publication . Article . 2017

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Lone Gram;
Open Access
  • Published: 29 Jun 2017 Journal: Frontiers in Microbiology, volume 8 (eissn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media SA
  • Country: Denmark
Abstract
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important when determining the ecophysiology of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurre...
Subjects
free text keywords: Photobacterium, Vibrionaceae, comparative genomics, pan-genome, core-genome, Microbiology, QR1-502, Original Research
Funded by
EC| BACTORY
Project
BACTORY
Biorefinery Training Platform: Bacterial Factories for Sustainable Chemical and Drug Production
  • Funder: European Commission (EC)
  • Project Code: 317058
  • Funding stream: FP7 | SP3 | PEOPLE
104 references, page 1 of 7

Andreoni F. Magnani M. (2014). Photobacteriosis: prevention and diagnosis. J. Immunol. Res. 2014:7. 10.1155/2014/793817 24982922 [OpenAIRE] [PubMed] [DOI]

Ast J. C. Cleenwerck I. Engelbeen K. Urbanczyk H. Thompsom F. L. De Vos P. . (2007). Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes. Int. J. Syst. Evol. Microbiol. 57, 2073–2078. 10.1099/ijs.0.65153-0 17766874 [OpenAIRE] [PubMed] [DOI]

Ast J. C. Dunlap P. V. (2004). Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi. Arch. Microbiol. 181, 352–361. 10.1007/s00203-004-0663-7 15034641 [OpenAIRE] [PubMed] [DOI]

Attar N. (2015). Structural biology: how CRISPR captures spacer invaders. Nat. Rev. Microbiol. 13, 15760. 10.1038/nrmicro3585 26548917 [OpenAIRE] [PubMed] [DOI]

Auch A. F. von Jan M. Klenk H.-P. Göker M. (2010). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2, 117–134. 10.4056/sigs.531120 21304684 [OpenAIRE] [PubMed] [DOI]

Aziz R. K. Bartels D. Best A. A. DeJongh M. Disz T. Edwards R. A. . (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 18261238 [OpenAIRE] [PubMed] [DOI]

Aziz R. K. Breitbart M. Edwards R. A. (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 38, 4207–4217. 10.1093/nar/gkq140 20215432 [OpenAIRE] [PubMed] [DOI]

Bjornsdottir-Butler K. McCarthy S. Dunlap P. V. Benner R. A. (2016). Photobacterium angustum and Photobacterium kishitanii : psychrotrophic high histamine-producing bacteria indigenous to Tuna. Appl. Environ. Microbiol. 82, 2167–2176. 10.1128/aem.02833-15 2682 6233 [OpenAIRE] [PubMed] [DOI]

Blom J. Albaum S. P. Doppmeier D. Pühler A. Vorhölter F.-J. Zakrzewski M. . (2009). EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10:154. 10.1186/1471-2105-10-154 19457249 [OpenAIRE] [PubMed] [DOI]

Campanaro S. Vezzi A. Vitulo N. Lauro F. M. D'Angelo M. Simonato F. . (2005). Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains. BMC Genomics 6:122. 10.1186/1471-2164-6-122 16162277 [OpenAIRE] [PubMed] [DOI]

Cascales E. Christie P. J. (2003). The versatile bacterial type IV secretion systems. Nat. Rev. Microbiol. 1, 137–149. 10.1038/nrmicro753 15035043 [OpenAIRE] [PubMed] [DOI]

Choi E. J. Nam S. J. Paul L. Beatty D. Kauffman C. A. Jensen P. R. . (2015). Previously uncultured marine bacteria linked to novel alkaloid production. Chem. Biol. 22, 1270–1279. 10.1016/j.chembiol.2015.07.014 26299672 [OpenAIRE] [PubMed] [DOI]

Dhillon B. K. Laird M. R. Shay J. A. Winsor G. L. Lo R. Nizam F. . (2015). IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res. 43, W104–W108. 10.1093/nar/gkv401 25916842 [OpenAIRE] [PubMed] [DOI]

Dunlap P. V. (2009). Bioluminescence, microbial, in Encyclopedia of Microbiology, 3rd Edn., ed Schaechter M. (Oxford: Academic Press), 45–61. 10.1016/B978-012373944-5.00066-3 [DOI]

Eloe E. A. Lauro F. M. Vogel R. F. Bartlett D. H. (2008). The deep-sea bacterium Photobacterium profundum SS9 utilizes separate flagellar systems for swimming and swarming under high-pressure conditions. Appl. Environ. Microbiol. 74, 6298–6305. 10.1128/AEM.01316-08 18723648 [OpenAIRE] [PubMed] [DOI]

104 references, page 1 of 7
Abstract
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important when determining the ecophysiology of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurre...
Subjects
free text keywords: Photobacterium, Vibrionaceae, comparative genomics, pan-genome, core-genome, Microbiology, QR1-502, Original Research
Funded by
EC| BACTORY
Project
BACTORY
Biorefinery Training Platform: Bacterial Factories for Sustainable Chemical and Drug Production
  • Funder: European Commission (EC)
  • Project Code: 317058
  • Funding stream: FP7 | SP3 | PEOPLE
104 references, page 1 of 7

Andreoni F. Magnani M. (2014). Photobacteriosis: prevention and diagnosis. J. Immunol. Res. 2014:7. 10.1155/2014/793817 24982922 [OpenAIRE] [PubMed] [DOI]

Ast J. C. Cleenwerck I. Engelbeen K. Urbanczyk H. Thompsom F. L. De Vos P. . (2007). Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes. Int. J. Syst. Evol. Microbiol. 57, 2073–2078. 10.1099/ijs.0.65153-0 17766874 [OpenAIRE] [PubMed] [DOI]

Ast J. C. Dunlap P. V. (2004). Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi. Arch. Microbiol. 181, 352–361. 10.1007/s00203-004-0663-7 15034641 [OpenAIRE] [PubMed] [DOI]

Attar N. (2015). Structural biology: how CRISPR captures spacer invaders. Nat. Rev. Microbiol. 13, 15760. 10.1038/nrmicro3585 26548917 [OpenAIRE] [PubMed] [DOI]

Auch A. F. von Jan M. Klenk H.-P. Göker M. (2010). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2, 117–134. 10.4056/sigs.531120 21304684 [OpenAIRE] [PubMed] [DOI]

Aziz R. K. Bartels D. Best A. A. DeJongh M. Disz T. Edwards R. A. . (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 18261238 [OpenAIRE] [PubMed] [DOI]

Aziz R. K. Breitbart M. Edwards R. A. (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res. 38, 4207–4217. 10.1093/nar/gkq140 20215432 [OpenAIRE] [PubMed] [DOI]

Bjornsdottir-Butler K. McCarthy S. Dunlap P. V. Benner R. A. (2016). Photobacterium angustum and Photobacterium kishitanii : psychrotrophic high histamine-producing bacteria indigenous to Tuna. Appl. Environ. Microbiol. 82, 2167–2176. 10.1128/aem.02833-15 2682 6233 [OpenAIRE] [PubMed] [DOI]

Blom J. Albaum S. P. Doppmeier D. Pühler A. Vorhölter F.-J. Zakrzewski M. . (2009). EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10:154. 10.1186/1471-2105-10-154 19457249 [OpenAIRE] [PubMed] [DOI]

Campanaro S. Vezzi A. Vitulo N. Lauro F. M. D'Angelo M. Simonato F. . (2005). Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains. BMC Genomics 6:122. 10.1186/1471-2164-6-122 16162277 [OpenAIRE] [PubMed] [DOI]

Cascales E. Christie P. J. (2003). The versatile bacterial type IV secretion systems. Nat. Rev. Microbiol. 1, 137–149. 10.1038/nrmicro753 15035043 [OpenAIRE] [PubMed] [DOI]

Choi E. J. Nam S. J. Paul L. Beatty D. Kauffman C. A. Jensen P. R. . (2015). Previously uncultured marine bacteria linked to novel alkaloid production. Chem. Biol. 22, 1270–1279. 10.1016/j.chembiol.2015.07.014 26299672 [OpenAIRE] [PubMed] [DOI]

Dhillon B. K. Laird M. R. Shay J. A. Winsor G. L. Lo R. Nizam F. . (2015). IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res. 43, W104–W108. 10.1093/nar/gkv401 25916842 [OpenAIRE] [PubMed] [DOI]

Dunlap P. V. (2009). Bioluminescence, microbial, in Encyclopedia of Microbiology, 3rd Edn., ed Schaechter M. (Oxford: Academic Press), 45–61. 10.1016/B978-012373944-5.00066-3 [DOI]

Eloe E. A. Lauro F. M. Vogel R. F. Bartlett D. H. (2008). The deep-sea bacterium Photobacterium profundum SS9 utilizes separate flagellar systems for swimming and swarming under high-pressure conditions. Appl. Environ. Microbiol. 74, 6298–6305. 10.1128/AEM.01316-08 18723648 [OpenAIRE] [PubMed] [DOI]

104 references, page 1 of 7
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