Metabolic dependencies drive species co-occurrence in diverse microbial communities.
Microbial communities populate most environments on earth and play a critical role in ecology and human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated in community assembly. The prevalence of metabolic interactions in microbial communities, however, has remained largely unknown. Here, we systematically survey, by using a genome-scale metabolic modeling approach, the extent of resource competition and metabolic exchanges in over 800 communities. We find that, despite marked resource competition at the level of whole assemblies, microbial communities harbor metabolically interdependent groups that recur across diverse habitats. By enumerating flux-balanced metabolic exchanges in these co-occurring subcommunities we also predict the likely exchanged metabolites, such as amino acids and sugars, that can promote group survival under nutritionally challenging conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence and hint at cooperative groups as recurring modules of microbial community architecture.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Aleksej
A
Zelezniak
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Sergej
S
Andrejev
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Olga
O
Ponomarova
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Daniel R
DR
Mende
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Peer
P
Bork
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany patil@embl.de.
Kiran Raosaheb
KR
Patil
D053858:Metabolic Networks and Pathways / Q000502:physiology*; D059013:Microbial Consortia / Q000235:genetics / Q000502:physiology*; D056265:Microbial Interactions / Q000502:physiology*; D008954:Models, Biological; D010802:Phylogeny; D013045:Species Specificity; D018709:Statistics, Nonparametric; D013559:Symbiosis
community metabolism; cooperation; metabolic modeling; naturalization theory; syntrophy