Abstract
The human gut microbiome exhibits characteristics of complex ecosystems,
including the ability to resist and compete with exogenous species or
communities. Understanding microbiome responses to such competition is
crucial, especially for fecal microbiota transplantation (FMT), where
success depends on microbial interactions. During these processes,
microbial communities undergo coalescence, combining and interacting in
ways that lead to complex ecological outcomes. In this study, we
investigated the coalescent dynamics of ten pairs of human gut
microbiota through in vitro co-culturing. Metaproteomic analysis
revealed that post-coalescence changes were not simply an average of the
initial microbiotas but instead, both coalescent microbiotas behaved as
cohesive structures, influencing the competitive outcome towards one of
them.. While taxonomic similarities were observed between co-cultured
communities and their parental samples, 23% of proteins showed
differential expression. Interestingly, the competitive outcomes
followed a “rock-paper-scissors” dynamic, with different species
contributing to competition outcomes across different pairs. This
highlights the complexity of microbial competition, suggesting that no
single factor consistently determines dominance. Pre-co-culturing may
thus be a promising method for predicting outcomes in FMT and other
ecological therapies.