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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The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Sara C. Di Rienzi,Itai Sharon,Kelly C. Wrighton,Omry Koren,Laura A. Hug,Brian C. Thomas,Julia K. Goodrich,Jordana T. Bell,Tim D. Spector,Jillian F. Banfield,Ruth E. Ley +10 more
TL;DR: This article used whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which they propose the designation "Melainabacteria".
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The role of the gut microbiome in systemic inflammatory disease
TL;DR: This review summarizes the preclinical and clinical evidence on how dietary, probiotic, prebiotic, and microbiome based therapeutics affect the understanding of wellness and disease, particularly in autoimmunity.
Journal ArticleDOI
Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes
Ling-Chun Kong,Julien Tap,Judith Aron-Wisnewsky,Véronique Pelloux,Arnaud Basdevant,Jean-Luc Bouillot,Jean-Daniel Zucker,Joël Doré,Karine Clément +8 more
TL;DR: An increase in gut microbiota richness and in the number of associations between gut microbiota and WAT genes after RYGB in obesity is shown, stimulating deeper explorations of the mechanisms linking gut microbiome and Wat pathological alterations in human obesity and its changes after weight loss.
Journal ArticleDOI
Captivity humanizes the primate microbiome.
Jonathan B. Clayton,Pajau Vangay,Hu Huang,Tonya Ward,Benjamin Hillmann,Gabriel A. Al-Ghalith,Dominic A. Travis,Ha Thang Long,Bui Van Tuan,Vo Van Minh,Francis Cabana,Tilo Nadler,Barbara Toddes,Tami Murphy,Kenneth E. Glander,Timothy J. Johnson,Dan Knights +16 more
TL;DR: It is found that captivity and loss of dietary fiber in nonhuman primates are associated with loss of native gut microbiota and convergence toward the modern human microbiome, suggesting that parallel processes may be driving recent loss of core microbial biodiversity in humans.
Journal ArticleDOI
The role of the bacterial microbiome in lung disease.
TL;DR: In this paper, the authors review and synthesize published reports of the lung microbiota of healthy and diseased subjects, discuss trends of microbial diversity and constitution across disease states, and look to the extrapulmonary microbiome for hypotheses and future directions for study.
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A human gut microbial gene catalogue established by metagenomic sequencing
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QIIME allows analysis of high-throughput community sequencing data.
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