Abstract
Rainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.
Highlights
An increasing global population has caused a concomitant increased demand for food
We isolated 174 bacterial strains from the skin mucus of rainbow trout spanning 18 genera. These strains were estimated to account for 4.95% of the total bacterial community in skin, it should be noted that this can be an overestimation considering the low taxonomic resolution of short-reads[38]
Spanggaard et al.[26] isolated 1,018 bacteria belonging to nine genera from skin, gill, and the gut of rainbow trout using TSA medium
Summary
An increasing global population has caused a concomitant increased demand for food. Aquaculture is the world’s fastest growing food production sector[1], partly fulfilling the food demand. Manipulation of the skin microbiome, such as increasing the abundance of specific antagonistic bacteria against pathogens might be effective. Such bacteria should be residing on the skin mucus rather than the gut of fish. More effort should be made to isolate diverse bacteria from fish skin for further understanding of skin microbiome and the screening of antagonistic bacteria. The present study aimed to analyze the skin microbiome of rainbow trout in order to culture a range of diverse bacteria for screening their antagonistic properties. We used 10 culture media containing different carbon sources or solidifying agents to isolate more diverse bacteria from the skin mucus of the rainbow trout. We compared our findings with published microbiome data of fish skin[29,31,32] to see whether similar sequences to the cultured isolates were found previously
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