fish gut metagenome Raw sequence reads. fish gut metagenome

Atlantic salmon have dynamic GI tract microbiomes influenced during their life stages. In the case of farmed Tasmanian salmon farms the gut microbiomes of most adult specimens contain mainly members of the family Vibrionaceae. In diet feeding trials with duplicated cage design evidence of systematic cage set replicate differences in community profiles was observed that suggested biases possibly from the experimental design or overriding farm-level influences. The primary differences involved 1-2 log10 unit differences in the relative abundances of mainly non-Vibrionaceae fermentative bacteria. Since farmed salmon faecal communities are dynamic over temporal scales we further investigated whether bacterial growth within the digesta as it resides in the hindgut is rapid enough that differences can occur on short time scales and thus reflect timing of sampling. It was also considered certain farm practices could destabilize the GI tract community such as freshwater bathing used to control amoebic gill disease (AGD). Analysis of samples from four separate feeding trials indicated the main driver of the gut microbiome structure was most likely related to growth of bacteria in the hind gut and the time digesta was present therein. This was evidenced by strong positive correlations of non-Vibrionaceae fermentative taxa with chloroplast derived 16S rRNA, the latter originating directly from the feed. This correlation was also characterized by an increase in species richness and an opposite relation to weighted average rRNA copy numbers. This indicated a classic community succession indicative of diversification of the microbiome community that we surmise that leads to the greater abundance of slower growing taxa. There was no evidence of gut community destabilization via freshwater bathing; diets have only minor influences, at least within short term applications; there was no link to changes in GI tract morphology; and the gut microbiome itself is qualitatively stable. There was also no connection found with farm performance data (feeding, feed conversion and specific growth rates) suggesting the phenomena observed is active in all individual fish. The results were corroborated with data obtained previously using different sequencing technology. The results here connect community structural fluxes to the digesta and gastric passage and could be useful in efforts to develop connections between the microbiome and farmed salmon physiology and behavior.