EVALUATING DIFFERENCES IN THE HOMEOSTATIC INTESTINAL MICROBIOME BETWEEN SELECTED STRAINS OF CHANNEL CATFISH Ictalurus punctatus AND BLUE CATFISH Ictalurus furctatus  

The intestinal microbiome (IM), or the community of commensal and pathogenic microbes living within the gut, have long been thought to play a large role in digestion and fish performance. Recently, high-throughput molecular sequencing has yielded insights into the importance of the IM in aquaculture species, and it has been shown that an imbalanced microbiome, or dysbiosis, can lead to disease or poor digestion. While it has been hypothesized that host (fish) genetics and immunity play a large role in maintaining the specific microbes within the microbiome, little data exists to elucidate this relationship in fish.

To improve upon this knowledge, we raised three strains of Channel Catfish Ictalurus punctatus and four strains of Blue Catfish Ictalurus furcatus from eggs, with equal feed and water conditions, to 193 days post hatch. At this time, fish were euthanized and the entire intestinal tract was removed and homogenized using sterile procedures. This allowed both allochthonous (fecal) and autochthonous (mucosal) bacteria to be captured for DNA extraction using a MoBio PowerFecal® DNA Extraction Kit. DNA was then added to the Fluidigm Access Array system for PCR amplification of the 16S rRNA gene, and preparation of a multiplexed sequencing library. Sequencing was then preformed on the MiSeq platform and data were analyzed using QIIME with the GreenGenes database used for picking of operational taxonomic units (OTUs). Poor quality reads and low abundance (≤0.5%) OTUs were removed, leaving 21 samples from both fish species for analysis.

From this data a total of 3,168,821 OTUs were identified from 14 distinct phylogentic clades. While the dominant OTUs (Fusobacteria and Proteobacteria) of the IMs are similar, the relative abundances of these OTUs are statistically different across the two species of Ictalurids. Alpha diversity rarefaction plots show Channel Catfish have only slightly more diverse microbiomes. This study provides insight on the relationship of fish genetics with the IM, and may help to explain differential susceptibility to disease in Ictalurids.