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Poster De Conférence Année : 2022

Construction of a reference genome catalog to decipher shared strains along an agrifood chain with shotgun metagenomic data

Résumé

Identifying fluxes of micro-organisms between successive compartments of an agrifood chain (soil, grass, litter, cow’s feces and rumen, cheese) is important to understand and control cheese production. A first step to identify shared micro-organisms is to perform a taxonomical assignation at the species level. However, the sub-species / strain resolution is very relevant for the precise analysis of the assembly process of microbiota across habitats. In order to study strain fluxes, and take into account intra-species polymorphism, we choose an approach based on mapping metagenomic reads using the BWA-MEM tool on a catalog of reference genomes to identify shared nucleotidic polymorphism across samples in our various ecosystems. The use of reference genomes instead of metagenomic assembled genomes allows capturing polymorphisms for more species than only the most abundant, and enables comparison across multiple datasets using a common reference. Construction of a genome reference database is a key part of our analysis framework and must be tailored to the ecosystems under study. We will present the construction of a dedicated catalog based on the RefSeq database with the addition of relevant genomes from different origins and projects to complete our database: metagenomic assembled genomes (MAGS) from previous experiments, and microbial genomes isolated from from cows’ rumen and feces, and cheese. In particular, the species in the reference catalog must be different enough to avoid ambiguous mapping of the metagenomic reads, which requires aggregating similar genomes and choosing a representative for groups of aggregated species. Once the metagenomic reads mapped on a common reference, we will strive to reconstruct the various strains present in an ecosystem for the most abundant species by adapting existing methods (e.g. DESMAN). Wherever coverage is insufficient to completely resolve strain genomes, we will use shared nucleotidic polymorphism between samples to compute similarity indices, based on Nei’s distance, adapted to metagenomics samples.
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Dates et versions

hal-04313747 , version 1 (29-11-2023)

Identifiants

  • HAL Id : hal-04313747 , version 1

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Solène Pety, Fiona Bottin, Sébastien Theil, Céline Delbès, Panagiotis Sapountzsis, et al.. Construction of a reference genome catalog to decipher shared strains along an agrifood chain with shotgun metagenomic data. JOBIM, Jul 2022, Rennes, France. ⟨hal-04313747⟩
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