Differences in the bacterial communities along the intestinal tract of channel (Ictalurus punctatus) and hybrid (I. punctatus × I. furcatus) catfish

Authors: Older, Caitlin; GOODMAN, PENELOPE - Mississippi State University; REIFERS, J - Mississippi State University; YAMAMOTO, FERNANDO - Mississippi State University

Submitted to: Physiological Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2025
Publication Date: 3/31/2025
Citation: Older, C.E., Goodman, P.M., Reifers, J.G., Yamamoto, F.Y. 2025. Differences in the bacterial communities along the intestinal tract of channel (Ictalurus punctatus) and hybrid (I. punctatus × I. furcatus) catfish. Physiological Genomics. 57(5)299-307. https://doi.org/10.1152/physiolgenomics.00008.2025.
DOI: https://doi.org/10.1152/physiolgenomics.00008.2025

Interpretive Summary: Hybrid catfish, produced by crossing a female channel and male blue catfish, display a number of advantages for production compared to either of its parent species, and thus has become the primary catfish cultured in the United States. Most management practices for hybrid catfish culture have been adopted from those used for channel catfish culture, with few adjustments specific for hybrid catfish. Utilizing management practices specifically designed for hybrids may improve production efficiency. The bacterial populations, or microbiota, in the gut play critical roles in host development and health, and thus are relevant to fish production. Scientists at the USDA ARS Warmwater Aquaculture Research Unit in collaboration with Mississippi State University characterized the gut microbiota in different segments of the intestines, and compared these communities between channel and hybrid catfish using DNA sequencing. Additionally, the microbiota was compared among the different intestinal segments within each fish species. Channels and hybrids were found to have significantly different microbiota, including higher abundances of Cetobacterium, a bacteria associated with some host benefits, in the middle intestinal segment of hybrids compared to channels. This bacteria was also found to have a trend of increasing abundance as you move along the intestinal tract. These results provide evidence of differences in the gut microbiota between channels and hybrids and insight into the bacterial communities along the catfish intestinal tract. Additional research will be valuable in understanding why differences between channel and hybrid catfish exist and how they may contribute to variation in gut microbiota-related production traits.

Technical Abstract: Hybrid catfish (Ictalurus punctatus × I. furcatus) is the preferred catfish for US aquaculture due to the heterosis exhibited in many production traits. Improvements in fry production protocols have enabled widespread adoption of these hybrids, with producers using management practices optimized for channel catfish. Research to consider differences, outside of production traits, which may exist between hybrids and their parent species is lacking. Utilizing management practices specifically designed for hybrids may improve production efficiency. The gut microbiome plays critical roles in host development and health and, thus, is relevant to production. In the present study, the microbiota in the anterior, middle, and posterior segments of the intestinal tract were compared between channel and hybrid catfish using high-throughput 16S rRNA gene sequencing. Bacterial community structure was different between channels and hybrids across all intestinal segments (P < 0.05) despite a lack of difference in community diversity. Cetobacterium spp. were found in higher abundances in the middle intestinal segment of hybrids compared with channels (q = 0.02) and found to have a trend of increasing abundance with increasingly distal segments in both channels and hybrids (q < 0.05). Vibrio spp., a low-abundance taxon, was similarly found in higher abundances in the anterior segment of hybrids. These results provide evidence of differences in the gut microbiomes of channels and hybrids and insight into the bacterial communities along the catfish intestinal tract. Additional research will be valuable in understanding why do differences between channel and hybrid catfish exist and how they may contribute to variation in gut microbiome-related production traits.