Characterization of the gut and skin microbiomes of wild-caught fishes from Lake Guntersville, Alabama

Abstract

In recent years, a paradigm shift has occurred in the area of organismal health. Where Koch and Hill’s fundamental postulates equating to “one microbe—one disease” were once regarded as the rule, research has now shifted to a more holistic view in which whole microbial communities give rise to and participate in complex interactions that can ultimately influence disease processes. The microbial communities that constitute fish microbiomes are now recognized as essential components of host health and defense from invading pathogens. Therefore, a better understanding of the natural bacterial communities of healthy individuals and how they interact with the host and other environmental factors is of critical importance. For this study, I hoped to expand the existing body of research on fish microbiomes to include the skin and gut microbiomes of important freshwater sport fishes. My objectives were to 1) 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, 2) compare intra- and interspecies differences in the composition of each microbiome, and 3) identify potential influences of seasonality on core microbial communities. 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 that in the skin indicating the gut microbiomes are more stable. Diversity of the skin was found to be significantly higher in August than in November and May.