Using functional annotations to study pairwise interactions in urinary tract infection communities

Elena G. Lara, Isabelle van der Windt, Douwe Molenaar, Marjon G.J. de Vos*, Chrats Melkonian

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.

Original languageEnglish
Article number1221
Pages (from-to)1-19
Number of pages19
JournalGenes
Volume12
Issue number8
Early online date6 Aug 2021
DOIs
Publication statusPublished - Aug 2021

Bibliographical note

Funding Information:
Funding: The research of C.M. is supported by a Grand Solution grant from Innovation Fund Denmark (grant no. 6150-00033B), The FoodTranscriptomics project. The research of M.G.J.d.V. was supported by a fellowship from the Netherlands Organisation for Scientific Research (NWO) Earth and Life Sciences (ALW) VENI Project 863.14.015.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

Keywords

  • Gene annotation
  • Microbial community
  • Microbial interaction
  • Urinary tract infection

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