Networks of energetic and metabolic interactions define dynamics in microbial communities

TLDR

Microbial communities are essential to global carbon cycling, especially in oxygen‑limited environments, but the prevalence of uncultured members hampers detailed study of their composition and interspecies interactions. The study aims to quantify interspecies interactions in methanogenic communities by integrating metagenomic binning, metatranscriptomics, and metabolic modeling. The authors combined metagenomic binning, metatranscriptomic profiling, and metabolic modeling to quantify interspecies interactions in methanogenic communities. The communities are structured by metabolic interactions, amino‑acid auxotrophies, and selective antimicrobial use that reinforces a tightly collaborative interspecies network.

Abstract

Significance Microbial communities are critical to global carbon cycling and particularly important in oxygen-limited environments, such as sediments and parts of the human microbiome. However, the uncultured members of these communities often hinder the study of community composition and interspecies interactions at a deeper level. Here, we integrate metagenomic binning, metatranscriptomic analysis, and metabolic modeling to obtain quantitative information about interspecies interactions between individual species present in methanogenic communities. We found that these communities are defined by not only metabolic interactions but also additional interdependencies, such as amino acid auxotrophies. Strategic usage of antimicrobials by specific community members further reinforces this intricate interspecies network, thereby enforcing strong collaboration among community members.