Core intestinal microbiomes of planktivorous and algae-farming coral reef damselfishes (Actinopterygii: Pomacentridae) reflects feeding behaviour

Abstract Background: Fish harbour diverse microbiomes within their gastro-intestinal system that effect the host’s digestion, nutrition and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome diversity and the factors that determine its structure and composition. Damselfish are important coral reef fish species that play a strong role in determining algae and coral structure of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we use 16s rRNA sequencing to interrogate the intestinal microbiome of 10 damselfish species (Pomacentridae) from the Great Barrier Reef to compare the composition of their intestinal bacterial assemblages across the planktivorous and algae-farming trophic guilds.Results: We identify core intestinal bacterial taxa for each host fish species. Gammaproteobacteria, belonging to the genus Actinobacillus, were detected in 80 % of sampled individuals and suggests a possible core member of pomacentrid microbiomes. Core microbiomes of algae-farming species were more diverse than planktivorous species with farming species sharing 35 ± 22 ASVs and planktivorous sharing 7 ± 3 ASVs. We also provide evidence for significant shifts in bacterial community composition along the intestines. We show that Bacteroidia, Clostridia and Mollicutes bacteria are more abundant in the anterior intestinal regions while Gammaproteobacteria are generally highest in the stomach. Finally, we highlight differences in microbiomes associated with both trophic guilds. Algae-farming and planktivorous damselfish host species significantly differed in their composition of bacteria belonging to Vibrionaceae, Lachnospiraceae and Pasteurellaceae.Conclusions: Our results demonstrate that core intestinal bacterial communities of damselfish reflect host species diet and feeding behaviour, whereby algae-farming hosts have larger and more diverse core microbiomes than planktivorous hosts. We suggest that the trophic guild of a host fish species is a strong determinant of microbiome structure.