Fish are not alone: characterization of the gut and skin microbiomes of Largemouth Bass (Micropterus salmoides), Bluegill (Lepomis macrochirus), and Spotted Gar (Lepisosteus oculatus)

The objective of this study was to characterize the gut and skin microbiomes of three common freshwater fishes including two important sport fishes, Largemouth Bass Micropterus salmoides and Bluegill Lepomis macrochirus as well as the distantly-related Spotted Gar Lepisosteus oculatus. Skin and gut samples were collected in August and November 2014, and May 2015. All samples were sequenced as paired-end reads of the 16S rRNA gene via the Illumina MiSeq platform. More than 5M reads were analyzed representing 4,130 and 2,744 OTUs from gut and skin samples, respectively. Approximately 51.84% of the total OTUs were shared between the skin and gut bacterial communities. Good’s coverage was higher than 98% in all samples. Spotted Gar exhibited the most diverse skin microbiome, while Largemouth Bass was the least diverse species in terms of both the skin and gut microbiome compositions. The highest diversity in the gut microbiome was observed in Bluegill; however, the bacterial communities of Spotted Gar were the most variable across seasons. Seasonal changes in bacterial community structures were also observed. For both the skin and the gut microbiomes, sampling date was found to exert a stronger influence on microbial composition than the species itself; however, season had a lesser impact on the gut microbiome than in the skin indicating the gut microbiomes are more stable. This study provides baseline data on the bacterial symbiont communities of three iconic freshwater fish species in North America. Our data could be used in future studies to identify environmental stressors that result unbalanced microbiomes and loss of homeostasis.