Finding functional differences between species in a microbial community: Case studies in wine fermentation and Kefir culture

Chrats Melkonian, Willi Gottstein, Sonja Blasche, Yongkyu Kim, Martin Abel-Kistrup, Hentie Swiegers, Sofie Saerens, Nathalia Edwards, Kiran R. Patil, Bas Teusink, Douwe Molenaar*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.

Original languageEnglish
Article number01347
Pages (from-to)1-14
Number of pages14
JournalFrontiers in Microbiology
Issue numberJUNE
Publication statusPublished - 25 Jun 2019


  • Computational biology
  • Genomes
  • Kefir
  • Lactic acid bacteria
  • Metagenomics
  • Microbial communities
  • Wine


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