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MEPS
Marine Ecology Progress Series

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MEPS 518:209-223 (2015)  -  DOI: https://doi.org/10.3354/meps11034

Comparison of the gut microbiomes of 12 bony fish and 3 shark species

Carrie E. Givens1,2, Briana Ransom1,3, Nasreen Bano1,4, James T. Hollibaugh1,*

1Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
2Present address: US Geological Survey Michigan Water Science Center, 6520 Mercantile Way, Lansing, MI 48911, USA
3Present address: Oglethorpe County High School, 749 Athens Rd, Lexington, GA 30648, USA
4Present address: USDA ARS, 950 College Station Rd, Athens, GA 30605, USA
*Corresponding author:

ABSTRACT: We used massively parallel sequencing (pyrosequencing) of 16S rRNA genes to compare the composition of microbial communities in the guts of 12 bony fish and 3 shark species. The species analyzed encompass herbivores and carnivores with varied digestive physiologies, are classified as pelagic and demersal species, and reside in estuarine to marine environments. We also compared the gut microbial assemblages of wild and cultured Fundulus heteroclitus and of juvenile and adult Lagodon rhomboides. A total of 1214355 sequences were filtered, denoised, trimmed, and then sorted into operational taxonomic units (OTUs) based on 97% sequence similarity. Bacteria representing 17 phyla were found among the sampled fish, with most fish hosting between 7 and 15 phyla. Proteobacteria OTUs were present in all fish and often dominated the libraries (3.0 to 98%; average: 61%). Firmicutes were also prevalent, but at a lower relative abundance, ranging between 1.3 and 45% (average: 17%). In most cases, the gut microflora of individual fish of a given species contained many of the same OTUs; however, some species (e.g. great barracuda) shared few OTUs among the individuals sampled. Although no single OTU was shared among all fish species, many of the OTUs present in one species’ core group were also found in the core groups of other species. Several OTUs were consistently found in the guts of multiple species, suggesting that these OTUs may be important contributors to fish gut functions such as digestion, nutrient absorption, and immune response.


KEY WORDS: Fish gut · Gut microbiome · 16S rRNA · Gut microflora · 454-pyrosequencing · Shark gut · Core gut microbiome


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Cite this article as: Givens CE, Ransom B, Bano N, Hollibaugh JT (2015) Comparison of the gut microbiomes of 12 bony fish and 3 shark species. Mar Ecol Prog Ser 518:209-223. https://doi.org/10.3354/meps11034

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