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The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

Nature Reviews Microbiology volume 11, pages 497–504 (2013)Cite this article

Subjects

Key Points

  • The human genome encodes only a small number of digestive glycoside hydrolases for the breakdown of sucrose, lactose and starch. Instead, the large diversity of complex polysaccharides in our diet is mainly digested by specialized enzymes encoded by the gut microbiome.

  • A model human microbiome was constructed from 177 microbial genomes in proportions that approximate their representation in the healthy adult gut, and this mini-microbiome was used to evaluate the diversity of carbohydrate-active enzymes (CAZymes) in the gut microbiota.

  • Gut bacteria from the phylum Bacteroidetes encode more CAZymes, and encode CAZymes from more families, than the other phyla represented in the model mini-microbiome. The large substrate range of these CAZymes is compatible with the diversity of the dietary plant cell wall polysaccharides that are presented to members of the microbiota.

Abstract

Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota.

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Figure 1: Glycoside hydrolases encoded by the human genome.
Figure 2: The mini-microbiome.
Figure 3: Carbohydrate-active enzyme composition of the mini-microbiome.
Figure 4: Glycoside hydrolases in the mini-microbiome.
Figure 5: Diversity of glycan-cleaving enzymes.

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Acknowledgements

A.E.K. was funded by La Fondation Infectiopôle Sud, France.

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Authors and Affiliations

  1. Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7257, Case 932, 163 Avenue de Luminy, Marseille cedex 9, 13288, France

    Abdessamad El Kaoutari & Bernard Henrissat

  2. CNRS UMR7278, Institut de Recherche pour le Développement 198, Institut National de la Santé et de la Recherche Médicale 1095, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, Faculté de Médecine, Marseille cedex 5, 13385, France

    Abdessamad El Kaoutari, Fabrice Armougom & Didier Raoult

  3. Center for Genome Sciences and Systems Biology, Washington University, St. Louis, 63108, Missouri, USA

    Jeffrey I. Gordon

  4. Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, DK-2200, Denmark

    Bernard Henrissat

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  1. Abdessamad El Kaoutari
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Correspondence to Bernard Henrissat.

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FURTHER INFORMATION

CAZy

HMP

IMG

IMG/M HMP

MetaHIT

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Supplementary information

Supplementary information S1 (table)

The genomes composing the mini-microbiome (PDF 304 kb)

Supplementary information S2 (table)

Abundance of each family of glycoside hydrolases (GH) and polysaccharide lyases (PL) in the bacterial strains composing the mini-microbiome (XLSX 85 kb)

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Kaoutari, A., Armougom, F., Gordon, J. et al. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 11, 497–504 (2013). https://doi.org/10.1038/nrmicro3050

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