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iScience
Volume 25 (2), 2022, 103761

An ensemble approach to the structure-function problem in microbial communities

Chandana Gopalakrishnappa1,4, Karna Gowda2,3,4, Kaumudi H. Prabhakara2,3,4, Seppe Kuehn2,3

Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Abstract

The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.

Keywords: Microbiology, Microbial metabolism, Biophysics.

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