A report of 42 unrecorded bacterial species isolated from fish intestines and clams in freshwater environments
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Nine fish and one clam species were collected from freshwater environments in Korea, including four lakes, two streams, and the Nakdong River, to investigate the host-associated bacteria. Hundreds of bacterial strains were isolated from the samples using a cell sorter and a dilution plating method. After identification of the bacterial strains using 16S rRNA gene sequences, 42 strains with greater than 98.7% sequence similarity with validly published species were determined to be unrecorded bacterial species in Korea. These strains were phylogenetically diverse and assigned to four phyla, six classes, 17 orders, 27 families, and 32 genera. At the genus level, the unrecorded species were classified as Corynebacterium, Mycobacterium, Mycolicibacterium, Gordonia, Williamsia, Modestobacter, Brachybacterium, Sanquibacter, Arthrobacter, and Mycolicibacterium of the class Actinobacteria; Empedobacter, and Flavobacterium of the class Flavobacteriia; Fictibacillus, Psychrobacillus, Cohnella, Paenibacillus, Rummeliibacillus, Enterococcus, and Vagococcus of the class Bacilli; Aquamicrobium, Paracoccus, and Sphingomonas of the class Alphaproteobacteria; Achromobacter, Delftia, and Deefgea of the class Betaproteobacteria; and Aeromonas, Providencia, Yersinia, Marinomonas, Acinetobacter, and Pseudomonas of the class Gammaproteobacteria. The 42 unrecorded species were subjected to further taxonomic characterization using gram staining, cellular and colony morphological determination, biochemical analyses, and phylogenetic analyses. This paper provides detailed descriptions of the 42 previously unrecorded bacterial species.
Abstract
Nine fish and one clam species were collected from freshwater environments in Korea, including four lakes, two streams, and the Nakdong River, to investigate the host-associated bacteria. Hundreds of bacterial strains were isolated from the samples using a cell sorter and a dilution plating method. After identification of the bacterial strains using 16S rRNA gene sequences, 42 strains with greater than 98.7% sequence similarity with validly published species were determined to be unrecorded bacterial species in Korea. These strains were phylogenetically diverse and assigned to four phyla, six classes, 17 orders, 27 families, and 32 genera. At the genus level, the unrecorded species were classified as Corynebacterium, Mycobacterium, Mycolicibacterium, Gordonia, Williamsia, Modestobacter, Brachybacterium, Sanquibacter, Arthrobacter, and Mycolicibacterium of the class Actinobacteria; Empedobacter, and Flavobacterium of the class Flavobacteriia; Fictibacillus, Psychrobacillus, Cohnella, Paenibacillus, Rummeliibacillus, Enterococcus, and Vagococcus of the class Bacilli; Aquamicrobium, Paracoccus, and Sphingomonas of the class Alphaproteobacteria; Achromobacter, Delftia, and Deefgea of the class Betaproteobacteria; and Aeromonas, Providencia, Yersinia, Marinomonas, Acinetobacter, and Pseudomonas of the class Gammaproteobacteria. The 42 unrecorded species were subjected to further taxonomic characterization using gram staining, cellular and colony morphological determination, biochemical analyses, and phylogenetic analyses. This paper provides detailed descriptions of the 42 previously unrecorded bacterial species.
참고문헌 (15)
- Banerjee G, "Bacterial symbiosis in the fish gut and its role in health and metabolism", Symbiosis, 72, pp.1~11 (2017)
- Felsenstein J, "Evolutionary trees from DNA sequences : a maximum likelihood approach", J. Mol. Evol, 17, pp.368~376 (1981)
- Felsenstein J, "Confidence limits on phylogenies : An approach using the bootstrap", Evolution, 39, pp.783~791 (1985)
- Fierer N, "The diversity and biogeography of soil bacterial communities", Proc. Natl. Acad. Sci. USA, 103, pp.626~631 (2006)
- Fitch WM, "Toward defining the course of evolution : minimum change for a specific tree topology", Syst. Zool, 20, pp.406~416 (1971)
- Jeon YS, "EzEditor : a versatile sequence alignment editor for both rRNA-and protein-coding genes", Int. J. Syst. Evol. Microbiol, 64, pp.689~691 (2014)
- Jukes TH, "Mammalian Protein Metabolism Vol. 3", pp.21~213 (1969), Academic Press
- Kumar S, "MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets", Mol. Biol. Evol., 33, pp.1870~1874 (2016)
- Liu H, "The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels", Sci. Rep, 6, pp.24340~ (2016)
- Llewellyn MS, "Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries", Front. Microbiol., 5, pp.207~ (2014)
- Ringø E, "Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story?", Aquac. Nutr., 22, pp.219~282 (2015)
- Saitou N, "The neighbor-joining method: a new method for reconstructing phylogenetic trees", Mol. Biol. Evol., 4, pp.406~425 (1987)
- Sullam KE, "Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis", Mol. Ecol., 21, pp.3363~3378 (2012)
- Wong S, "Intestinal microbiota composition in fishes is influenced by host ecology and environment", Mol. Ecol., 21, pp.3100~3102 (2012)
- Yoon SH, "Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies", Int. J. Syst. Evol. Microbiol., 67, pp.1613~1617 (2017)