Disruption of the skin, gill, and gut mucosae microbiome of gilthead seabream fingerlings after bacterial infection and antibiotic treatment

Abstract

The activity of the microbiome of fish mucosae provides functions related to immune response, digestion, or metabolism. Several biotic and abiotic factors help maintaining microbial homeostasis, with disruptions leading to dysbiosis. Diseases and antibiotic administration are known to cause dysbiosis in farmed fish. Pathogen infections gr eatl y affect the production of gilthead sea br eam, and antibiotic treatment is still fr equentl y r equir ed. Her e , w e employ ed a 16S rRN A high-thr oughput metataxonomics appr oach to c har acterize c hang es in the gut, skin, and g ill microbiomes occurring due to infection with Photobacterium damselae subsp. piscicida and subsequent antibiotic treatment with oxytetracycline (OTC), as well as during r ecov er y. Although micr obiota r esponse differ ed betw een studied tissues, over all c hanges in composition, di v ersity, structur e, and pr edicted function wer e observ ed in all m ucosae. The skin and gill microbiomes of diseased fish became largely dominated by taxa that have been frequently linked to secondary infections, whereas in the gut the genus Vibrio , known to include pathogenic bacteria, increased with OTC treatment. The study highlights the negati v e impacts of disease and antibiotic treatment on the microbiome of farmed fish. Our results also suggest that fish transportation operations may have profound effects on the fish microbiome, but further studies are needed to accurately evaluate their impact.