Gut microbiome community dynamics in captive juvenile chum salmon: the influences of development, diet, and seawater transition

Background The development of host-associated microbiota evolves from birth to adulthood, with distinct microbial signatures influencing host biological processes. This study aims to analyze how bacterial communities in the digestive tracts of chum salmon are structured during the first 90 days post-hatching (DPH), encompassing the embryonic stage, feeding, and the transition from freshwater to seawater under controlled conditions. Results Gut microbiota was analyzed using high-throughput 16S rRNA gene amplicon sequencing. Our results indicated that bacterial communities were highly dynamic, with significant shifts occurring after feeding began (35 DPH), as diet heavily influenced gut microbiota stability. Upon transferring to seawater, dominant taxa shifted to include Aliivibrio , Colwellia , Bartonella , and Enterococcus , signifying the establishment of a marine microbial population. Core taxa, including Bartonella , Enterococcus , and Acinetobacter , were consistent across almost all fish samples regardless of the freshwater or seawater environment, suggesting these microbes may perform essential functions for the host. Notably, seawater taxa appeared in the gut as fish adapted to the hyperosmotic environment, yet the proportion of diet- and water-derived bacteria declined over time. Conclusions These findings indicate a strong host selection process in community assembly, highlighting the importance of active interactions in shaping gut microbiota, alongside passive environmental uptake. This study provides critical insights into the stability of the gut microbial community during the early development of chum salmon, with implications for aquaculture practices, particularly in hatchery programs, and the potential modification of gut microbiota through probiotics.