Human gut microbiome viewed across age and geography
Tanya Yatsunenko,Federico E. Rey,Mark J. Manary,Mark J. Manary,Indi Trehan,Indi Trehan,Maria Gloria Dominguez-Bello,Monica Contreras,Magda Magris,Glida Hidalgo,Robert N. Baldassano,Andrey P. Anokhin,Andrew C. Heath,Barbara B. Warner,Jens Reeder,Justin Kuczynski,J. Gregory Caporaso,Catherine A. Lozupone,Christian L. Lauber,Jose C. Clemente,Dan Knights,Rob Knight,Jeffrey I. Gordon +22 more
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TLDR
The need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization is underscored, as distinctive features of the functional maturation of the gut microbiome are evident in early infancy as well as adulthood.Abstract:
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.read more
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Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice
Alexandra E. Livanos,Thomas U. Greiner,Pajau Vangay,Wimal Pathmasiri,Delisha A. Stewart,Susan McRitchie,Huilin Li,Jennifer Chung,Jiho Sohn,Sara Kim,Zhan Gao,Cecily M. Barber,Joanne Kim,Sandy Ng,Arlin B. Rogers,Susan Sumner,Xue-Song Zhang,Ken Cadwell,Dan Knights,Alexander V. Alekseyenko,Fredrik Bäckhed,Fredrik Bäckhed,Martin J. Blaser,Martin J. Blaser +23 more
TL;DR: Findings show that early-life antibiotic treatments alter the gut microbiota and its metabolic capacities, intestinal gene expression and T-cell populations, accelerating T1D onset in non-obese diabetic mice.
Journal ArticleDOI
Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes
Robert R. Dunn,Noah Fierer,Noah Fierer,Jessica B. Henley,Jonathan W. Leff,Holly L. Menninger +5 more
TL;DR: The presence of dogs had a significant effect on bacterial community composition in multiple locations within homes as the homes occupied by dogs harbored more diverse communities and higher relative abundances of dog-associated bacterial taxa.
Journal ArticleDOI
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut.
Ann C. Gregory,Olivier Zablocki,Ahmed A. Zayed,Allison Howell,Benjamin Bolduc,Matthew B. Sullivan +5 more
TL;DR: The GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any “disease” effect at the population level, and document how viral diversity changes from human infancy into senescence.
Journal ArticleDOI
Anti-Infective Activities of Lactobacillus Strains in the Human Intestinal Microbiota: from Probiotics to Gastrointestinal Anti-Infectious Biotherapeutic Agents
TL;DR: The current knowledge concerning the experimental antibacterial activities, including antibiotic-like and cell-regulating activities, and therapeutic effects demonstrated in well-conducted, placebo-controlled, randomized clinical trials of these probiotic Lactobacillus strains are described.
Journal ArticleDOI
Application of metagenomics in the human gut microbiome
TL;DR: Functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations.
References
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more