The Long-Term Stability of the Human Gut Microbiota
Jeremiah J. Faith,Janaki L. Guruge,Mark R. Charbonneau,Sathish Subramanian,Henning Seedorf,Andrew L. Goodman,Jose C. Clemente,Rob Knight,Rob Knight,Andrew C. Heath,Rudolph L. Leibel,Michael Rosenbaum,Jeffrey I. Gordon +12 more
TLDR
Low-error sequencing data suggest that initial microbial colonizers of infant guts could persist over the life span of an individual, and members of Bacteroidetes and Actinobacteria are significantly more stable components than the population average.Abstract:
A low-error 16S ribosomal RNA amplicon sequencing method, in combination with whole-genome sequencing of >500 cultured isolates, was used to characterize bacterial strain composition in the fecal microbiota of 37 U.S. adults sampled for up to 5 years. Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Shared strains were recovered from family members but not from unrelated individuals. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain composition were better predicted by changes in weight than by differences in sampling interval. This combination of stability and responsiveness to physiologic change confirms the potential of the gut microbiota as a diagnostic tool and therapeutic target.read more
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Journal ArticleDOI
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Vanessa K. Ridaura,Jeremiah J. Faith,Federico E. Rey,Jiye Cheng,Alexis E. Duncan,Andrew L. Kau,Nicholas W. Griffin,Vincent Lombard,Bernard Henrissat,Bernard Henrissat,James R. Bain,Michael J. Muehlbauer,Olga Ilkayeva,Clay F. Semenkovich,Katsuhiko Funai,David K. Hayashi,Barbara J. Lyle,Margaret C. Martini,Luke K. Ursell,Jose C. Clemente,Will Van Treuren,William A. Walters,Rob Knight,Rob Knight,Christopher B. Newgard,Andrew C. Heath,Jeffrey I. Gordon +26 more
TL;DR: The results reveal that transmissible and modifiable interactions between diet and microbiota influence host biology and that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids.
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Proteobacteria: Microbial signature of dysbiosis in gut microbiota
TL;DR: This work reviews studies that explored the association between an abnormal expansion of Proteobacteria and a compromised ability to maintain a balanced gut microbial community and proposes that an increased prevalence of ProTeobacteria is a potential diagnostic signature of dysbiosis and risk of disease.
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Gut biogeography of the bacterial microbiota
TL;DR: Novel hypotheses for how nutrient selection, immune activation and other mechanisms control the biogeography of bacteria in the gut are considered, and the relevance of this spatial heterogeneity to health and disease is discussed.
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An integrated catalog of reference genes in the human gut microbiome
Junhua Li,Huijue Jia,Xianghang Cai,Huanzi Zhong,Qiang Feng,Shinichi Sunagawa,Manimozhiyan Arumugam,Jens Roat Kultima,Edi Prifti,Trine Nielsen,Agnieszka S. Juncker,Chaysavanh Manichanh,Bing Chen,Wenwei Zhang,Florence Levenez,Juan Wang,Xun Xu,Liang Xiao,Suisha Liang,Dongya Zhang,Zhaoxi Zhang,Weineng Chen,Hailong Zhao,Jumana Y. Al-Aama,Sherif Edris,Huanming Yang,Jian Wang,Torben Hansen,Henrik Nielsen,Søren Brunak,Karsten Kristiansen,Francisco Guarner,Oluf Pedersen,Joël Doré,S. Dusko Ehrlich,Peer Bork,Jun Wang +36 more
TL;DR: The integrated gene catalog (IGC) is established comprising 9,879,896 genes, which includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs.
Journal ArticleDOI
The ecology of the microbiome: Networks, competition, and stability
TL;DR: This finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability, and indicates that stability is promoted by limiting positive feedbacks and weakening ecological interactions.
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