Salmonid alphavirus infection causes skin dysbiosis in Atlantic salmon (Salmo salar L.) post-smolts

Abstract

Interactions among host, microbiota and viral pathogens are complex and poorly understood. The goal of the present study is to assess the changes in the skin microbial community of Atlantic salmon (Salmo salar L.) in response to experimental infection with salmonid alphavirus (SAV). The salmon skin microbial community was determined using 16S rDNA pyrosequencing in five different experimental groups: control, 7 days after infection with low-dose SAV, 14 days after infection with low-dose SAV, 7 days after infection with high-dose SAV, and 14 days after infection with high-dose SAV. Both infection treatment and time after infection were strong predictors of the skin microbial community composition. Skin samples from SAV3 infected fish showed an unbalanced microbiota characterized by a decreased abundance of Proteobacteria such as Oleispira sp. and increased abundances of opportunistic taxa including Flavobacteriaceae, Streptococcaceae and Tenacibaculum sp. These results demonstrate that viral infections can result in skin dysbiosis likely rendering the host more susceptible to secondary bacterial infections.

Environmental conditions and neutral processes shape the skin microbiome of European catfish (Silurus glanis) populations of Southwestern France

“…and Supporting Information S12). We found more than 900 potentially pathogenic ESVs in catfish skin microbiome, which together could attain high abundance on hosts, i.e., up to 33.1% of abundance on a single host (Reid et al ., ). 17% of such ESVs showed >97% identity with the major freshwater fish pathogens, Flavobacterium columnare , F. branchiophilum and F. psychrophilum (Austin and Austin, ).…”

Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata)

“…At the same time, infectious diseases that frequently affect farmed fish can also induce dysbiosis, generally favouring increased abundance of opportunistic bacteria creating complex feedback mechanisms (e.g. Llewellyn et al, 2017;Reid et al, 2017).…”

“…Moreover, previous disease history (e.g. Llewellyn et al, 2017;Tapia-Paniagua et al, 2018;Reid et al, 2017) and host physiology (e.g. Apprill et al, 2014) may have influenced the composition of fish skin microbiomes.…”

Using fish models to investigate the links between microbiome and social behaviour: The next step for translational microbiome research?

“…Disentangling the links between microbiome and fish health is a hot topic, particularly given the growth of the aquaculture industry. In this respect, the effects of pathogens, antibiotics and probiotics on microbiome composition have been subject of several studies showing that significant changes take place (e.g., Carlson, Leonard, Hyde, Petrosino, & Primm, 2017;Gonçalves & Gallardo-Escarate, 2017;Hennersdorf et al, 2016;Li et al, 2016;Llewellyn et al, 2017;Reid et al, 2017).…”