Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism
The genus <i>Photobacterium</i> is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. <i>Photobacterium</i> sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the ge...
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MDPI AG
2022-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/17/9712 |
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| author | Nyok-Sean Lau Wooi Liang Heng Noorizan Miswan Nor Azura Azami Go Furusawa |
| author_facet | Nyok-Sean Lau Wooi Liang Heng Noorizan Miswan Nor Azura Azami Go Furusawa |
| author_sort | Nyok-Sean Lau |
| collection | DOAJ |
| description | The genus <i>Photobacterium</i> is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. <i>Photobacterium</i> sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 <i>Photobacterium</i> strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with <i>P. galatheae</i>, forming a distinct clade with <i>P. halotolerans</i>, <i>P. salinisoli</i>, and <i>P. arenosum</i>. The core genome of <i>Photobacterium</i> was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against <i>Vibrio</i> spp. Intriguingly, clustering based on BGCs profiles grouped <i>P. galatheae</i>, <i>P. halotolerans</i>, <i>P. salinisoli</i>, <i>P. arenosum</i>, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich <i>Photobacterium</i> strains represent great potential for bioactive secondary metabolites production and sources for novel compounds. |
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| last_indexed | 2024-03-10T01:45:01Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-38a2dba50c5741b696e4dc80b5adbe4f2023-11-23T13:15:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-08-012317971210.3390/ijms23179712Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with AntagonismNyok-Sean Lau0Wooi Liang Heng1Noorizan Miswan2Nor Azura Azami3Go Furusawa4Centre for Chemical Biology, Universiti Sains Malaysia, Penang 11900, MalaysiaCentre for Chemical Biology, Universiti Sains Malaysia, Penang 11900, MalaysiaCentre for Chemical Biology, Universiti Sains Malaysia, Penang 11900, MalaysiaCentre for Chemical Biology, Universiti Sains Malaysia, Penang 11900, MalaysiaCentre for Chemical Biology, Universiti Sains Malaysia, Penang 11900, MalaysiaThe genus <i>Photobacterium</i> is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. <i>Photobacterium</i> sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 <i>Photobacterium</i> strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with <i>P. galatheae</i>, forming a distinct clade with <i>P. halotolerans</i>, <i>P. salinisoli</i>, and <i>P. arenosum</i>. The core genome of <i>Photobacterium</i> was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against <i>Vibrio</i> spp. Intriguingly, clustering based on BGCs profiles grouped <i>P. galatheae</i>, <i>P. halotolerans</i>, <i>P. salinisoli</i>, <i>P. arenosum</i>, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich <i>Photobacterium</i> strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.https://www.mdpi.com/1422-0067/23/17/9712<i>Photobacterium</i>comparative genomicspan-genome analysissecondary metabolitesantagonism |
| spellingShingle | Nyok-Sean Lau Wooi Liang Heng Noorizan Miswan Nor Azura Azami Go Furusawa Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism International Journal of Molecular Sciences <i>Photobacterium</i> comparative genomics pan-genome analysis secondary metabolites antagonism |
| title | Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism |
| title_full | Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism |
| title_fullStr | Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism |
| title_full_unstemmed | Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism |
| title_short | Comparative Genomic Analyses of the Genus <i>Photobacterium</i> Illuminate Biosynthetic Gene Clusters Associated with Antagonism |
| title_sort | comparative genomic analyses of the genus i photobacterium i illuminate biosynthetic gene clusters associated with antagonism |
| topic | <i>Photobacterium</i> comparative genomics pan-genome analysis secondary metabolites antagonism |
| url | https://www.mdpi.com/1422-0067/23/17/9712 |
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