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Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration

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Abstract

The human gastrointestinal (GI) tract contains communities of microbes (bacteria, fungi, viruses) that vary by anatomic location and impact human health. Microbial communities differ in composition based on age, diet, and location in the gastrointestinal tract. Differences in microbial composition have been associated with chronic disease states. In terms of function, microbial metabolites provide key signals that help maintain healthy human physiology. Alterations of the healthy gastrointestinal microbiome have been linked to the development of various disease states including inflammatory bowel disease, diabetes, and colorectal cancer. While the definition of a healthy GI microbiome cannot be precisely identified, features of a healthy gut microbiome include relatively greater biodiversity and relative abundances of specific phyla and genera. Microbes with desirable functional profiles for the human host have been identified, in addition to specific metabolic features of the microbiome. This article reviews the composition and function of the healthy human GI microbiome, including the relative abundances of different bacterial taxa and the specific metabolic pathways and classes of microbial metabolites contributing to human health and disease prevention.

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Abbreviations

GI:

Gastrointestinal

HMP:

Human Microbiome Project

MetaHIT:

Metagenomics of the Human Intestinal Tract

IBD:

Inflammatory bowel disease

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Funding

This study was supported by the NIH T32 Grant 5T32DK007664-28 awarded to WR, NIH U01CA170930 Grant awarded to JV, the NLM Training Program in Biomedical Informatics and Data Science T15LM007093 (SCD) awarded to JV, and the Digestive Diseases Center which is funded by NIH/NIDDK P30 DK56338-06A2 Grant awarded to JV.

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Authors and Affiliations

  1. Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA

    Wenly Ruan

  2. Section of Gastroenterology, Hepatology, and Nutrition, Texas Children’s Hospital, Houston, TX, USA

    Wenly Ruan

  3. Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA

    Melinda A. Engevik, Jennifer K. Spinler & James Versalovic

  4. Department of Pathology, Texas Children’s Hospital, 1102 Bates St., Feigin Tower Suite 830, Houston, TX, 77030, USA

    Melinda A. Engevik, Jennifer K. Spinler & James Versalovic

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  1. Wenly Ruan
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  2. Melinda A. Engevik
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  3. Jennifer K. Spinler
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  4. James Versalovic
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Correspondence to James Versalovic.

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JV receives unrestricted research support from BioGaia AB, a Swedish probiotics company. JV serves on the scientific advisory board of Seed, a USA-based probiotics/prebiotics company. JV serves on the scientific advisory board of Biomica, an Israeli informatics enterprise, and on the scientific advisory board of Plexus Worldwide, a USA-based nutrition company.

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Ruan, W., Engevik, M.A., Spinler, J.K. et al. Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration. Dig Dis Sci 65, 695–705 (2020). https://doi.org/10.1007/s10620-020-06118-4

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