Carbohydrate foraging by gut bacteria: inputs of functional metagenomics - IRSD

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Carbohydrate foraging by gut bacteria: inputs of functional metagenomics

Glycosides are produced by all living cells and are keystones in metabolism. They also play a fundamental role in the interactions between eukaryotes, bacteria and even viruses. Microorganisms face their structural complexity and diversity by producing a broad range of glycoside utilization machineries, involving carbohydrate active enzymes and transporters. In order to better understand how glycosides are metabolized in the human gut, we have developed versatile high- and ultra- high throughput functional metagenomics approaches, exploiting the last advances in nanotechnologies and microfluidics. We exploited them to explore the vast world of still uncultured microorganisms from the human gut, in order to decipher, up to the molecular level, the glycan-mediated interactions between gut microbes, the host, and food.
We identified a panel of dietary, microbial and mucin glycan metabolizing pathways from commensal gut bacteria, including beneficial and non-beneficial species from different genera. The discovered loci, which encode a battery of glycoside-hydrolases, and also glycoside-phosphorylases and transporters from various families, are, for most of them, highly prevalent and abundant in the gut microbiome, and explain the metabolic flexibility of bacteria feeding both on dietary and human glycans. Others are disease-associated, and represent novel targets to explore the mucus-driven interactions between the human gut microbiota and the host in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. In addition to opening up new perspectives for the control of the microbiota functioning, the new enzymes and transporters identified represent biotechnological tools of interest for synthetic biology.

Gabrielle Potocki-Veronese is a Research Director at the French National Research Institute for Agriculture, Food and Environment (INRAE). She is specialist in enzyme discovery through functional metagenomics. She obtained her PhD in biotechnology at the Institut National des Sciences Appliquees of Toulouse (INSAT, France) in 1999. After working as Associate Professor at INSAT and as post-doc in molecular oncology at the French Atomic Energy Commission (Fontenay aux Roses, France), she held a research scientist position at INRAE in 2001. She now leads the DiscOmics group (“metaomics for function discovery”) at the Toulouse Biotechnology Institute. She coordinated or participated in 28 national and international projects in the field of enzyme discovery and microbiomics. She is currently the TBI PI in the H2020 projects Zelcor and RadicalZ. She is also the coordinator of two projects in collaboration with Céline Deraison at IRSD: the ANR project CAZIBD and the CULTISSIMDROP project funded by Toulouse White Biotechnology.