Ontogenetic characterization of the intestinal microbiota of channel catfish through 16S rRNA gene sequencing reveals insights on temporal shifts and the influence of environmental microbes

Authors: BELDSOE, JACOB - University Of Idaho; Peterson, Brian; SWANSON, KELLY - University Of Illinois; SMALL, BRIAN - University Of Idaho

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2016
Publication Date: 12/8/2016
Citation: Beldsoe, J., Peterson, B.C., Swanson, K., Small, B. 2016. Ontogenetic characterization of the intestinal microbiota of channel catfish through 16S rRNA gene sequencing reveals insights on temporal shifts and the influence of environmental microbes. PLoS One. 11(11):e0166379. DOI: 10.1371/journal.pone.0166379.

Interpretive Summary: To continue increasing fish production the industry is looking for ways of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate changes that may occur throughout development of the host. Intestinal microbiota were surveyed with high-throughput sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (DPH), while also characterizing the environmental microbes derived from the culture water and diets fed. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 DPH when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 DPH. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the bacterium Cetobacterium somerae and Plesiomonas shigelloides dominating the catfish microbiota after 3 DPH. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained separate from the overall microbial communities present in diets and water, although there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Results have implications on the management of catfish aquaculture, such as aiding in the development and timing of pre- and probiotic supplementations, as well as yielding further basic insights into the microbiota of fish.

Technical Abstract: Aquaculture recently overtook capture fisheries as the largest producer of food fish; however, to continue increasing fish production the industry is looking for ways of improving fish health and growth. Pre- and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate temporal changes that may occur throughout ontogenetic development of the host. Intestinal microbiota were surveyed with high-throughput sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (DPH), while also characterizing the environmental microbes derived from the culture water and diets fed. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 DPH when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 DPH. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the bacterium Cetobacterium somerae and Plesiomonas shigelloides dominating the catfish microbiota after 3 DPH. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained as a niche habitat, separate from the overall microbial communities present in diets and water, although there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Results have implications on the management of catfish aquaculture, such as aiding in the development and timing of pre- and probiotic supplementations, as well as yielding further basic insights into ontogenetic effects on teleost microbiota.