Functional genomics analyses of symbiotic ciliates of herbivorous mammals suggests microbial niche partitioning and more efficiency in rumen environment

Abstract

Abstract Herbivorous mammals have evolved symbiotic relationships with ciliates, either as mutualists or as parasites. Here, we investigate the ecological roles and metabolic impacts of ciliates across different gastrointestinal environments (rumen, caecum, and large intestine) through a functional genomic analysis. Functional analysis revealed that most rumen and caecum ciliates shared similar metabolic profiles, whereas the parasitic ­Balantioides coli displayed genes associated with energy metabolism and pathogenicity, suggesting a shift from mutualism to parasitism. Carbohydrate-active enzyme profiling showed rumen ciliates to be more metabolically diverse, supporting niche partitioning, enhancing ecological balance in the rumen environment.