Abstract
Species utilizing the same resources ultimately do not coexist for long periods of time. Such competitive exclusion mechanisms potentially underly dynamics of microbiomes, causing breakdowns of communities constituted by species with similar genetic backgrounds of resource use. Nonetheless, it remains a major challenge to integrate genomics and ecology for understanding deterministic processes of species coexistence in species-rich communities. We here show that community-scale analyses of functional gene redundancy provide statistical platforms for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of coexisting bacterial species. We then reconstructed ecological niche space based on the multivariate analysis of the genome compositions in order to evaluate potential shifts in the level of niche overlap between species through time. Specifically, we hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was explained by the magnitude of metabolic pathway (gene repertoire) overlaps among bacterial species. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).
Competing Interest Statement
The authors have declared no competing interest.