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An insider's perspective: Bacteroides as a window into the microbiome

Nature Microbiology volume 2, Article number: 17026 (2017) Cite this article

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Abstract

Over the last decade, our appreciation for the contribution of resident gut microorganisms—the gut microbiota—to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium. While genome and metagenome sequences are being produced at breakneck speed, the Bacteroides provide a significant ‘jump-start’ on uncovering the guiding principles that govern microbiota–host and inter-bacterial associations in the gut that will probably extend to many other members of this ecosystem.

Microbial life thrives in the anaerobic environment of the human gastrointestinal tract, which represents one of the densest microbial communities known in nature. With a collective microbial gene count (the ‘microbiome’) exceeding that of the host by more than 100-fold, the microorganisms living within our gut (the ‘microbiota’) in many ways represent an additional metabolic organ that contributes substantially to our physiology—including nutrient absorption, metabolism, disease resistance and susceptibility, and response to xenobiotics1–5. More than a decade's worth of 16S rRNA sequencing and metagenomic analyses of hundreds of human gut microbiomes collected over numerous geographical locations have shown that each individual harbours a unique assemblage of microbial life that first establishes itself when we are born, changes markedly over the first two to three years of life, and then remains fairly stable throughout our adult lives6–9. These communities include representatives from all three domains of life, with hundreds of species and strains occupying and competing for limited space and resources.

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Figure 1: Global distributions and abundances of human gut microorganisms at the phylum and genus levels.
Figure 2: Consumption and production of polysaccharides in Bacteroides.
Figure 3: Commensal colonization of colonic crypts.
Figure 4: Mechanisms of inter-bacterial cooperation and antagonism among Bacteroides.

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Acknowledgements

We thank W. Schofield and B. Lim for careful reading of the manuscript. Support for this work was provided by the National Institutes of Health (GM105456 and GM118159), the Pew Scholars Program, and the Burroughs Wellcome Fund to A.L.G. A.G.W. is supported by a fellowship from the Gruber Foundation.

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  1. Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, 06510, Connecticut, USA

    Aaron G. Wexler & Andrew L. Goodman

  2. Microbial Sciences Institute, Yale University School of Medicine, West Haven, 06516, Connecticut, USA

    Aaron G. Wexler & Andrew L. Goodman

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  1. Aaron G. Wexler
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A.G.W. drafted the manuscript and prepared figures. A.G.W. and A.L.G. edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to Andrew L. Goodman.

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Wexler, A., Goodman, A. An insider's perspective: Bacteroides as a window into the microbiome. Nat Microbiol 2, 17026 (2017). https://doi.org/10.1038/nmicrobiol.2017.26

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