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MICROBIOTA

Rules of engagement in the gut microbiome

Nature Medicine volume 24, pages 1642–1644 (2018)Cite this article

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In humans, niche-specific gastrointestinal microbiomes influence the colonization success of probiotic microbes. Microbiome reconstitution following antimicrobial perturbation is most successful using preperturbation autofecal microbial transplant.

The microbial carrying capacity of humans is both substantial and plastic. It increases rapidly in early life and is shaped by a range of environmental exposures. In turn, microbial strains and their bioactive products, particularly those housed in the gut microbiome, impact physiological development1 and local and remote immune cell populations2,3 and influence organ function4,5,6,7. This relatively new appreciation of the microbiome as an ancillary and malleable component critical to the health of humans has sparked renewed interest in gut microbiome manipulation for prevention, treatment and management of disease. Though consumption of fecal microbes to promote health originates in 4th century Chinese culture and approaches using defined probiotic species hark back to the research of Eli Metchnikoff in the early 20th century8, the rules of engagement following microbial introduction to the gastrointestinal tract have remained elusive. Recent companion manuscripts by Suez et al.9 and Zmora et al.10 in Cell shed light on the factors that influence microbial colonization success along the length of the gastrointestinal tract following either autologous fecal microbial transplant (aFMT; transplant of feces collected prior to antimicrobial administration) or a commercially available mix of 11 probiotic bacterial strains belonging to the Bifidobacteria, Lactobacillus, Lactococcus and Streptococcus genera.

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Fig. 1: The effect of auto-FMT and probiotics on microbiome colonization.

Change history

  • 12 November 2018

    In the version of this article that was originally published, the names of the authors appeared at the beginning of the standfirst. This was an error, and their names have now been removed from the standfirst.

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  1. Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA

    Elze Rackaityte & Susan V. Lynch

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  1. Elze Rackaityte
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  2. Susan V. Lynch
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Correspondence to Susan V. Lynch.

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The authors declare no competing interests.

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Rackaityte, E., Lynch, S.V. Rules of engagement in the gut microbiome. Nat Med 24, 1642–1644 (2018). https://doi.org/10.1038/s41591-018-0242-0

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