Gut Microbiome Changes in Senescing Chinook Salmon

In addition to the juvenile experimental fish, we collected analogous anal vent swabs from adult Chinook salmon carcasses immediately after fish were artificially spawned for propagation at Willamette Hatchery in Oakridge, Oregon, USA (43°73′84.9″N, − 122°43′77.2″W) in September of 2020. Samples were immediately placed on ice and were frozen at − 80 within 3 h of collection. To evaluate senescence via histology, we preserved lower intestine and pyloric caeca samples in Dietrich’s fixative for histology and evaluated the integrity of the epithelium by measuring the percent of intact gut epithelium remaining³⁵ . Scoring of gut samples was conducted by an experienced fish pathologist with forty years of experience conducting histological analysis of salmonids. We previously demonstrated that loss of integrity of the intestinal epithelium correlates closely with the timing of senescence and mortality in adult freshwater phase Chinook salmon^{35 ,36 (link)}. Therefore, to explore potential differences in gut microbiota between adult fish at early versus late stages of gut senescence, we used epithelial integrity scores to select four adult males with extremely degraded gut epithelia (“senescent”) and three adult males with mostly intact gut epithelia (“pre-senescent”) for microbiome sequencing. Fish designated as senescent had 5–10% epithelial integrity, and fish designated as pre-senescent had 70–80% epithelial integrity.