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

Hybrid catfish (<i>Ictalurus punctatus</i> × <i>I. furcatus</i>) 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 (<i>P</i> < 0.05) despite a lack of difference in community diversity. <i>Cetobacterium</i> spp. were found in higher abundances in the middle intestinal segment of hybrids compared with channels (<i>q</i> = 0.02) and found to have a trend of increasing abundance with increasingly distal segments in both channels and hybrids (<i>q</i> < 0.05). <i>Vibrio</i> 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.<b>NEW & NOTEWORTHY</b> Hybrid and channel catfish are inhabited by gut bacterial communities of similar overall diversity but of significantly different structure and composition. <i>Cetobacterium</i> spp., a genus previously shown to confer benefits in other hosts, was found in higher abundances in the middle intestinal segment of hybrids and was found to have increasing abundance along the intestinal tract of both channels and hybrids.