Background: The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein rich mucus that influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) across three time-points to identify links between microbial groups and host metabolism. Our aims include 1) describing the variation of microbiome taxa over time and identify those members which are recurrent (present across all time-points, 2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points, 3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and 4) identifying whether the metabolisms are share across microbial genera or found in specific taxa.
Results: Microbial members of the microbiome showed high similarity between all individuals (average similarity: 82.74) with relative abundance of those members varying across years, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter and Sphingopxis being consistently abundance across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relative abundant genera forming three recurrent groups. The microbiome also displayed high functional similarity between individuals (average similarity: 97.65) with gene function composition being consistent across time-points.
Conclusion: These results show that while presence of microbial genera exhibit consistency across time-points, their abundances do fluctuate. Functions however remain stable across time points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We hypothesize this may be the result of the host’s epidermal attributes structuring the microbiome. In addition, we show the co-existence of many microbial genera that carry genes which may enable the microbes to use the nutrients provided by the elasmobranch’s metabolism.