Food-borne bacteria undercover: MAG reconstruction can reveal the biases in cultured food bacterial isolates and help identifying new species and strains - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
Conference Poster Year : 2022

Food-borne bacteria undercover: MAG reconstruction can reveal the biases in cultured food bacterial isolates and help identifying new species and strains

Abstract

Background: Food-borne bacteria are considered non-recalcitrant to isolation on culture medium. However, recent studies on food microbiota using 16S amplicon sequencing has revealed that this paradigm deserves to be re-evaluated scientifically. The most obvious bias concerns the search for subdominant species (or even strains), the most part of which pass under the detection filter of isolation practices (requirement for non-canonical growth conditions, or less competitive than dominant strains), although these taxa may represent an important functional role, or participate in certain processes in a transient manner (dynamic succession of populations). Method: The comparative analysis of food metagenomes, in particular of MAG (Metagenomic Assembled Genome) and genomes of isolates represents, in this context, a promising strategy to evaluate this cultural bias and to estimate the heritage of functions carried by naturally occurring strains in food and those carried by the genomes of cultivated strains. Results: We applied this strategy to 50 metagenomes obtained from cured-meat products and focused our analysis on two methodologies: (1) phylogenomic analysis based on the isolates/MAGs core genome using various evolutionary models. (2) Comparative analysis of the variable genomic heritage of the MAGs and genomes of sequenced strains. We could demonstrate that the bias is highly species-dependent and determined four situations: the species is very clonal (both isolates and MAGs); the species is very panmictic (both isolates and MAGs); isolates show more diversity than MAGs (selective pressure of food) and finally MAGs help in characterizing additional unsuspected strains diversity, including the discovery of novel candidate species.
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hal-04283313 , version 1 (13-11-2023)

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  • HAL Id : hal-04283313 , version 1

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Sybille Tabuteau, Stéphane Chaillou. Food-borne bacteria undercover: MAG reconstruction can reveal the biases in cultured food bacterial isolates and help identifying new species and strains. ISME18 - 18th International Symposium on Microbial Ecology, Aug 2022, Lausanne ( CH), Switzerland. . ⟨hal-04283313⟩
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