Previous studies have identified that the hindgut microbiota of juvenile rainbow trout (Oncorhynchus mykiss) is predominately comprised of Citrobacter gillenii, Obesumbacterium proteus, Kluyvera intermedia, Shewanella spp., and Lactobacillus lactis, whilst within adult fish, Aeromonas, Pseudomonas and Enterobacteriaceae dominate. To date no study has assessed the composition of the microbiota in rainbow trout farmed in Australia. Previous studies have also not compared fish at the freshwater hatchery and those at harvest following a marine growout phase. In this study, the hindgut samples were collected from female diploid (n= 5) and triploid (n=5) fish from a hatchery and from female diploid (n= 5) and triploid (n=5) rainbow trout at harvest from a fish farm on the west coast (Macquarie Harbour) of Tasmania, Australia. Using 16S rRNA sequencing we analyzed microbial communities of the hindgut contents and the epithelium of these fish using diversity profiling. Results showed that in the hindgut of both female diploid and triploid rainbow trout the dominant genera were Vibrio, Aliivibrio and Photobacterium spp. whereas the microbiota of juvenile trout at the hatchery was dominated by Cetobacterium somerae, Clostridium and Pediococcus acidilactici with the latter two species only present in diploid fish. Variations in the number of less prevalent bacterial species between individual fish were also present. Comparison of the microbial communities showed that only some of the microorganisms found in the hindgut were present on the gut epithelium.
These differences are likely to be an effect of the transfer from fresh water to seawater however may also a result of a shift to a more stable community, something which should investigated further.