Shifting seas and first feeds: gut microbiome dynamics in juvenile chum salmon (Oncorhynchus keta) and their climate...

The early development of host-associated microbiota is crucial for host health and resilience. In migratory fish like chum salmon, the transition from freshwater to seawater and the onset of feeding are critical life stages that may be susceptible to environmental stressors, including those related to climate change. However, the relative influence of diet versus environment on microbiome stabilization remains unclear under ecologically relevant conditions. This study investigated the dynamics of gut bacterial communities in juvenile chum salmon during the first 90 days post-hatching, exploring how first feeding and freshwater-to-seawater transition shape the gut microbiota, with implications for climate sensitivity.

High-throughput 16S rRNA gene amplicon sequencing revealed highly dynamic gut/body microbiota. Prior to feeding, bacterial communities exhibited considerable fluctuations and lacked compositional stability. However, following the onset of feeding at 35 days post-hatching (DPH), the gut microbiota rapidly stabilized, indicating a strong influence of dietary microbes. Dominant taxa in freshwater stages included Aeromonas, Vibrio, Acinetobacter, and members of the Rhizobiaceae family. Upon transfer to seawater, the microbial community underwent a significant shift, with Aliivibrio and Colwellia emerging as dominant taxa, alongside the sustained presence of core taxa like Bartonella and Enterococcus. Interestingly, while many of the stabilized gut taxa post-feeding were derived from the feed, the microbial composition in the gut differed significantly from that of the feed itself, highlighting strong host-mediated selection. This selective filtering was further evidenced by the consistent presence of core bacterial taxa, including Bartonella, Enterococcus, and Acinetobacter across both freshwater and seawater environments, suggesting these microbes potentially provide essential functions to the host.

This study demonstrates that the gut microbiota in juvenile chum salmon is assembled by both environmental microbial input from diet and water, and is ultimately filtered by the host. This selective process highlights potential vulnerabilities of chum salmon to shifts in feed and ambient microbial communities, both of which are sensitive to environmental changes. Our findings underscore the importance of understanding host-microbe-environment triads for predicting climate-related vulnerabilities in wild salmon and for guiding future microbiome-based aquaculture strategies.