The microbiota of teleost fish has gained a great deal of research attention within the past decade, with experiments suggesting that both host-genetics and environment are strong ecological forces shaping the bacterial assemblages of fish microbiomes. Despite representing great commercial and scientific importance, the catfish within the family Ictaluridae, specifically the blue and channel catfish, have received very little research attention directed toward their gut-associated microbiota using 16S rRNA gene sequencing. Within this study we utilize multiple genetically distinct strains of blue and channel catfish, verified via microsatellite genotyping, to further quantify the role of host-genetics in shaping the bacterial communities in the fish gut, while maintaining environmental and husbandry parameters constant. Comparisons of the gut microbiota among the two catfish species showed no differences in bacterial species richness (observed and Chao1) or overall composition (weighted and unweighted UniFrac) and UniFrac distances showed no correlation with host genetic distances (Rst) according to Mantel tests. The microbiota of environmental samples (diet and water) were found to be significantly more diverse than that of the catfish gut associated samples, suggesting that factors within the host were further regulating the bacterial communities, despite the lack of a clear connection between microbiota composition and host genotype. The catfish gut communities were dominated by the phyla Fusobacteria, Proteobacteria, and Firmicutes; however, differential abundance analysis between the two catfish species using analysis of composition of microbiomes detected two differential genera, Cetobacterium and Clostridium XI. The metagenomic pathway features inferred from our dataset suggests the catfish gut bacterial communities possess pathways beneficial to their host such as those involved in nutrient metabolism and antimicrobial biosynthesis, while also containing pathways involved in virulence factors of pathogens. Testing of the inferred KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways by DESeq2 revealed minor difference in microbiota function, with only two metagenomic pathways detected as differentially abundant between the two catfish species. As the first study to characterize the gut microbiota of blue catfish, our study results have direct implications on future ictalurid catfish research. Additionally, our insight into the intrinsic factors driving microbiota structure has basic implications for the future study of fish gut microbiota.

Background: Mucosal surfaces of fish provide cardinal defense against environmental pathogens and toxins, yet these external mucosae are also responsible for maintaining and regulating beneficial microbiota. To better our understanding of interactions between host, diet, and microbiota in finfish and how those interactions may vary across mucosal tissue, we used an integrative approach to characterize and compare immune biomarkers and microbiota across three mucosal tissues (skin, gill, and gut) in Atlantic salmon receiving a control diet or diets supplemented with mannan-oligosaccharides, coconut oil, or both. Dietary impacts on mucosal immunity were further evaluated by experimental ectoparasitic sea lice (Lepeophtheirus salmonis) challenge. Results: Fish grew to a final size of 646.5 g ± 35.8 during the 12-week trial, with no dietary effects on growth or sea lice resistance. Bacterial richness differed among the three tissues with the highest richness detected in the gill, followed by skin, then gut, although dietary effects on richness were only detected within skin and gill. Shannon diversity was reduced in the gut compared to skin and gill but was not influenced by diet. Microbiota communities clustered separately by tissue, with dietary impacts on phylogenetic composition only detected in the skin, although skin and gill communities showed greater overlap compared to the gut according to overall composition, differential abundance, and covariance networks. Inferred metagenomic functions revealed preliminary evidence for tissue-specific host–microbiota coadaptation, as putative microbiota functions showed ties to the physiology of each tissue. Immune gene expression profiles displayed tissue-specific signatures, yet dietary effects were also detected within each tissue and peripheral blood leukocytes. Procrustes analysis comparing sample-matched multivariate variation in microbiota composition to that of immune expression profiles indicated a highly significant correlation between datasets. Conclusions: Diets supplemented with functional ingredients, namely mannan-oligosaccharide, coconut oil, or a both, resulted in no difference in Atlantic salmon growth or resistance to sea lice infection. However, at the molecular level, functional ingredients caused physiologically relevant changes to mucosal microbiota and host immune expression. Putative tissue-specific metagenomic functions and the high correlation between expression profiles and microbiota composition suggest host and microbiota are interdependent and coadapted in a tissue-specific manner.

The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (Oncorhynchus mykiss) is one such species in which the strain ARS-Sel has been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth and plasma and digesta metabolomes between ARS-Sel and two commercial strains (CS-1 and CS-2), when fed plant-protein (PM) and fishmeal-based (FM) diets, and to correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-Sel fish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma and digesta metabolite profiles of ARS-Sel and CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of enteritis development, which was confirmed by intestinal histology. As reported in previous studies, the ARS-Sel strain performed better than the commercial strains when fed the PM diet. Our findings also suggest that metabolomic profiles of plasma and digesta, samples of which can be obtained through non-lethal methods, offer valuable insight in monitoring the occurrence of enteritis in carnivorous aquaculture species due to plant-based diets.

Biofloc technology is an aquaculture production system that has gained popularity with tilapia production. Probiotics provide benefits for the host and/or aquatic environments by both regulating and modulating microbial communities and their metabolites. When a probiotic feed is combined with a biofloc system, the production amount may be improved through better fish growth, disease resistance, and/or improved water quality by reducing organic matter and stabilizing metrics such as pH and components of the nitrogen cycle. Two research trials measured Nile tilapia ( Oreochromis niloticus ) growth performance and composition of the microbial communities in the water and within the fish fecal material, following feeding with top‐coated probiotic treatments. Trial A incorporated tilapia (71.4 ± 4.4 g), and a commercial diet (Control) that was top coated with either Bacillus velenzensis AP193 (AP193; 1 × 10 ⁷ CFU g ¹ ) and BiOWiSH Feedbuilder Syn3 (BW; 3.6 × 10 ⁴ CFU g ⁻¹ ). In Trial B, juvenile tilapia (5.34 ± 0.42 g) were fed treatment diets top coated with two different concentrations of BiOWiSH Feedbuilder Syn3 at final concentrations of 3.6 × 10 ⁴ CFU g ⁻¹ (BWx1) and 7.2 × 10 ⁴ CFU g ⁻¹ (BWx2). Tilapia were offered commercial feed (38% protein floating tilapia feed) as a control diet for both trials. Results from both growth trials indicated no differences in growth performance due to the probiotic additions, except for feed conversion ratio (FCR) in Trial B. Both BWx1 and BWx2 showed improved survival, water quality, solids management, and bacterial composition of water and fecal matter. Even though growth performance results presented no significant differences, results could differ based on the probiotic concentration, the route of probiotic administration, or their impact on the microbial community of the biofloc system culture water. Trial results indicated that testing on a larger scale with varied probiotic doses may be necessary to achieve an effective dosage for improving tilapia growth performance.

Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal morbidity especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure bacterial population dynamics during P. salmonis infection. We observed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicated that coinfection with other pathogens may enhance P. salmonis pathogenicity.