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The ancestral and industrialized gut microbiota and implications for human health


Human-associated microbial communities have adapted to environmental pressures. Doses of antibiotics select for a community with increased antibiotic resistance, inflammation is accompanied by expansion of community members equipped to flourish in the presence of immune effectors and Western diets shift the microbiota away from fibre degraders in favour of species that thrive on mucus. Recent data suggest that the microbiota of industrialized societies differs substantially from the recent ancestral microbiota of humans. Rapid modernization, including medical practices and dietary changes, is causing progressive deterioration of the microbiota, and we hypothesize that this may contribute to various diseases prevalent in industrialized societies. In this Opinion article, we explore whether individuals in the industrialized world may be harbouring a microbial community that, while compatible with our environment, is now incompatible with our human biology.

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Nature Reviews Microbiology thanks R. Carmody and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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E.D.S. and J.L.S. researched data for the article, wrote the article and reviewed and/or edited the manuscript before submission.

Correspondence to Erica D. Sonnenburg or Justin L. Sonnenburg.

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Fig. 1: Changes in host–microbiota interactions over evolutionary time.
Fig. 2: Loss of VANISH taxa in industrialized populations.
Fig. 3: Population-wide and personalized strategies to manipulate the gut microbiota to improve health.