Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting

Lharbi Dridi, Fernando Altamura, Emmanuel Gonzalez, Olivia Lui, Ryszard Kubinski, Reilly Pidgeon, Adrian Montagut, Jasmine Chong, Jianguo Xia, Corinne F. Maurice () and Bastien Castagner ()
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Lharbi Dridi: McGill University
Fernando Altamura: McGill University
Emmanuel Gonzalez: McGill Genome Center
Olivia Lui: McGill University
Ryszard Kubinski: McGill University
Reilly Pidgeon: McGill University
Adrian Montagut: McGill University
Jasmine Chong: McGill University
Jianguo Xia: McGill University
Corinne F. Maurice: McGill University
Bastien Castagner: McGill University

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract The composition and metabolism of the human gut microbiota are strongly influenced by dietary complex glycans, which cause downstream effects on the physiology and health of hosts. Despite recent advances in our understanding of glycan metabolism by human gut bacteria, we still need methods to link glycans to their consuming bacteria. Here, we use a functional assay to identify and isolate gut bacteria from healthy human volunteers that take up different glycans. The method combines metabolic labeling using fluorescent oligosaccharides with fluorescence-activated cell sorting (FACS), followed by amplicon sequencing or culturomics. Our results demonstrate metabolic labeling in various taxa, such as Prevotella copri, Collinsella aerofaciens and Blautia wexlerae. In vitro validation confirms the ability of most, but not all, labeled species to consume the glycan of interest for growth. In parallel, we show that glycan consumers spanning three major phyla can be isolated from cultures of sorted labeled cells. By linking bacteria to the glycans they consume, this approach increases our basic understanding of glycan metabolism by gut bacteria. Going forward, it could be used to provide insight into the mechanism of prebiotic approaches, where glycans are used to manipulate the gut microbiota composition.

Date: 2023
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DOI: 10.1038/s41467-023-36365-8

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