Abstract
The gut microbiome is an important regulator of nutrition and immunity in fish, but it is highly sensitive to common aquaculture stressors (such as temperature shocks and air exposure during handling and transport) and influenced by host genetic factors, including immune function and mucus production. Triploid fish are commonly produced in aquaculture as they are sterile and have potentially higher growth rates. However, compared with their diploid counterparts, triploids have differences in morphology and susceptibility to stress, which could be related to the composition and diversity of the gut microbiome. Here, we exposed diploid and triploid rainbow trout (
Oncorhynchus mykiss
) to an early life stressor (cold shock) and assessed its effects on the composition and diversity of the gut microbiome five months later, through 16S rRNA sequencing. We found substantial differences in baseline microbiome diversity and composition between diploid and triploid fish, as well as in the microbiota′s response to stress. Triploidy was associated with significantly reduced microbial richness and phylogenetic diversity, potential reduction in lactic acid producing bacteria, increased abundance of facultative pathogenic taxa from the family
Enterobacteriaceae
and elevated mortality. Early life acute stress caused shifts in microbiome communities in later life, promoting an increase in the relative abundance of
Enterobacteriaceae
and a reduction of potential probiotic taxa, which are more evident in triploids. Our results indicate that early life stress has long term consequences for the gut microbiome composition of rainbow trout, with disproportionately greater effects in triploids compared with diploids.