Date of Award


Degree Name

Master of Science


Animal Science

First Advisor

Small, Brian


The intestinal microbiome (IM) or the community of commensal and pathogenic microbes that inhabit the intestinal tract of fish has long been of interest in aquaculture because of its hypothesized role in nutrient digestion and fish immunity. Artificial improvement to the IM of fish with pre- and probiotics has been shown to have benefits in some studies; however, the mechanisms behind these supplements are poorly understood because of a lack of knowledge on the basic structure of the IM of fish. The research described here aims to characterize the IM of the highly studied and commercially important Icatlurid catfish, channel catfish Ictalurus punctatus and blue catfish I. furcatus. In this study we evaluated differences between the homeostatic IM, across genotype (Objective 1) and developmental ontogeny (Objective 2), using high-throughput sequencing of 16S rRNA gene amplicons. We compared the IM of four selected strains of blue catfish and three selected strains of channel catfish at 193 days post-hatch (DPH) in Objective 1 (n = 40); while the influence of developmental ontogeny was evaluated by observing the IM of a single family of channel catfish at 3, 65, 125, and 193 DPH Objective 2 (n = 20). The bacterial phyla Fusobacteria, Firmicutes, and Proteobacteria were detected in all fish strains and developmental time points; however, at the genus level the abundances of different bacteria varied among experimental units, as well as being rather variable between individuals. At 3 DPH (n = 5) the IM of channel catfish sac-fry larvae showed the most variation between individuals; with bacteria from the genus Bradyrhizobium dominating the IM of two sac-fry (84% and 88%), and Flavobacterium, Lactobacillus, Comamonadaceae dominating the IM of the remaining three sac-fry analyzed (86%, 99%, and 97% respectively). The dominant bacteria in the gut of all other fish analyzed (n = 55), was Cetobacterium somerae (mean ± SD, 41.4% ± 36%), a commensal microbe that is known to produce vitamin B12. Statistical differences in the abundance of three different bacteria within the order Clostridiales (P ≤ 0.039) were detected in Objective 1, with more of these OTUs inhabiting the gut of channel catfish than that of blue catfish. Statistical differences in the abundance of Edwardsiella, a genus of bacteria known to cause disease in catfish, were detected across the two species of Ictalurid catfish in Objective 1 (P = 0.038), and across developmental ontogeny in Objective 2 (P = 0.021); however, these bacteria were detected at low abundance (0.002% - 0.004%). Comparisons of beta diversity showed significant differences between many strains of Ictalurids, with a highly significant difference between channel catfish and blue catfish (P = 0.001); however, few differences were detected when comparing beta diversity across the four time points over the first 193 DPH in Objective 2, with only 3 DPH and 125 DPH showing significant differences (P = 0.022). Overall these data suggest host-genotype, and to a lesser extent developmental ontogeny, influence the structure of the IM of Ictalurid catfish. As the first study to be conducted on the IM of these fish species, these results have performance implications on the culture of these commercially important catfish, while also enhancing our basic knowledge on the dynamics of the fish microbiome.




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