Uncovering the strain-level genetic variation of major gut microbiota components

This abstract was selected by our Scientific Committee to pitch on the programme in the R2B session (PM).

The intestinal microbiota is composed of multiple species of microorganisms that have important metabolic, immunological and protective functions for the human host. Traditionally, the gut microbiota has been studied by sequencing specific gene markers or the entire DNA from the community, revealing what species are present in the ecosystem and which functions they encode. However, this holistic approach fails to capture the extensive strain-level genetic diversity of the microbiota components, a major limitation in the microbiome field considering that independent strains of the same species may harbour different pathogenic and/or metabolic capabilities.

In this study, we aimed to characterize the intra-individual genetic diversity of three highly prevalent and abundant gastrointestinal species with probiotic or infective potential. Using the anaerobic culturomics platform implemented in our lab, we isolated and whole-genome sequenced over 200 colonies of Bifidobacterium adolescentis, Bacteroides vulgatus and Bacteroides uniformis from a dozen of volunteers. Additionally, we sequenced the metagenomes of the faecal samples from which bacteria were isolated. A combination of metagenomic and single-isolate genomic analyses revealed that the gastrointestinal tract is more frequently represented by a single or a few dominant strains of each species. In addition, inter-individual comparisons showed that people carry distinct strains that considerably differ in their genomic content and the metabolic functions they encode. Future in vitro experiments will help us to understand the strain-level variation dynamics observed in the gut. Overall, these analyses will be highly valuable for the rational design of probiotics and for the treatment of gut-associated infectious diseases.


Rodrigo Bacigalupe
Anais Biclot
Geert Huys
Jeroen Raes


VIB - KU Leuven Center for Microbiology

Presenting author

Rodrigo Bacigalupe, Postdoctoral Scientist, VIB - KU Leuven Center for Microbiology
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