Biotic and abiotic factors influencing channel catfish egg and gut microbiome dynamics during early life stages

This study quantified the effects of pond rearing environments on microbial community composition in larval channel catfish (Ictalurus punctatus) gastrointestinal (GI) tracts across early developmental stages. Larvae were reared under standard industry conditions and sampled at five developmental stages (Egg, Swim-up, Day of stocking, 24 h post-stocking, and 21 d post-stocking). Massive-parallel sequencing of a segment of the 16S rRNA gene was conducted using an Illumina MiSeq platform to characterize the diversity and taxonomic composition of gut and water microbial communities. PERMANOVA analyses of differences in egg and gut microbial community composition across stages indicated a significant interaction between nursery pond environment, and family (P < 0.05) during the last two stages. Proteobacteria and Firmicutes genera along with genera including Vibrio, Aeromonas and Flavobacterium were associated with differences in gut bacterial community composition during larval development before and after pond stocking. Our study demonstrates that the aquatic rearing environment is an important factor influencing the transfer of microbes from water or food into the gut, and provides insight concerning the niche and ecological adaptability of microbes inside the channel catfish gut. Findings demonstrating that catfish gut community composition is highly variable over time indicates probiotic treatments may be possible, however gut community manipulation would require concurrent manipulation of pond or other environmental regimes and microbial communities.