Infection and antibiotic treatment have prolonged effects on gut microbiota, muscle and hepatic fatty acids in rainbow trout (Oncorhynchus mykiss).

Aims: The aim of the present study was to investigate the gastrointestinal (GI) microbiota and bacterium-specific fatty acid occurrence in the muscle and hepatic lipids of rainbow trout Oncorhynchus mykiss (Walbaum, 1792), both healthy and those naturally infected with bacterial pathogens.

Methods And Results: From June 2017 (L1) to September 2018 (L8), 74 specimens of rainbow trout Oncorhynchus mykiss (with an average weight from 139.2 ± 7.1 g (L1) to 2191.7 ± 85.1 g (L8)) were studied. Amplicon sequencing targeted to the V3-V4 region of 16S rRNA gene fragments is used for the identification of the taxonomic composition of gut bacterial communities. Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Fusobacteria were the major phyla. Besides behavioural and physiological manifestations of the bacterial mixed disease (yersiniosis, pseudomonosis and flavobacteriosis), some disorders induced by both the infection and followed antibiotic treatment were detected in the host organism, including (1) a progressive decrease in the content of odd-chain saturated fatty acids of bacterial origin within the trout lipid molecules and (2) abnormalities in trout GI tract microbiota, such as the elimination of LAB and progressive occurrence of certain bacterial taxa, particularly Mycoplasmataceae.

Conclusions: The GI bacterial flora varied principally due to Mycoplasmataceae and Lactobacillaceae, which could be considered in the search for bioindicators. The content of specific bacterium-derived fatty acids incorporated into the lipids of trout muscle and hepatic seems to be related to the prevalence of bacterial taxa, and their deficit could be regarded as an early warning sign of microbiota disturbance.

Significance And Impact Of Study: Our results demonstrated that infectious disease and antibiotic treatment of reared species can cause a pertinent imbalance in their gut microbiota and reduce the abundance of specific fatty acids. This can be useful for the sustainable aquaculture industry due to the development of early indication technologies for rapid disease diagnosis.