Comparison of channel catfish and blue catfish gut microbiota assemblages shows minimal effects of host genetics on microbial structure and inferred function

Authors: BLEDSOE, JAKE - University Of Idaho; Waldbieser, Geoffrey - Geoff; SWANSON, KELLY - University Of Illinois; Peterson, Brian; SMALL, BRIAN - University Of Idaho

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2018
Publication Date: 5/23/2018
Citation: Bledsoe, J., Waldbieser, G.C., Swanson, K., Peterson, B.C., Small, B. 2018. Comparison of channel catfish and blue catfish gut microbiota assemblages shows minimal effects of host genetics on microbial structure and inferred function. Frontiers in Microbiology. 9:1073.

Interpretive Summary: While channel and blue catfish have different performance traits in commercial culture, and their hybrid offspring are valued for commercial production, little is known whether there is a difference in the microbial content in the gut of these two species, or strains within each species. A. ARS scientists at the Warmwater Aquaculture Research Unit in Stoneville, MS, and the National Cold Water Marine Aquaculture Center in Franklin, ME, collaborated with scientists from the University of Idaho to culture fish from three channel and three blue catfish strains in a common environment with the same diet. Gut samples were collected at 193 days post-hatch and DNA sequencing was used to determine the types of bacteria present in each sample. Statistical analyses showed no significant differences in overall microbial diversity between fish strains or species, although there was enrichment of 39 species of Firmicutes, Proteobacteria, and Fusobacteria in channel catfish whereas only one species of Vibrio was enriched in the blue catfish gut. This experiment provided a background survey of microbial content in the catfish gut and pointed to differences in microbial gut populations between channel and blue catfish that could be enhanced to improve production.

Technical Abstract: Channel catfish (Ictalurus punctatus) represent the greatest market share in U.S. aquaculture production, both in terms of total economic value and numbers produced. The blue catfish (I. furcatus) is also of great interest to U.S. aquaculture, because interspecific crosses (I. punctatus x I. furcatus) produce offspring with hybrid vigor and desirable phenotypes such as increased disease resistance and fillet yield. Ictalurid catfish have received much breeding attention, and multiple aquaculture strains with unique performance traits exist within both species, yet there is a paucity of knowledge regarding their gut microbiota. As such, we aimed to characterize and compare the gut microbiota of six distinct strains of ictalurids (3 I. punctatus, 3 I. furcatus; strain nested within species) using 16S rRNA V4 sequencing, to determine if gut microbiota are involved in the observed differences in performance traits among these strains. Fish were reared in a common flow-through system and received the same diets up to the time of sampling (193 days post hatch) to control for sources of variation other than host genetics. In addition, host genetic data were gathered from separate individuals from each strain (n=20) in the form of 20 microsatellite loci to quantify and compare genetic distance among the hosts to that of their respective microbiota. Results indicate that a shared environment (water and diet) overcomes differences in host-genotype in shaping the assemblage of gut microbiota, as no significant differences in alpha- (ANOVA; p = 0.05) or beta-diversity (PERMANOVA; p = 0.05) were detected and no significant correlation (Mantel test; p = 0.05) was found between host genetic distance (Rst) and microbiota distance (UniFrac). However, DESeq2 identified 40 differentially abundant (FDR q = 0.05) microbes among the two fish species, including taxa from Aeromonadaceae, Enterobacteriaceae, and Pseudomonas. While differences in microbiota were minimal, differentially abundant microbes among these heterospecific strains reared in the same environment indicate that differences in host-genotype do have an indirect influence on the gut microbiota assemblages in these teleostean fish.