Most probiotics used in aquaculture are borrowed from terrestrial livestock systems and therefore may not be the most effective strains. We evaluate and explore a broad range of vertebrates contrasting differences in the microbiomes of fish with mammals. The host-associated gut microbiome in vertebrates is shaped by a variety of biological factors including phylogeny, diet, age along with environmental factors such as geography, habitat, and climate. Here we perform a meta-analysis, comparing the hindgut microbiomes of 569 unique species of vertebrates. We then compare factors which drive the mucosal microbiomes (gill, skin, midgut, and hindgut) across 115 species of wild marine fish. Gamma diversity metrics show that while mammals have the highest diversity amongst vertebrate classes when comparing hindgut, the lion’s share of microbial diversity in fish exists in other body sites including the midgut, gill, and skin and that when included collectively have much higher microbial diversity than other vertebrate classes (Figure 1a-d). To quantify impacts of host phylogeny, trophic level, habitat type, swim performance, and body site we compare the gill, skin, midgut, and hindgut microbiomes from 25% of the total marine fish diversity from Southern California including 101 species.
Total microbial diversity across vertebrate hindguts and within multiple body sites of fish. a) Hindgut microbiome samples from 569 species of vertebrates were rarified to 5000 reads and unique or shared ASVs (amplified sequence variants) determined for each class. b) The percent of unique ASVs only found in a given class as compared. c) Rarefaction of cumulative gamma diversity as a function of unique vertebrate species. Included is a single fish species, Scomber japonicus, sampled over three years ‘black dots’ and the unrarified FMP samples which had detectable bacteria in all four body sites (gill, skin, midgut, and hindgut). d) Gamma diversity of 68 fish species across four body sites. e) Percentage of unique ASVs associated with a given body site across the 68 fish species. f) Rarefaction curve of increasing gamma diversity (inclusive of four body sites) as a function of increasing fish species.
Distribution of putative probiotic ASVs grouped by genera: Bacillus or Lactobacillus. a) The total percentage of samples within a given body site having either a Bacillus ASV or Lactobacillus ASV. b) The relative abundances of Bacillus and Lactobacillus ASVs within each body site (including samples with 0 counts).