Deposit‐feeding sea cucumbers repeat ingestion of sediments and excretion of feces daily and consequently increase bacterial abundance in sediments and promote organic matter mineralization. Such ecological roles are expected to be collaborative activities of sea cucumbers and the gut microbiota. Here we performed a spatiotemporally‐broad 16S rRNA gene analysis using 109 samples from sea cucumber feces and habitat sediments to explore potential contribution of their gut microbiota to the ecological roles. Most operational taxonomic units (OTUs) observed in the fecal samples were shared with the sediment samples, nevertheless fecal and sediment microbiota differed from each other in UniFrac analysis. Lower bacterial diversity and increased relative abundance of specific OTUs in the fecal microbiota strongly suggest selective enrichment of ingested sediment microbiota in their guts. Interestingly, representative fecal OTUs were more abundant in sea cucumber‐populated sediments than in un‐inhabited sediments, indicating bacteria selectively enriched in the guts were spread on ambient sediments via feces. Moreover, the predicted microbial community metabolic potential showed a higher abundance of genes related to carbohydrate and xenobiotics metabolisms in feces than in sediments. Our study suggests the repeated selective enrichment transforms ambient sediment microbial communities and maintains the host's ecological roles by promoting organic matter mineralization.
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