Community context reshapes microbial proteomes and reduces functional overlap

Microbial coexistence in complex communities requires mechanisms that minimize competition and optimize resource use. However, the mechanisms by which these ecological strategies are executed remain poorly understood. Here we show that bacteria modulate protein abundance in response to specific community members, reducing functional redundancy and promoting metabolic complementarity. Using synthetic gut-derived consortia exposed to distinct carbon sources, we systematically profiled proteomic responses of individual species across isolate, pairwise and 4-member communities. We found that biotic interactions, rather than abiotic conditions, were the dominant drivers of proteomic variation. These interactions led to reproducible, partner-specific expression shifts that significantly reduced functional overlap and were frequently associated with increased community productivity. Together, these findings highlight gene expression as a means by which microbes implement ecological strategies in community contexts. Through this regulatory plasticity, microbes dynamically reshape their realized niche through protein abundance modulation, enabling them to partition metabolic space and stabilize community structure.