Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Microbiology Spectrum Year : 2024

Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables

Abstract

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the “stochastic block model” method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes ofcommunity succession among different bacterial assemblages. IMPORTANCE Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.
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Thursday, November 21, 2024
Embargoed file
Thursday, November 21, 2024
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hal-04581000 , version 1 (21-05-2024)

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Romane Junker, Florence Valence, Michel-Yves Mistou, Stéphane Chaillou, Helene Chiapello. Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables. Microbiology Spectrum, 2024, 12 (6), pp.e00312-24. ⟨10.1128/spectrum.00312-24⟩. ⟨hal-04581000⟩
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