Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15
Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, G...
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| Format: | Article |
| Language: | English |
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Elsevier
2020
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| Online Access: | http://psasir.upm.edu.my/id/eprint/89117/1/BACT.pdf |
| _version_ | 1796982084904943616 |
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| author | Roslan, Noordiyanah Nadhirah Ngalimat, Mohamad Syazwan Thean, Adam Chor Leow Oslan, Siti Nurbaya Baharum, Syarul Nataqain Sabri, Suriana |
| author_facet | Roslan, Noordiyanah Nadhirah Ngalimat, Mohamad Syazwan Thean, Adam Chor Leow Oslan, Siti Nurbaya Baharum, Syarul Nataqain Sabri, Suriana |
| author_sort | Roslan, Noordiyanah Nadhirah |
| collection | UPM |
| description | Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15. |
| first_indexed | 2024-03-06T10:47:09Z |
| format | Article |
| id | upm.eprints-89117 |
| institution | Universiti Putra Malaysia |
| language | English |
| last_indexed | 2024-03-06T10:47:09Z |
| publishDate | 2020 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | upm.eprints-891172021-09-03T22:28:46Z http://psasir.upm.edu.my/id/eprint/89117/ Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 Roslan, Noordiyanah Nadhirah Ngalimat, Mohamad Syazwan Thean, Adam Chor Leow Oslan, Siti Nurbaya Baharum, Syarul Nataqain Sabri, Suriana Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15. Elsevier 2020 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/89117/1/BACT.pdf Roslan, Noordiyanah Nadhirah and Ngalimat, Mohamad Syazwan and Thean, Adam Chor Leow and Oslan, Siti Nurbaya and Baharum, Syarul Nataqain and Sabri, Suriana (2020) Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15. Microbiological Research, 233. art. no. 126410. pp. 1-8. ISSN 0944-5013; ESSN: 1618-0623 https://www.sciencedirect.com/science/article/pii/S0944501319310894 10.1016/j.micres.2020.126410 |
| spellingShingle | Roslan, Noordiyanah Nadhirah Ngalimat, Mohamad Syazwan Thean, Adam Chor Leow Oslan, Siti Nurbaya Baharum, Syarul Nataqain Sabri, Suriana Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 |
| title | Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 |
| title_full | Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 |
| title_fullStr | Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 |
| title_full_unstemmed | Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 |
| title_short | Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15 |
| title_sort | genomic and phenomic analysis of a marine bacterium photobacterium marinum j15 |
| url | http://psasir.upm.edu.my/id/eprint/89117/1/BACT.pdf |
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