with CDI+. We also detected a variety of genes and pathways that differed significantly (Kruskal-Wallis p ≤ 0.05, log(LDA) ≥ 2) based on CDI status. Notably, differential genes associated with biofilm formation were expressed by C. difficile. This provides evidence of another possible contributor to C. difficile's resistance to antibiotics and frequent recurrence in vivo. Furthermore, the greater number of CDI+ associated fungal taxa constitute additional evidence that the mycobiome is important to CDI pathogenesis. Future work will focus on establishing if C. difficile is actively producing biofilms during infection and if any specific fungal taxa are particularly influential in CDI.},
}

@article {pmid38680886,
year = {2024},
author = {Nimnoi, P and Pirankham, P and Srimuang, K and Ruanpanun, P},
title = {Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17289},
pmid = {38680886},
issn = {2167-8359},
mesh = {Animals ; Thailand ; *Oryza/microbiology/parasitology ; *Rhizosphere ; *Soil Microbiology ; *Nematoda/microbiology ; Bacteria/classification/isolation & purification/genetics ; Microbiota ; Soil/parasitology/chemistry ; Biodiversity ; Southeast Asian People ; },
abstract = {Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.},
}

Animals
Thailand
*Oryza/microbiology/parasitology
*Rhizosphere
*Soil Microbiology
*Nematoda/microbiology
Bacteria/classification/isolation & purification/genetics
Microbiota
Soil/parasitology/chemistry
Biodiversity
Southeast Asian People

@article {pmid38680731,
year = {2024},
author = {Song, Y and Yao, S and Li, X and Wang, T and Jiang, X and Bolan, N and Warren, CR and Northen, TR and Chang, SX},
title = {Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems.},
journal = {Eco-Environment & Health},
volume = {3},
number = {2},
pages = {227-237},
pmid = {38680731},
issn = {2772-9850},
abstract = {Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.},
}

@article {pmid38680700,
year = {2024},
author = {Xu, YW and Tian, J and Song, Y and Zhang, BC and Wang, J},
title = {Metabolic syndrome's new therapy: Supplement the gut microbiome.},
journal = {World journal of diabetes},
volume = {15},
number = {4},
pages = {793-796},
pmid = {38680700},
issn = {1948-9358},
abstract = {This letter to the editor discusses the publication on gut microbiome supplementation as therapy for metabolic syndrome. Gut microbiome dysbiosis disrupts intestinal bacterial homeostasis and is related to chronic inflammation, insulin resistance, cardiovascular diseases, type 2 diabetes mellitus, and obesity. Previous research has found that increasing the abundance of beneficial microbiota in the gut modulates metabolic syndrome by reducing chronic inflammation and insulin resistance. Prebiotics, probiotics, synbiotics, and postbiotics are often used as supplements to increase the number of beneficial microbes and thus the production of short-chain fatty acids, which have positive effects on the gut microbiome and metabolic syndrome. In this review article, the author summarizes the available supplements to increase the abundance of beneficial gut microbiota and reduce the abundance of harmful microbiota in patients with metabolic disorders. Our group is also researching the role of the gut microbiota in chronic liver disease. This article will be of great help to our research. At the end of the letter, the mechanism of the gut microbiota in chronic liver disease is discussed.},
}

@article {pmid38680610,
year = {2024},
author = {Duarte, MJ and Tien, PC and Kardashian, A and Ma, Y and Hunt, P and Kuniholm, MH and Adimora, AA and Fischl, MA and French, AL and Topper, E and Konkle-Parker, D and Minkoff, H and Ofotokun, I and Plankey, M and Sharma, A and Price, JC},
title = {Microbial Translocation and Gut Damage Are Associated With an Elevated Fast Score in Women Living With and Without HIV.},
journal = {Open forum infectious diseases},
volume = {11},
number = {5},
pages = {ofae187},
pmid = {38680610},
issn = {2328-8957},
abstract = {BACKGROUND: Steatohepatitis is common in persons living with HIV and may be associated with gut microbial translocation (MT). However, few studies have evaluated the gut-liver axis in persons living with HIV. In the Women's Interagency HIV Study, we examined the associations of HIV and circulating biomarkers linked to MT and gut damage using the FibroScan-aspartate aminotransferase (FAST) score, a noninvasive surrogate for steatohepatitis with advanced fibrosis.

METHODS: Among 883 women with HIV and 354 without HIV, we used multivariable regression to examine the associations of HIV and serum biomarkers linked to MT and gut damage (kynurenine and tryptophan ratio, intestinal fatty acid-binding protein, soluble CD14, and soluble CD163) with a log-transformed FAST score after adjusting for key covariates. We used a path analysis and mediation models to determine the mediating effect of each biomarker on the association of HIV with FAST.

RESULTS: HIV infection was associated with a 49% higher FAST score. MT biomarker levels were higher in women with HIV than women without HIV (P < .001 for each). MT biomarkers mediated 13% to 32% of the association of HIV and FAST score.

CONCLUSIONS: Biomarkers linked to MT and gut damage are associated with a higher FAST score and mediate the association of HIV with a higher FAST score. Our findings suggest that MT may be an important mechanism by which HIV increases the risk of steatohepatitis with advanced fibrosis.},
}

@article {pmid38680585,
year = {2024},
author = {Dornbier, RA and Doshi, CP and Desai, SC and Bajic, P and Van Kuiken, M and Khemmani, M and Farooq, AV and Bresler, L and Turk, TMT and Wolfe, AJ and Baldea, KG},
title = {Metabolic syndrome and the urinary microbiome of patients undergoing percutaneous nephrolithotomy.},
journal = {Asian journal of urology},
volume = {11},
number = {2},
pages = {316-323},
pmid = {38680585},
issn = {2214-3882},
abstract = {OBJECTIVE: To identify possible stone-promoting microbes, we compared the profiles of microbes grown from stones of patients with and without metabolic syndrome (MetS). The association between MetS and urinary stone disease is well established, but the exact pathophysiologic relationship remains unknown. Recent evidence suggests urinary tract dysbiosis may lead to increased nephrolithiasis risk.

METHODS: At the time of percutaneous nephrolithotomy, bladder urine and stone fragments were collected from patients with and without MetS. Both sample types were subjected to expanded quantitative urine culture (EQUC) and 16 S ribosomal RNA gene sequencing.

RESULTS: Fifty-seven patients included 12 controls (21.1%) and 45 MetS patients (78.9%). Both cohorts were similar with respect to demographics and non-MetS comorbidities. No controls had uric acid stone composition. By EQUC, bacteria were detected more frequently in MetS stones (42.2%) compared to controls (8.3%) (p=0.041). Bacteria also were more abundant in stones of MetS patients compared to controls. To validate our EQUC results, we performed 16 S ribosomal RNA gene sequencing. In 12/16 (75.0%) sequence-positive stones, EQUC reliably isolated at least one species of the sequenced genera. Bacteria were detected in both "infectious" and "non-infectious" stone compositions.

CONCLUSION: Bacteria are more common and more abundant in MetS stones than control stones. Our findings support a role for bacteria in urinary stone disease for patients with MetS regardless of stone composition.},
}

@article {pmid38680177,
year = {2024},
author = {Druzhinin, VG and Baranova, ED and Demenkov, PS and Matskova, LV and Larionov, AV},
title = {Composition of the sputum bacterial microbiome of patients with different pathomorphological forms of non-small-cell lung cancer.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {2},
pages = {204-214},
doi = {10.18699/vjgb-24-25},
pmid = {38680177},
issn = {2500-0462},
abstract = {Recent studies have shown that the bacterial microbiome of the respiratory tract influences the development of lung cancer. Changes in the composition of the microbiome are observed in patients with chronic inflammatory processes. Such microbiome changes may include the occurrence of bacteria that cause oxidative stress and that are capable of causing genome damage in the cells of the host organism directly and indirectly. To date, the composition of the respiratory microbiome in patients with various histological variants of lung cancer has not been studied. In the present study, we determined the taxonomic composition of the sputum microbiome of 52 patients with squamous cell carcinoma of the lung, 52 patients with lung adenocarcinoma and 52 healthy control donors, using next-generation sequencing (NGS) on the V3-V4 region of the bacterial gene encoding 16S rRNA. The sputum microbiomes of patients with different histological types of lung cancer and controls did not show significant differences in terms of the species richness index (Shannon); however, the patients differed from the controls in terms of evenness index (Pielou). The structures of bacterial communities (beta diversity) in the adenocarcinoma and squamous cell carcinoma groups were also similar; however, when analyzed according to the matrix constructed by the Bray-Curtis method, there were differences between patients with squamous cell carcinoma and healthy subjects, but not between those with adenocarcinoma and controls. Using the LEFse method it was possible to identify an increase in the content of Bacillota (Streptococcus and Bacillus) and Actinomycetota (Rothia) in the sputum of patients with squamous cell carcinoma when compared with samples from patients with adenocarcinoma. There were no differences in the content of bacteria between the samples of patients with adenocarcinoma and the control ones. The content of representatives of the genera Streptococcus, Bacillus, Peptostreptococcus (phylum Bacillota), Prevotella, Macellibacteroides (phylum Bacteroidota), Rothia (phylum Actinomycetota) and Actinobacillus (phylum Pseudomonadota) was increased in the microbiome of sputum samples from patients with squamous cell carcinoma, compared with the control. Thus, the sputum bacterial microbiome of patients with different histological types of non-small-cell lung cancer has significant differences. Further research should be devoted to the search for microbiome biomarkers of lung cancer at the level of bacterial species using whole-genome sequencing.},
}

@article {pmid38679911,
year = {2024},
author = {Fahad, M and Tariq, L and Muhammad, S and Wu, L},
title = {Underground Communication: Long Noncoding RNA Signaling in the Plant Rhizosphere.},
journal = {Plant communications},
volume = {},
number = {},
pages = {100927},
doi = {10.1016/j.xplc.2024.100927},
pmid = {38679911},
issn = {2590-3462},
abstract = {Long non-coding RNAs (lncRNAs) have emerged as integral gene expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous and dynamic rhizosphere, plants use interconnected regulatory mechanisms to optimally fine-tune gene expression governing interactions with soil biota, nutrient acquisition, and heavy metal tolerance. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues. Here, we examine lncRNA biogenesis, classification, and mode of action, highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors. We then discuss studies that revealed lncRNA significance and target genes during developmental plasticity and stress responses at the rhizobium interface. Thus, a comprehensive understanding of specific lncRNAs, their regulatory targets, and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals. As we look ahead, we foresee that single-cell dissection of cell type-specific lncRNA regulatory dynamics will enhance our understanding of precise developmental modulation mechanisms enabling plant rhizosphere adaptation. Overcoming future challenges through multi-omics and genetic approaches will better reveal the integral lncRNA roles governing plant adaptation to the belowground environment.},
}

@article {pmid38679353,
year = {2024},
author = {Bai, F and You, L and Lei, H and Li, X},
title = {Association between increased and decreased gut microbiota abundance and Parkinson's disease: A systematic review and subgroup meta-analysis.},
journal = {Experimental gerontology},
volume = {191},
number = {},
pages = {112444},
doi = {10.1016/j.exger.2024.112444},
pmid = {38679353},
issn = {1873-6815},
abstract = {OBJECTIVE: The objective of the study was to systematically investigate the association between gut microbiota (GM) abundance and Parkinson's disease (PD).

METHODS: PubMed, Medline, Cochrane Library and other literature datebase platforms were searched for eligible studies in the English-language from conception to March 1, 2024. Studies evaluating the association between GM and PD were included. The results of the included studies were analyzed using a random effects model with calculation of the mean difference (MD) with the 95 % confidence interval to quantify the incidence of differences in abundance of various bacterial families in PD patients. Continuous models were used to analyze the extracted data.

RESULTS: A total of 14 studies with 1045 PD cases and 821 healthy controls were included for data extraction and meta-analysis. All the included studies exhibited reasonable quality. The included studies reported the data on the ratios of 10 families of GM. Of these 10 microbiota families, Bifidobacteriaceae, Ruminococcaceae, Rikenellaceae, Lactobacillaceae, Verrucomicrobiaceae and Christensenellaceae were found to have increased ratios according to the pooled ratios, while Prevotellaceae, Lachnospiraceae, Erysipelotrichaceae and Faecalibacterium were decreased in PD cases.

CONCLUSION: Patients in the PD cohort exhibited distinctive microbiota compositions compared to healthy individuals, with unique differential patterns in gut microbiome abundance at the phylum, family, and genus levels that may be associated wtih PD pathogenesis.},
}

@article {pmid38679133,
year = {2024},
author = {Pei, L and Weiye, W and Ka Fung, Y and Raymond Wai Man, T and Xiaoli, G and Edward Chin Man, L and May Chun Mei, W},
title = {Can Oral Microbiome Predict Low Birth Weight Infant Delivery?.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105018},
doi = {10.1016/j.jdent.2024.105018},
pmid = {38679133},
issn = {1879-176X},
abstract = {OBJECTIVES: This study aimed to identify the oral microbiota factors contributing to low birth weight (LBW) in Chinese pregnant women and develop a prediction model using machine learning.

METHODS: A nested case-control study was conducted in a prospective cohort of 580 Chinese pregnant women, with 23 LBW cases and 23 healthy delivery controls matched for age and smoking habit. Saliva samples were collected at early and late pregnancy, and microbiome profiles were analyzed through 16S rRNA gene sequencing.

RESULTS: The relative abundance of Streptococcus was over-represented (median 0.259 vs. 0.116) and Saccharibacteria_TM7 was under-represented (median 0.033 vs. 0.068) in the LBW case group than in controls (p<0.001, p=0.015 respectively). Ten species were identified as microbiome biomarkers of LBW by LEfSe analysis, which included 7 species within the genus of Streptococcus or as part of 'nutritionally variant streptococci' (NVS), 2 species of opportunistic pathogen Leptotrichia buccalis and Gemella sanguinis (all LDA score>3.5) as risk biomarkers, and one species of Saccharibacteria TM7 as a beneficial biomarker (LDA= -4.5). The machine-learning model based on these 10 distinguished oral microbiota species could predict LBW, with an accuracy of 82%, sensitivity of 91%, and specificity of 73% (AUC-ROC score 0.89, 95% CI: 0.75-1.0). Results of α-diversity showed that mothers who delivered LBW infants had less stable salivary microbiota construction throughout pregnancy than the control group (measured by Shannon, p=0.048; and Pielou's, p=0.021), however the microbiome diversity did not improve the prediction accuracy of LBW.

CONCLUSIONS: A machine-learning oral microbiome model shows promise in predicting low-birth-weight delivery. Even in cases where oral health is not significantly compromised, opportunistic pathogens or rarer taxa associated with adverse pregnancy outcomes can still be identified in the oral cavity.

CLINICAL SIGNIFICANCE: This study highlights the potential complexity of the relationship between oral microbiome and pregnancy outcomes, indicating that mechanisms underlying the association between oral microbiota and adverse pregnancy outcomes may involve complex interactions between host factors, microbiota, and systemic conditions. Using machine learning to develop a predictive model based on specific oral microbiota biomarkers provides a potential for personalized medicine approaches. Future prediction models should incorporate clinical metadata to be clinically useful for improving maternal and child health.},
}

@article {pmid38679108,
year = {2024},
author = {Dang, P and Lu, C and Huang, T and Zhang, M and Yang, N and Han, X and Xu, C and Wang, S and Wan, C and Qin, X and Siddique, KHM},
title = {Enhancing intercropping sustainability: Manipulating soybean rhizosphere microbiome through cropping patterns.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172714},
doi = {10.1016/j.scitotenv.2024.172714},
pmid = {38679108},
issn = {1879-1026},
abstract = {Understanding the responses of soybean rhizosphere and functional microbiomes in intercropping scenarios holds promise for optimizing nitrogen utilization in legume-based intercropping systems. This study investigated three cropping layouts under film mulching: sole soybean (S), soybean-maize intercropping in one row (IS), and soybean-maize intercropping in two rows (IIS), each subjected to two nitrogen levels: 110 kg N ha[-1] (N110) and 180 kg N ha[-1] (N180). Our findings reveal that cropping patterns alter bacterial and nifh communities, with approximately 5 % of soybean rhizosphere bacterial amplicon sequence variants (ASVs) and 42 % of rhizosphere nifh ASVs exhibiting altered abundances (termed sensitive ASVs). Root traits and soil properties shape these communities, with root traits exerting greater influence. Sensitive ASVs drive microbial co-occurrence networks and deterministic processes, predicting 85 % of yield variance and 78 % of partial factor productivity of nitrogen, respectively. These alterations impact bacterial and nifh diversity, complexity, stability, and deterministic processes in legume-based intercropping systems, enhancing performance in terms of yield, nitrogen utilization efficiency, land equivalent ratio, root nodule count, and nodule dry weight under IIS patterns with N110 compared to other treatments. Our findings underscore the importance of field management practices in shaping rhizosphere-sensitive ASVs, thereby altering microbial functions and ultimately impacting the productivity of legume-based intercropping systems. This mechanistic understanding of soybean rhizosphere microbial responses to intercropping patterns offers insights for sustainable intercropping enhancements through microbial manipulation.},
}

@article {pmid38679006,
year = {2024},
author = {Wang, K and Fu, Y and Li, L and Zhang, L and Huang, M and Yan, W and Shan, X and Yan, Z and Lu, Y},
title = {Gut microbiota moderates multimodal brain structure-function integration and behavioral cognition in growth hormone deficient children.},
journal = {Neuroendocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000539097},
pmid = {38679006},
issn = {1423-0194},
abstract = {Background Previous brain studies of growth hormone deficiency (GHD) often used single-mode neuroimaging, missing the complexity captured by multimodal data. Growth hormone affects gut microbiota and metabolism in GHD. However, from a gut-brain axis perspective, the relationship between abnormal GHD brain development and microbiota alterations remains unclear. The ultimate goal is to uncover the manifestations underlying gut-brain axis (GBA) abnormalities in GHD and idiopathic short stature (ISS). Methods Participants included 23 GHD and 25 ISS children. The fusion independent component analysis was applied to integrat multimodal brain datas (high resolution structural, diffusion tensor, and resting state functional MRI) covering regional homogeneity (ReHo), amplitude of low frequency fluctuations (ALFF), and White matter fractional anisotropy (FA). Gut microbiome diversity and metabolites were analyzed using 16S sequencing and proton nuclear magnetic resonance (1H-NMR). Associations between multimodal neuroimaging and cognition were assessed using moderation analysis. Results Six components (ReHo, ALFF, and FA) differed significantly between GHD and ISS patients, with three functional components linked to processing speed. GHD individuals showed higher levels of acetate in microbiota metabolism. Higher alpha diversity in GHD strengthened connections between ReHo-IC1, ReHo-IC5, ALFF-IC1, and processing speed, while increasing Agathobacter levels in ISS weakened the link between ALFF-IC1 and speech comprehension. Conclusions Our findings uncover differing brain structure and functional fusion in GHD, alongside microbiota metabolism of short-chain fatty acids. Additionally, microbiome influences connections between neuroimaging and cognition, offering insight into diverse gut-brain axis patterns in GHD and ISS, enhancing our understanding of the disease's pathophysiology and interventions.},
}

@article {pmid38678973,
year = {2024},
author = {Hoepers, PG and Nunes, PLF and Almeida-Souza, HO and Martins, MM and Carvalho, RDO and Dreyer, CT and Aburjaile, FF and Sommerfeld, S and Azevedo, V and Fonseca, BB},
title = {Harnessing probiotics capability to combat Salmonella Heidelberg and improve intestinal health in broilers.},
journal = {Poultry science},
volume = {103},
number = {7},
pages = {103739},
doi = {10.1016/j.psj.2024.103739},
pmid = {38678973},
issn = {1525-3171},
abstract = {The poultry industry faces significant challenges in controlling Salmonella contamination while reducing antibiotic use, particularly with the emergence of Salmonella Heidelberg (SH) strains posing risks to food safety and public health. Probiotics, notably lactic acid bacteria (LAB) and Saccharomyces boulardii (SB) offer promising alternatives for mitigating Salmonella colonization in broilers. Understanding the efficacy of probiotics in combating SH and their impact on gut health and metabolism is crucial for improving poultry production practices and ensuring food safety standards. This study aimed to assess the inhibitory effects of LAB and SB against SH both in vitro and in vivo broilers, while also investigating their impact on fecal metabolites and caecal microbiome composition. In vitro analysis demonstrated strong inhibition of SH by certain probiotic strains, such as Lactiplantibacillus plantarum (LP) and Lacticaseibacillus acidophilus (LA), while others like SB and Lactobacillus delbrueckii (LD) did not exhibit significant inhibition. In vivo testing revealed that broilers receiving probiotics had significantly lower SH concentrations in cecal content compared to the positive control (PC) at all ages, indicating a protective effect of probiotics against SH colonization. Metagenomic analysis of cecal-content microbiota identified predominant bacterial families and genera, highlighting changes in microbiota composition with age and probiotic supplementation. Additionally, fecal metabolomics profiling showed alterations in metabolite concentrations, suggesting reduced oxidative stress, intestinal inflammation, and improved gut health in probiotic-supplemented birds. These findings underscore the potential of probiotics to mitigate SH colonization and improve broiler health while reducing reliance on antibiotics.},
}

@article {pmid38678950,
year = {2024},
author = {He, Y and Zhu, Y and Shui, X and Huang, Z and Li, K and Lei, W},
title = {Gut microbiome and metabolomic profiles reveal the antiatherosclerotic effect of indole-3-carbinol in high-choline-fed ApoE[-/-] mice.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {129},
number = {},
pages = {155621},
doi = {10.1016/j.phymed.2024.155621},
pmid = {38678950},
issn = {1618-095X},
abstract = {BACKGROUND: The metabolites produced from choline contribute to atherosclerosis (AS) pathogenesis, and the gut microbiota is redundantly essential for this process. Indole-3-carbinol (I3C), found in cruciferous vegetables such as broccoli, cabbage, cauliflower and brussels sprouts, helps prevent hyperlipidemia, maintain the gut microbiota balance, and decrease the production of trimethylamine-N-oxide (TMAO) from choline in the diet.

PURPOSE: The objective of this research was to investigate the impact of I3C on choline-induced AS and to further elucidate the underlying mechanism involved.

METHODS: AS models of high-choline-induced ApoE[-/-] mice and TMAO-promoted foamy macrophages were established to observe the effect of I3C on the formation of atherosclerotic plaques and foam cells and changes in AS-related indicators (including blood biochemical indicators, TMA, TMAO, SRA, and SRB1), and integrated analyses of the microbiome and metabolome were used to reveal the mechanism of action of I3C.

RESULTS: We found that I3C inhibited high-choline-induced atheroma formation (50-100 mg/kg/d, in vivo) and slightly improved the lipid profile (15 mg/kg/d, in vivo). Moreover, I3C suppressed lipid influx at a concentration of 40 µmol/L in vitro, enhanced the diversity of the gut microbiota and the abundance of the phylum Verrucomicrobia, and consequently modified the gut microbial metabolites at a dosage of 50 mg/kg/d in the mice. Associative analyses based on microbiome and metabolomics revealed that 1-methyladenosine was a key modulator of the protective effect of I3C against AS in high-choline-induced ApoE[-/-] mice.

CONCLUSION: These findings demonstrate for the first time that I3C ameliorates AS progression through remodeling of the gut microbiome and metabolomics, which paves the way for the possible therapeutic use of this vegetable-derived natural compound and may reduce the clinical severity of AS-related cardiovascular diseases.},
}

@article {pmid38678728,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {A metagenome-wide association study of gut microbiome in patients with AMD, ASD, RA, T2D & VKH diseases.},
journal = {Computational biology and chemistry},
volume = {110},
number = {},
pages = {108076},
doi = {10.1016/j.compbiolchem.2024.108076},
pmid = {38678728},
issn = {1476-928X},
abstract = {Clinical studies have already illustrated the associations between gut microbes and diseases, yet fundamental questions remain unclear that how we can universalize this knowledge. Considering the important role of human gut microbial composition in maintaining overall health, it is important to understand the microbial diversity and altered disease conditions of the human gut. Metagenomics provides a way to analyze and understand the microbes and their role in a community manner. It provides qualitative as well as quantitative measurements, in terms of relative abundance. Various studies are already going on to find out the association between microbes and diseases; still, the mined knowledge is limited. Considering the current scenario, using the targeted metagenomics approach, we analyzed the gut microbiome of 99 samples from healthy and diseased individuals. Our metagenomic analysis mainly targeted five diseased microbiomes (i.e., Age-related macular degeneration, Autism spectrum disorder, Rheumatoid arthritis, Type 2 diabetes and Vogt-Koyanagi harada), with compare to healthy microbiome, and reported disease-associated microbiome shift in different conditions.},
}

@article {pmid38678496,
year = {2024},
author = {Li, Y and Ding, Z and Xu, T and Wang, Y and Wu, Q and Song, T and Wei, X and Dong, J and Lin, Y},
title = {Synthetic consortia of four strains promote Schisandra chinensis growth by regulating soil microbial community and improving soil fertility.},
journal = {Planta},
volume = {259},
number = {6},
pages = {135},
pmid = {38678496},
issn = {1432-2048},
support = {2021YFD1000203//the National Key Research and Development Program of China/ ; },
mesh = {*Schisandra/growth & development/metabolism/physiology ; *Soil Microbiology ; *Soil/chemistry ; *Fertilizers ; Rhizosphere ; Biomass ; Microbial Consortia ; Plant Roots/microbiology/growth & development ; Microbiota ; Chlorophyll/metabolism ; },
abstract = {Synthetic consortia performed better in promoting Schisandra chinensis growth than individual strains, and this result provides valuable information for the development of synthetic microbial fertilizers. Schisandra chinensis is an herbal medicine that can treat numerous diseases. However, the excessive reliance on chemical fertilizers during the plantation of S. chinensis has severely restricted the development of the S. chinensis planting industry. Plant growth-promoting rhizobacteria (PGPR) can promote the growth of a wide range of crops, and synthetic consortia of them are frequently superior to those of a single strain. In this study, we compared the effects of four PGPR and their synthetic consortia on S. chinensis growth. The pot experiment showed that compared with the control, synthetic consortia significantly increased the plant height, biomass, and total chlorophyll contents of S. chinensis, and their combined effects were better than those of individual strains. In addition, they improved the rhizosphere soil fertility (e.g., TC and TN contents) and enzyme activities (e.g., soil urease activity) and affected the composition and structure of soil microbial community significantly, including promoting the enrichment of beneficial microorganisms (e.g., Actinobacteria and Verrucomicrobiota) and increasing the relative abundance of Proteobacteria, a dominant bacterial phylum. They also enhanced the synergistic effect between the soil microorganisms. The correlation analysis between soil physicochemical properties and microbiome revealed that soil microorganisms participated in regulating soil fertility and promoting S. chinensis growth. This study may provide a theoretical basis for the development of synthetic microbial fertilizers for S. chinensis.},
}

*Schisandra/growth & development/metabolism/physiology
*Soil Microbiology
*Soil/chemistry
*Fertilizers
Rhizosphere
Biomass
Microbial Consortia
Plant Roots/microbiology/growth & development
Microbiota
Chlorophyll/metabolism

@article {pmid38678226,
year = {2024},
author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A},
title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {78},
pmid = {38678226},
issn = {2049-2618},
support = {818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; *Food Microbiology ; Bacteria/classification/genetics ; Caves/microbiology ; Corynebacterium/genetics ; Longitudinal Studies ; Metagenome ; Lactococcus/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/classification ; Food Safety ; },
abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.

RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.

CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.},
}

*Cheese/microbiology
*Microbiota/genetics
*Food Microbiology
Bacteria/classification/genetics
Caves/microbiology
Corynebacterium/genetics
Longitudinal Studies
Metagenome
Lactococcus/genetics/classification
RNA, Ribosomal, 16S/genetics
Staphylococcus/genetics/classification
Food Safety

@article {pmid38678223,
year = {2024},
author = {Konovalovas, A and Armalytė, J and Klimkaitė, L and Liveikis, T and Jonaitytė, B and Danila, E and Bironaitė, D and Mieliauskaitė, D and Bagdonas, E and Aldonytė, R},
title = {Human nasal microbiota shifts in healthy and chronic respiratory disease conditions.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {150},
pmid = {38678223},
issn = {1471-2180},
support = {01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; 01.2.2-LMT-K-718-03-0079//Lietuvos Mokslo Taryba/ ; },
mesh = {Humans ; *Microbiota ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Chronic Disease ; Bronchoalveolar Lavage Fluid/microbiology ; Nasopharynx/microbiology ; Respiratory Tract Diseases/microbiology ; Lithuania ; Nose/microbiology ; Aged ; Young Adult ; Nasal Cavity/microbiology ; Sequence Analysis, DNA/methods ; Healthy Volunteers ; },
abstract = {BACKGROUND: An increasing number of studies investigate various human microbiotas and their roles in the development of diseases, maintenance of health states, and balanced signaling towards the brain. Current data demonstrate that the nasal microbiota contains a unique and highly variable array of commensal bacteria and opportunistic pathogens. However, we need to understand how to harness current knowledge, enrich nasal microbiota with beneficial microorganisms, and prevent pathogenic developments.

RESULTS: In this study, we have obtained nasal, nasopharyngeal, and bronchoalveolar lavage fluid samples from healthy volunteers and patients suffering from chronic respiratory tract diseases for full-length 16 S rRNA sequencing analysis using Oxford Nanopore Technologies. Demographic and clinical data were collected simultaneously. The microbiome analysis of 97 people from Lithuania suffering from chronic inflammatory respiratory tract disease and healthy volunteers revealed that the human nasal microbiome represents the microbiome of the upper airways well.

CONCLUSIONS: The nasal microbiota of patients was enriched with opportunistic pathogens, which could be used as indicators of respiratory tract conditions. In addition, we observed that a healthy human nasal microbiome contained several plant- and bee-associated species, suggesting the possibility of enriching human nasal microbiota via such exposures when needed. These candidate probiotics should be investigated for their modulating effects on airway and lung epithelia, immunogenic properties, neurotransmitter content, and roles in maintaining respiratory health and nose-brain interrelationships.},
}

Humans
*Microbiota
Female
Male
*RNA, Ribosomal, 16S/genetics
Middle Aged
Adult
*Bacteria/classification/genetics/isolation & purification
Chronic Disease
Bronchoalveolar Lavage Fluid/microbiology
Nasopharynx/microbiology
Respiratory Tract Diseases/microbiology
Lithuania
Nose/microbiology
Aged
Young Adult
Nasal Cavity/microbiology
Sequence Analysis, DNA/methods
Healthy Volunteers

@article {pmid38678061,
year = {2024},
author = {DeClercq, V and Wright, RJ and Nearing, JT and Langille, MGI},
title = {Oral microbial signatures associated with age and frailty in Canadian adults.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9685},
pmid = {38678061},
issn = {2045-2322},
mesh = {Humans ; Middle Aged ; Female ; Male ; Aged ; Adult ; *Frailty/microbiology ; *Microbiota ; Canada ; *RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation & purification ; Aging ; Age Factors ; },
abstract = {This study aimed to assess the association between the oral microbiome, age, and frailty. Data and saliva samples were obtained from male and female participants aged 35-70 years (n = 1357). Saliva samples were analysed by 16S rRNA gene sequencing and differences in microbial diversity and community compositions were examined in relation to chronological age and the frailty index (FI). Most alpha diversity measures (Richness, Shannon Diversity, Faith's Phylogenetic Diversity) showed an inverse association with frailty, whereas a positive association was observed with age and Shannon Diversity and Evenness. A further sex-stratified analysis revealed differences in measures of microbial diversity and composition. Multiple genera were detected as significantly differentially abundant with increasing frailty and age by at least two methods. With age, the relative abundance of Veillonella was reduced in both males and females, whereas increases in Corynebacterium appeared specific to males and Aggregatibacter, Fusobacterium, Neisseria, Stomatobaculum, and Porphyromonas specific to females. Beta diversity was significantly associated with multiple mental health components of the FI. This study shows age and frailty are differentially associated with measures of microbial diversity and composition, suggesting the oral microbiome may be a useful indicator of increased risk of frailty or a potential target for improving health in ageing adults.},
}

Humans
Middle Aged
Female
Male
Aged
Adult
*Frailty/microbiology
*Microbiota
Canada
*RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
*Saliva/microbiology
Bacteria/genetics/classification/isolation & purification
Aging
Age Factors

@article {pmid38678008,
year = {2024},
author = {Bamba, M and Akyol, TY and Azuma, Y and Quilbe, J and Andersen, SU and Sato, S},
title = {Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae056},
pmid = {38678008},
issn = {1574-6941},
abstract = {The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype [G], soil microbiome [M], and growth conditions (environment) [E] are the core factors shaping root microbiome, their relationships remain unclear. In this study we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.},
}

@article {pmid38678007,
year = {2024},
author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z},
title = {The role of rhizosphere phages in soil health.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae052},
pmid = {38678007},
issn = {1574-6941},
abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.},
}

@article {pmid38677827,
year = {2024},
author = {Rahman, S and Lu, E and Patel, RK and Tsikitis, VL and Martindale, RG},
title = {Colorectal Disease and the Gut Microbiome: What a Surgeon Needs to Know.},
journal = {The Surgical clinics of North America},
volume = {104},
number = {3},
pages = {647-656},
doi = {10.1016/j.suc.2023.12.004},
pmid = {38677827},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Colorectal Neoplasms/microbiology ; Dysbiosis/microbiology ; Inflammatory Bowel Diseases/microbiology ; Clostridium Infections/therapy/microbiology ; Constipation/microbiology/etiology ; Anastomotic Leak/microbiology/etiology ; },
abstract = {The gut microbiome is defined as the microorganisms that reside within the gastrointestinal tract and produce a variety of metabolites that impact human health. These microbes play an intricate role in human health, and an imbalance in the gut microbiome, termed gut dysbiosis, has been implicated in the development of varying diseases. The purpose of this review is to highlight what is known about the microbiome and its impact on colorectal cancer, inflammatory bowel disease, constipation, Clostridioides difficile infection, the impact of bowel prep, and anastomotic leaks.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Colorectal Neoplasms/microbiology
Dysbiosis/microbiology
Inflammatory Bowel Diseases/microbiology
Clostridium Infections/therapy/microbiology
Constipation/microbiology/etiology
Anastomotic Leak/microbiology/etiology

@article {pmid38677612,
year = {2024},
author = {Zhang, X and Zheng, W and Shao, W and Yu, W and Yang, Y and Qin, F and Zhou, W and Gong, C and Hu, X},
title = {Environmental concentrations of microplastic-induced gut microbiota and metabolite disruption in silkworm, Bombyx mori.},
journal = {Chemosphere},
volume = {358},
number = {},
pages = {142126},
doi = {10.1016/j.chemosphere.2024.142126},
pmid = {38677612},
issn = {1879-1298},
abstract = {Microplastics (MPs) existing extensively in various ecosystems can be ingested by marine organisms and enter the food chain, resulting the health risks from the presence of MPs in aquatic and terrestrial ecosystems. In the present study, an ideal model for Lepidoptera, the silkworm, Bombyx mori, was exposed to environmental concentrations (0.125 μg, 0.25 μg or 0.5 μg/diet) of MPs for 5 days, and the global changes in gut microbes and metabolites were subsequently examined via 16S rDNA sequencing and GC‒MS-based metabolomics. The results showed that MPs exposure did not seriously threaten survival but may regulate signaling pathways involved in development and cocoon production. MPs exposure induced gut microbiota perturbation according to the indices of α-diversity and β-diversity, and the functional prediction of the altered microbiome and associated metabolites demonstrated the potential roles of the altered microbiome following MPs exposure in the metabolic and physiological states of silkworm. The metabolites markedly altered following MPs exposure may play vital biological roles in energy metabolism, lipid metabolism, xenobiotic detoxification and the immune system by directly or indirectly affecting the physiological state of silkworms. These findings contribute to assessing the health risks of MPs exposure in model insects and provide novel insight into the toxicity mechanism of MPs.},
}

@article {pmid38677585,
year = {2024},
author = {Herman, K and Brough, HA and Pier, J and Venter, C and Järvinen, KM},
title = {Prevention of IgE-Mediated Food Allergy: Emerging Strategies through Maternal and Neonatal Interventions.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2024.04.029},
pmid = {38677585},
issn = {2213-2201},
abstract = {While the early introduction of highly allergenic foods has been shown to be effective at preventing the onset of food allergy (FA) in high-risk infants, sensitization to food antigens can occur prior to complementary food introduction and thus additional, earlier FA prevention strategies are urgently needed. Currently, aside from early introduction of peanut and egg, no therapies are strongly recommended by international professional allergy societies for the primary prevention of FA. This review focuses on maternal- and neonatal-directed interventions that are being actively investigated and developed, including maternal dietary factors and supplementation, specific elimination diets, breastfeeding, cow's milk formula supplementation, microbiome manipulations, bacterial lysate therapy, and skin barrier therapies. Evaluating how these factors and various prenatal/early life environmental exposures may impact the development of FA is crucial for accurately counseling caregivers in the prevention of FA.},
}

@article {pmid38677520,
year = {2024},
author = {Bhave, VM and Ament, Z and Levy, DE and Thorndike, AN and Kimberly, WT},
title = {Workplace food purchases, dietary intake, and gut microbial metabolites in a secondary analysis of the ChooseWell 365 study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2024.04.022},
pmid = {38677520},
issn = {1938-3207},
abstract = {BACKGROUND: Dietary choices can affect human health through alterations in gut microbial metabolism, and gut microbial metabolites could serve as biomarkers for disease risk conferred by dietary intake. However, self-reported dietary intake may not reflect true intake.

OBJECTIVE: We identified circulating metabolites, including gut microbiome-related metabolites, associated with adherence to a healthy diet in the ChooseWell 365 study. In this randomized clinical trial, the dietary choices of hospital employees were assessed over 24 months using not only 24-hour dietary recalls, but also electronic records of hospital cafeteria purchases.

METHODS: Plasma metabolites were profiled from 470 participants. Two targeted metabolomics methods were developed and implemented to expand detection coverage for metabolites related to gut microbial activity. Linear regression models were used to associate metabolites with Healthy Purchasing Scores (HPS) derived from cafeteria purchases and Healthy Eating Index-2015 (HEI-15) scores derived from dietary recalls.

RESULTS: Fourteen metabolites were concordantly associated with the HPS and HEI-15 scores in multivariable models adjusted for age, sex, and race, including the gut microbiome-related metabolites indole-3-propionic acid (HPS, β=0.16, 95% CI [0.07, 0.26], p=7.32x10[-4]; HEI-15, β=0.16, 95% CI [0.07, 0.25], p=6.79x10[-4]), hippuric acid (HPS, β=0.11, 95% CI [0.02, 0.21], p=1.97x10[-2]; HEI-15, β=0.10, 95% CI [0.01, 0.19], p=3.14x10[-2]), and indoxyl sulfate (HPS, β= -0.13, 95% CI [-0.23, -0.03], p=8.21x10[-3]; HEI-15, β= -0.12, 95% CI [-0.22, -0.03], p=8.50x10[-3]). These gut microbial metabolites were associated with the intake of specific food groups, such as whole fruits. These metabolites were also associated with clinical variables, including blood pressure, diabetes or prediabetes, and body mass index.

CONCLUSIONS: In a secondary analysis of the ChooseWell 365 study, associations between circulating gut microbiome-related metabolites and a healthy diet were confirmed using both objective and subjective measures of consumption. Accurate identification of diet-associated metabolites may help guide dietary or microbiome-based interventions aimed at disease prevention.},
}

@article {pmid38677518,
year = {2024},
author = {Maitin-Shepard, M and O'Tierney-Ginn, P and Kraneveld, AD and Lyall, K and Fallin, D and Arora, M and Fasano, A and Mueller, NT and Wang, X and Caulfield, LE and Dickerson, AS and Diaz Heijtz, R and Tarui, T and Blumberg, JB and Holingue, C and Schmidt, RJ and Garssen, J and Almendinger, K and Lin, PD and Mozaffarian, D},
title = {Report of a Meeting: Food, Nutrition, and Autism: From Soil to Fork.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2024.04.020},
pmid = {38677518},
issn = {1938-3207},
abstract = {Food and nutrition-related factors have the potential to impact development of autism spectrum disorder (ASD) and quality of life for people with ASD, but gaps in evidence exist. On November 10, 2022, Tufts University's Friedman School of Nutrition Science and Policy and Food and Nutrition Innovation Institute hosted a one-day meeting to explore the evidence and evidence gaps regarding the relationships of food and nutrition with ASD. This meeting report summarizes the presentations and deliberations from the meeting. Topics addressed included prenatal and child dietary intake, the microbiome, obesity, food-related environmental exposures, mechanisms and biological processes linking these factors and ASD, food-related social factors, and data sources for future research. Presentations highlighted evidence for protective associations with prenatal folic acid supplementation and ASD development, increases in risk of ASD with maternal gestational obesity, and the potential for exposure to environmental contaminants in foods and food packaging to influence ASD development. The importance of the maternal and child microbiome in ASD development or ASD-related behaviors in the child was reviewed, as was the role of discrimination in leading to disparities in environmental exposures and psychosocial factors that may influence ASD. The role of child diet and high prevalence of food selectivity in children with ASD and its association with adverse outcomes were also discussed. Priority evidence gaps identified by participants include further clarifying ASD development, including biomarkers and key mechanisms; interactions among psychosocial, social, and biological determinants; interventions addressing diet, supplementation, and the microbiome to prevent and improve quality of life for people with ASD; and mechanisms of action of diet-related factors associated with ASD. Participants developed research proposals to address the priority evidence gaps. The workshop findings serve as a foundation for future prioritization of scientific research to address evidence gaps related to food, nutrition, and ASD.},
}

@article {pmid38677439,
year = {2024},
author = {Luo, X and Hounmanou, YMG and Ndayisenga, F and Yu, Z},
title = {Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172712},
doi = {10.1016/j.scitotenv.2024.172712},
pmid = {38677439},
issn = {1879-1026},
abstract = {The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.},
}

@article {pmid38677413,
year = {2024},
author = {Yokoyama, D and Tsuboi, Y and Abe, H and Nagahata, R and Konno, H and Yoshida, M and Kikuchi, J},
title = {Quantification of microbial community assembly processes during degradation on diverse plastispheres based on physicochemical characters and phylogenetic bin-based null model analysis.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172401},
doi = {10.1016/j.scitotenv.2024.172401},
pmid = {38677413},
issn = {1879-1026},
abstract = {To understand the differences in degradation processes depending on the chemical properties of polymers, it is necessary to both quantify the microbiome composition and evaluate the process of microbial turnover (i.e., community assembly processes) in a variety of polymer materials. In this study, using a phylogenetic bin-based null model analysis (i.e., iCAMP), we evaluated community assembly processes from original estuary water to 37 types of polymers, which provide overwhelmingly diverse niches for microbes, in 14-day incubation experiments. First, we evaluated the polymer properties related to degradation rates. Polymers with higher adipic acid (AdA) monomer exhibited higher motility, hydrophilicity, and degradation rates, whereas those with higher aromatic monomer exhibited the opposite trends. Second, microbiome composition analysis was performed, and the microbiomes were significantly changed by the AdA or aromatic content. This was consistent with the polymer properties, suggesting that polymer motility and hydrophilicity attributable to the first-order structure modify the accessibility of the enzyme to the reaction site and hence the degradation rate, resulting in differences in microbiome community composition. Finally, we determined community assembly processes from estuary water to plastics using a phylogenetic bin-based null model analysis. The importance of heterogeneous selection was higher in mobile, hydrophilic, and fast-degrading polymers, while that of homogeneous selection was lower. This suggests that the environmental difference between before and after incubation becomes significant under rapid degradation, which select microbes adapted to biofilm environments. In addition, the more stochastic turnover prevailed, the more variation in the communities (i.e., β-diversity) increased. This suggests that turnover processes not dictated by the environment lead to instability in community compositions.},
}

@article {pmid38677385,
year = {2024},
author = {Wang, YC and Fu, HM and Shen, Y and Wang, J and Wang, N and Chen, YP and Yan, P},
title = {Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis.},
journal = {Bioresource technology},
volume = {401},
number = {},
pages = {130740},
doi = {10.1016/j.biortech.2024.130740},
pmid = {38677385},
issn = {1873-2976},
abstract = {Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.},
}

@article {pmid38677092,
year = {2024},
author = {ShanTian, and Guo, Y and Lan, Q and Li, J and Hu, J and Qiu, M and Guo, C and Dong, W},
title = {Association between ascites Gustave Roussy immune score and the intratumoural microbiome in malignant ascites secondary to hepatocellular carcinoma.},
journal = {International immunopharmacology},
volume = {133},
number = {},
pages = {112097},
doi = {10.1016/j.intimp.2024.112097},
pmid = {38677092},
issn = {1878-1705},
abstract = {BACKGROUNDS: The Gustave Roussy Immune (GRIm) score predicts survival outcomes in several cancers. However, the prognostic significance of the GRIm score in patients with malignant ascites has not yet been investigated.

METHODS: Clinical samples were collected from a cohort of patients with malignant ascites secondary to hepatocellular carcinoma (HCC). We calculated serum GRIm (sGRIm) and ascites GRIm (aGRIm) scores and divided the samples into low and high GRIm score groups. Survival analysis was used to compare the prognostic significance of the sGRIm and aGRIm scores. 16S rRNA sequencing was performed to determine the profiles of the intratumoral microbiota in the groups. A fluorescent multiplex immunohistochemistry (mIHC) assay was used to detect the expression of different immune cells by labeling seven markers of malignant ascites.

RESULTS: 155 patients with HCC and malignant ascites were enrolled in this study. Survival analysis revealed that the aGRIm score showed a superior prognostic significance compared to the sGRIm score. Microbial analysis demonstrated that the bacterial richness and diversity were higher in the low aGRIm score group than in the high aGRIm score group. LefSe analysis revealed that certain bacteria were correlated with high aGRIm scores. Fluorescent mIHC displayed the tumor microenvironment of malignant ascites and found that the density of CD8 + T cells was significantly higher in the low aGRIm score group than in the high aGRIm score group.

CONCLUSIONS: Our present study identified a novel scoring system (aGRIm score) that can predict the survival outcome of patients with malignant ascites secondary to HCC.},
}

@article {pmid38676863,
year = {2024},
author = {Xiang, F and Han, L and Jiang, S and Xu, X and Zhang, Z},
title = {Black soldier fly larvae mitigate greenhouse gas emissions from domestic biodegradable waste by recycling carbon and nitrogen and reconstructing microbial communities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38676863},
issn = {1614-7499},
support = {42377002//Major Research Plan/ ; 32171466//Major Research Plan/ ; },
abstract = {Black soldier fly larvae have been proven to reduce greenhouse gas emissions in the treatment of organic waste. However, the microbial mechanisms involved have not been fully understood. The current study mainly examined the dynamic changes of carbon and nitrogen, greenhouse gas emissions, the succession of microbial community structure, and changes in functional gene abundance in organic waste under larvae treatment and non-aeration composting. Thirty percent carbon and 55% nitrogen in the organic waste supplied were stored in larvae biomass. Compared to the non-aeration composting, the larvae bioreactor reduced the proportion of carbon and nitrogen converted into greenhouse gases (CO2, CH4, and N2O decreased by 62%, 87%, and 95%, respectively). 16S rRNA sequencing analysis indicated that the larvae bioreactor increased the relative abundance of Methanophaga, Marinobacter, and Campylobacter during the bioprocess, enhancing the consumption of CH4 and N2O. The metagenomic data showed that the intervention of larvae reduced the ratio of (nirK + nirS + nor)/nosZ in the residues, thereby reducing the emission of N2O. Larvae also increased the functional gene abundance of nirA, nirB, nirD, and nrfA in the residues, making nitrite more inclined to be reduced to ammonia instead of N2O. The larvae bioreactor mitigated greenhouse gas emissions by redistributing carbon and nitrogen and remodeling microbiomes during waste bioconversion, giving related enterprises a relative advantage in carbon trading.},
}

@article {pmid38676838,
year = {2024},
author = {Allogmanny, S and Probst, Y},
title = {Dietary Modification Combined with Nutrition Education and Counseling for Metabolic Comorbidities in Multiple Sclerosis: Implications for Clinical Practice and Research.},
journal = {Current nutrition reports},
volume = {},
number = {},
pages = {},
pmid = {38676838},
issn = {2161-3311},
abstract = {PURPOSE OF REVIEW: Metabolic comorbidities such as obesity, diabetes, hypertension, and dyslipidemia are common to multiple sclerosis (MS) and are associated with negative outcomes of the disease. Dietary intervention has the potential to improve MS co-morbidities; thus, it is a high priority for people living with MS to self-manage their disease. The present review aimed to summarize the recent evidence on the impacts of combining dietary modification with nutrition education and counseling on managing metabolic comorbidity markers in MS.

RECENT FINDINGS: Evidence suggests important roles for tailored dietary change strategies and nutrition education and counseling in managing metabolic comorbidities for MS. There is also indirect evidence suggesting a relationship between dietary fiber, the gut microbiome, and improved metabolic markers in MS, highlighting the need for more research in this area. For people living with MS, addressing both barriers and facilitators to dietary changes through behavior change techniques can help them achieve sustainable and tailored dietary behavior changes. This will support person-centered care, ultimately improving metabolic comorbidity outcomes. Metabolic comorbidities in MS are considered modifiable diseases that can be prevented and managed by changes in dietary behavior. However, the impact of targeted dietary interventions on mitigating MS-related metabolic comorbidities remains inadequately explored. Therefore, this review has provided insights into recommendations to inform future best practices in MS. Further well-designed studies based on tailored dietary strategies applying behavior change theories are needed to address the underlying determinants of dietary practice in this population.},
}

@article {pmid38676678,
year = {2024},
author = {Naydenova, IL and Danilov, AB and Simonova, AV and Pilipovich, AA and Filatova, EG},
title = {[A comparative assessment of microbiocenosis of saliva and oropharynx in patients with migraine].},
journal = {Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova},
volume = {124},
number = {4},
pages = {55-62},
doi = {10.17116/jnevro202412404155},
pmid = {38676678},
issn = {1997-7298},
mesh = {Humans ; *Saliva/microbiology ; Adult ; Female ; Male ; Middle Aged ; *Migraine Disorders/microbiology/diagnosis ; *Oropharynx/microbiology ; *Microbiota ; Young Adult ; },
abstract = {OBJECTIVE: To identify changes in the microbiome of saliva and to compare it with the microbiome of the oropharynx of patients with migraine.

MATERIAL AND METHODS: Sixty patients with migraine (21-56 years old), were examined using a headache diary, MIDAS and VAS. A microbiological examination of saliva and smear from the mucosa of the posterior wall of the oropharynx with evaluation by the method of mass spectrometry of microbial markers (MSMM) with the determination of 57 microorganisms was performed. All patients had comorbid chronic diseases of the gastrointestinal tract and upper respiratory tract (URT), according to anamnestic data and examination by specialists.

RESULTS: A significant increase in the content of markers of resident (conditionally pathogenic) microorganisms characteristic of chronic diseases of URT (strepto- and staphylococci); markers of transient microorganisms characteristic of intestinal microflora (clostridia, gram-negative rods, anaerobes) that are normally absent; viral markers of cytomegaloviruses and herpes groups; a decrease in the content of fungi were identified in saliva. A comparative analysis of the microbiome of saliva and oropharynx showed: 1) a significant decrease in the concentration of coccal flora Enterococcus spp., Streptococcus mutans, Staphylococcus aureus, anaerobic bacteria Clostridium difficile and Clostridium perfringens in saliva; enterobacteria Helicobacter pylori; gram-negative rods Kingella spp., fungi and Epstein-Barr virus; 2) an increase in salivary concentrations of Staphylococcus epidermidis, anaerobic Clostridium ramosum and Fusobacterium spp./Haemophilus spp. and gram-negative bacilli Porphyromonas spp.

CONCLUSION: A comparative assessment of the microbiota of a smear from the posterior wall of the oropharynx and saliva using MMSM showed the presence of dysbiosis both in the oropharynx and in the saliva of patients with migraine. However, there were fewer deviations from the norm in saliva, therefore, for diagnostic purposes, a smear from the posterior wall of the oropharynx is more significant as a biomarker for patients with migraine.},
}

Humans
*Saliva/microbiology
Adult
Female
Male
Middle Aged
*Migraine Disorders/microbiology/diagnosis
*Oropharynx/microbiology
*Microbiota
Young Adult