Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)

Daniela Rosado,Marcos Pérez-Losada,Jo Cable,Ricardo Severino,Fernando Tavares,Raquel Xavier

doi:10.1038/s41598-019-55314-4

Daniela Rosado, Marcos Pérez-Losada + Show 4 more

Open Access

https://doi.org/10.1038/s41598-019-55314-4

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Abstract

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.

Highlights

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens
A shift in the abundance of such pathogens on the fish mucosae can lead to microbial imbalance and disease[21], which is usually accompanied by a reduction in bacterial diversity[6,14,22]
We describe the dysbiosis caused by disease and antibiotic treatment in microbial diversity of both mucosae over 3 weeks

Summary

Introduction

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. The European seabass Dicentrarchus labrax is one of the main farmed fish species in southern Europe, totaling 103.476 tons in landings (10% of global aquaculture production) between 2002 and 201123 This important food resource is susceptible to several bacterial pathogens: Photobacterium damselae, which causes photobacteriosis, Vibrio spp. causing vibriosis, and Tenacibaculum maritimum causing tenacibaculosis, just to name a few[24]. A decrease in microbial diversity was detected[42,46], along with an increased susceptibility to secondary infection, reduced host growth[41,44] and higher mortality[43] These studies reported bacterial pathogens acquiring resistance after antibiotic treatment, suggesting that farmed fish microbiomes could become reservoirs for antibiotic resistant genes[42,43,44]. Several studies showed an increase in resistance to tetracycline and streptomycin antibiotics in strains of P. damselae sampled from both wild and farmed fish hosts[35,38,47,48]

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