NGS reveals initial diet strongly influences northern pike gut microbiota in an aquaculture setting

Session: Application of Genomic Tools to Inform Management of the Great Lakes (4)

Benjamin Gallo, State University of New York College of Environmental Science and Forestry, [email protected]
John Farrell, SUNY-ESF, [email protected]
Brian Leydet, State University of New York College of Environmental Science and Forestry, [email protected]

Abstract

The emergence of Next Generation Sequencing has uncovered the enormous diversity of microbes inhabiting the vertebrate gut. Gut microbiota has been explored in a limited number of fish species, and further evidence is needed to elucidate the effect diet may have on a fish’s gut microbiota composition. We designed an experiment testing the influence initial diet has on the gut microbiota composition in Northern Pike (Esox lucius) by rearing larval fish and feeding cohorts Artemia spp. or zooplankton. Both groups were then transitioned to a dry-food diet. Intestinal samples were collected temporally and sequenced on an Illumina MiSeq. Results revealed significant differences in the gut microbiome between initial diet groups and after the switch to the dry food diet. Further analysis revealed selection and dominance of Lelliottia spp.and Plesiomonas spp.in the Artemia and zooplankton fed fish respectively. Sampling from wild pike also revealed significant colonization by Plesiomonas spp. but no Lelliottia spp., suggesting the importance of Plesiomonas spp. during early development in the fish. Our findings support the effect of diet on gut microbiota structure, while raising questions as to what effect the absence of ‘natural’ microbes may have on the development of fish in an aquaculture setting.