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

Abstract

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.

Bacterial diversity of smoked and smoked‐dried fish from West Africa: A metagenomic approach

“…Bacterial strains present on the surface (or within) fish can also be affected by fish species and geographical location as previously indicated by several authors (Parlapani, 2021;Parlapani et al, 2018;Pimentel et al, 2017;Zotta et al, 2019). Important inter-individual variation in the composition of bacterial communities among fishes of the same species has also been previously reported (Arias et al, 2019;Boutin et al, 2014). The detection of the genus Photobacterium in sea fish with relative abundance higher than in lake fish, and the presence of Salinicoccus, Marinobacter, and Marinobacterium genera exclusively in sea fish is likely due to the fact that these bacteria are halophilic, as previously reported (Chen et al, 2007;Durán-Viseras et al, 2021;Grimaud, 2010).…”

“…Similarly, Arias et al. (2019) have reported Proteobacteria as the most common phylum on skin of Micropterus salmoides , Lepomis macrochirus , and Lepisosteus oculatus , while Parlapani et al. (2018) found Proteobateria and Firmicutes as the most abundant phyla in sea bream flesh.…”

“…Proteobateria has also been reported as the most common phylum associated with the skin and gill of teleost fish (Llewellyn et al, 2014), including the skin microbiome of sea bass and sea bream (Chiarello et al, 2015;Rosado et al, 2018). Similarly, Arias et al (2019) have reported Proteobacteria as the most common phylum on skin of Micropterus salmoides, Lepomis macrochirus, and Lepisosteus oculatus, while Parlapani et al (2018) found Proteobateria and Firmicutes as the most abundant phyla in sea bream flesh. These two bacterial phyla were also noticed as dominant in hongoe, a traditional Korean fermented fish product (Jang et al, 2017;Zhao & Eun, 2020).…”

Effects of Lysophospholipid Supplementation in Feed with Low Protein or Lipid on Growth Performance, Lipid Metabolism, and Intestinal Flora of Largemouth Bass (Micropterus salmoides)

“…The complex microbial ecosystem in the gut exhibits a vital role in the nutrition and health of the host [ 44 , 45 ]. Indeed, the composition of the intestinal flora can be influenced by factors such as feed and environment [ 46 , 47 ]. Iced trash fish and artificial diets could affect the diversity and composition of gut microbes in largemouth bass [ 48 , 49 ].…”

Gut dysbiosis induced by florfenicol increases susceptibility to Aeromonas hydrophila infection in Zebrafish Danio rerio after the recommended withdrawal period

“…The fish gut is colonized by a complex microbial community that is essential in maintaining host homeostasis (Lozupone et al 2012;Clements et al 2014;Ghanbari et al 2015;Tarnecki et al 2017;Ray et al 2019). It provides the host with complementary genetic resources, including genes involved in energy harvesting and the production of essential vitamins, bioelements, and other essential metabolites (Caporaso et al 2011;Faith et al 2013;Shin et al 2015).…”