An ecological insight into the spatial arrangement in the gut bacterial community of the algivorous sea urchin Tripneustes gratilla elatensis will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. We hypothesized that alterations in the bacterial compositional structure under different diets and along the gut are associated with the potential contribution to food digestion. Toward this goal, we investigated the bacterial communities in the sea urchin’s esophagus, stomach, and intestine when fed a mono-specific diet of either Ulva fasciata or Gracillaria conferta, or an algal-free aquafeed. The study combined 16S rRNA amplicon sequencing, followed by bioinformatics analyses of community structure, interactions, and the prediction of their functional genes.
Sea urchins fed with U. fasciata grew faster, and their gut microbiome network was rich in bacterial associations (edges) and networking clusters. Bacteroidetes was the keystone phylum in the gut, with few microbes being central hub nodes that maintained community connectivity. Communities with distinct features in the esophagus and intestine evidenced spatial distribution. Bacteria that can contribute to Ulva digestion are common in the stomach and intestine and consist of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. The various bacterial genes for the degradation of algal polysaccharides may be valuable for biomass biorefinery processes.