Fish skin microbiota under health and disease conditions

Background: The welfare of farmed fish is influenced by environmental and management factors, their skin being an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). Highly sensitive S. aurata, were challenged with Vibrio harveyi (Gram-negative bacteria). In addition, and to provide a wider range of infection, both fish species were infected with Streptococcus iniae (Gram-positive bacteria), comparing the highly sensitive L. calcarifer and the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks. Results: Swabs samples taken from different areas on fish skin (lateral lines, abdomen and gills) before, 24, 48 and 72 h, 5 days, one week and 1 month after controlled infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed a similar bacterial composition present naturally on all sites of fish skin sampled but the bacterial composition changed following the controlled infections (T1) resulting in changes in bacterial community on fish skin. Moreover, when the skin naturally occurring microbiome did not recover, it led to fish mortality mostly following T1 (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water between fish reared in non-UV and UV treated water under health and disease conditions. Conclusions: Based on the experimental findings presented, modifications and balance in fish skin flora (in sick and health conditions) are better understood, and can be harnessed for providing beneficial tools for commercial fish farmers; methods and compositions can be developed for predicting and preventing fish diseases and increasing fish health and welfare, thus, enhancing commercial fish yields.