Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis

Abstract

Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.

Feed Regime Slightly Modifies the Bacterial but Not the Fungal Communities in the Intestinal Mucosal Microbiota of Cobia Fish (Rachycentron canadum)

“…The phylum Proteobacteria dominated the bacterial community in all cobia fish which was consistent with previous studies.Proteobacteria have been reported in larval [ 11 , 48 ], juvenile [ 10 , 11 , 13 ] and adult [ 12 ] healthy cobia, and other tropical marine aquaculture fish [ 62 , 63 , 64 ]. The most abundant genera were Photobacterium , Vibrio , Catenococcus and Enterovibrio , independently of the diet.…”

“…It is a tropical and subtropical species widely distributed worldwide except in the eastern Pacific [ 9 ]. A few studies have described the bacterial components of the cobia gut microbiota using 16S rRNA metabarcoding, revealing different compositions according to rearing conditions and fish development stages [ 10 , 11 , 12 , 13 ]. In these studies, cobia were reared in China, India and the South Caribbean Sea of Colombia.…”