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Genomic Characterization of the Uncultured Bacteroidales Family S24-7 Inhabiting the Guts of Homeothermic Animals Kate L
Ormerod et al. Microbiome (2016) 4:36 DOI 10.1186/s40168-016-0181-2 RESEARCH Open Access Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals Kate L. Ormerod1, David L. A. Wood1, Nancy Lachner1, Shaan L. Gellatly2, Joshua N. Daly1, Jeremy D. Parsons3, Cristiana G. O. Dal’Molin4, Robin W. Palfreyman4, Lars K. Nielsen4, Matthew A. Cooper5, Mark Morrison6, Philip M. Hansbro2 and Philip Hugenholtz1* Abstract Background: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. Results: Here, we provide the first whole genome exploration of this family, for which we propose the name “Candidatus Homeothermaceae,” using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of “Ca. Homeothermaceae” to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. Conclusions: “Ca. Homeothermaceae” representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. -
Supplementary Table 8 Spearman's Correlations Between Targeted Urinary Urolithins and Microbiota
Supplementary material Gut Supplementary Table 8 Spearman's correlations between targeted urinary urolithins and microbiota. Urolithin- Urolithin- Urolithin- Total A- B- C- Urolithins Family level Taxonomy glucuronid glucuronid glucuronid (A+B+C) e e e Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium adolescentis_msp_0263 -0.18 -0.09 -0.16 -0.18 Bifidobacteriaceae Bifidobacterium; Bifidobacterium adolescentis Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium bifidum_msp_0419 -0.12 -0.2 -0.08 -0.13 Bifidobacteriaceae Bifidobacterium; Bifidobacterium bifidum Actinobacteria; Coriobacteriia; Coriobacteriales; Coriobacteriaceae; Collinsella; Collinsella aerofaciens_msp_1244 -0.15 -0.06 -0.04 -0.18 Coriobacteriaceae Collinsella aerofaciens Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Adlercreutzia; unclassified Adlercreutzia_msp_0396 0.09 0.01 0.16 0.12 Eggerthellaceae unclassified Adlercreutzia Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Eggerthella; Eggerthella lenta_msp_0573 0.03 -0.15 0.08 0.03 Eggerthellaceae Eggerthella lenta Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Gordonibacter; Gordonibacter urolithinfaciens_msp_1339 0.19 -0.05 0.18 0.19 Eggerthellaceae Gordonibacter urolithinfaciens Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; Bacteroides cellulosilyticus_msp_0003 0.12 0.11 0.15 0.15 Bacteroidaceae Bacteroides cellulosilyticus Bacteroidetes; Bacteroidia; Bacteroidales; -
A Case–Control Study
www.nature.com/scientificreports OPEN Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study Deborah Traversi1,8*, Ivana Rabbone2,7, Giacomo Scaioli1,8, Camilla Vallini2, Giulia Carletto1,8, Irene Racca1, Ugo Ala5, Marilena Durazzo4, Alessandro Collo4,6, Arianna Ferro4, Deborah Carrera3, Silvia Savastio3, Francesco Cadario3, Roberta Siliquini1,8 & Franco Cerutti1,2 Type 1 diabetes (T1D) is a common autoimmune disease that is characterized by insufcient insulin production. The onset of T1D is the result of gene-environment interactions. Sociodemographic and behavioural factors may contribute to T1D, and the gut microbiota is proposed to be a driving factor of T1D. An integrated preventive strategy for T1D is not available at present. This case–control study attempted to estimate the exposure linked to T1D to identify signifcant risk factors for healthy children. Forty children with T1D and 56 healthy controls were included in this study. Anthropometric, socio-economic, nutritional, behavioural, and clinical data were collected. Faecal bacteria were investigated by molecular methods. The fndings showed, in multivariable model, that the risk factors for T1D include higher Firmicutes levels (OR 7.30; IC 2.26–23.54) and higher carbohydrate intake (OR 1.03; IC 1.01–1.05), whereas having a greater amount of Bifdobacterium in the gut (OR 0.13; IC 0.05 – 0.34) was a protective factor for T1D. These fndings may facilitate the development of preventive strategies for T1D, such as performing genetic screening, characterizing the gut microbiota, and managing nutritional and social factors. Type 1 diabetes (T1D) is a multifactor disease caused by β-cell destruction (which is mostly immune-medi- ated) and absolute insulin defciency. -
Integrated Analysis of the Gut Microbiota and Their Fermentation Products in Mice Treated with the Longevity Enhancing Drug Acarbose
Integrated Analysis of the Gut Microbiota and Their Fermentation Products in Mice Treated with the Longevity Enhancing Drug Acarbose by Byron J. Smith A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in the University of Michigan 2019 Doctoral Committee: Professor Thomas M. Schmidt, Chair Professor Gregory J. Dick Professor Meghan A. Duffy Professor Aaron A. King Byron J. Smith [email protected] ORCID iD: 0000-0002-0182-404X © Byron J. Smith 2019 ACKNOWLEDGMENTS This work is supported by The Glenn Foundation for Medical Research, the Host Microbiome Initiative at the University of Michigan, and an Integrated Training in Microbial Systems fellowship. Additional funding came from the Department of Ecology and Evolutionary Biology at the University of Michi- gan. I want to thank my advisor, Tom, for his wonderful mentorship over the entirety of my PhD. His advising style—usually hands off, and often more of a collaborator than a director of his students’ work—has been integral to my graduate school experience. Given the freedom and time to explore the field on my own, I have developed more as an individual scientist than I would have imagined possible. I know that I was not always the easiest trainee to work with, but he has been patient throughout. Similarly, I need to thank the myriad other mentors, including the members of my committee, whose feedback and optimism have been a vital resource. Aaron, Greg, and Meg have each had important impacts on not only my science, but also how I think about my PhD and my future career. -
Bacteroidales Species Are a Reservoir of Phase-Variable Antibiotic Resistance Genes in the Human Gut Microbiome
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.26.441444; this version posted April 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Bacteroidales species are a reservoir of phase-variable antibiotic resistance genes in the human gut microbiome Wei Yana, A. Brantley Hallb,c, and Xiangfang Jianga a National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA b Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA c Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA Address correspondence to Xiaofang Jiang: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.26.441444; this version posted April 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Phase-variable antibiotic resistance genes (ARGs) can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of phase-variable ARGs remains poorly understood. Here, we sought to assess the threat posed by phase-variable ARGs by systematically searching for phase-variable ARGs in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified phase-variable ARGs and categorized them into three classes based on the invertase regulating phase variation.