Bacterial diversity and community structure of the intestinal microbiome of Channel Catfish (Ictalurus punctatus) during ontogenesis

Abstract The acquisition of gut microbes does not occur randomly and is highly dependent on host factors, environmental cues, and self-assembly rules exerted by the microbes themselves. The main objective of this project was to characterize how the gut microbiome develops during the early life stages of Channel Catfish and to identify i) which bacteria are the main constituents of the gut microbiome at different ontogenesis stages, and ii) at which time point(s) the gut microbiome stabilizes. High-throughput Illumina Miseq DNA sequencing of the V4 domain of the 16S rRNA gene was used to assess the microbial community composition during the life stages of Channel Catfish along with water and feed samples. Microbiomes from fertilized eggs, sac fry, swim up fry, pre-fingerlings, and fingerlings were all significantly distinct. OTUs analyses showed that the phylum Proteobacteria, Firmicutes, Fusobacteria and Cyanobacteria dominated the Channel Catfish gut microbiome. During the early stages of ontogenesis, the fish microbiome was dynamic and highly diverse, with significant shifts occurring between fertilized eggs to sac fry (6 dph), and from sac fry to swim up fry (15 dph). The gut microbiome stabilized between the pre-fingerlings and fingerlings stage (≤90 dph) with an observed reduction in species richness. Feed had a more significantly contribution to the microbial colonization of the gut than water. We have identified the period in which the gut microbiome changes rapidly from 15 dph until 21 dph before stabilizing after 90 dph.