Networks of energetic and metabolic interactions define dynamics in microbial communities

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.