The intestinal microbiome of Australian abalone, Haliotis laevigata and Haliotis laevigata × Haliotis rubra, over a 1-year period in aquaculture.

Abstract

The digestive tract microbiome aids its host in food digestion, immune system function, development, and health. In marine organisms and habitats, microbiome research is limited. In Australia, abalone aquaculture is an economically important industry; however, little is known about the relationship between abalone and their microbiome. This study investigated the intestinal microbiomes of hybrid, or Tiger, (Haliotis laevigata x H. rubra) and greenlip (Haliotis laevigata) abalone over a one-year production period, grown at two commercial farms. Abalone samples (n = 30 for each species) were collected every three months, for a total of five sampling periods, mimicking seasonal change (i.e. Autumn, Winter, Spring, Summer, Autumn) for each farm. The intestinal samples were sequenced (16S rRNA gene, Illumina MiSeq) and the intestinal microbiomes were analysed. The intestinal microbiomes of hybrid and greenlip abalone were dominated by four genera: Psychrilyobacter, Vibrio, Mycoplasma, and to a lesser extent Formosa. The dominance of the digestive tract by four genera (≥88%) indicates that the abalone gut is a niche environment with unique selective pressures. The intestinal microbiomes were significantly impacted by the sampling date, which is associated with seasonal changes and abalone age.