Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential
A novel marine actinomycete, designated strain MCN248T, was isolated from the coastal sediment in Songkhla Province, Thailand. Based on the 16S rRNA gene sequences, the new isolate was closely related to Nonomuraea harbinensis DSM45887T (99.2%) and Nonomuraea ferruginea DSM43553T (98.6%). Phylogenet...
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1226945/full |
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| author | Chananan Ngamcharungchit Chananan Ngamcharungchit Atsuko Matsumoto Atsuko Matsumoto Chanwit Suriyachadkun Watanalai Panbangred Yuki Inahashi Yuki Inahashi Bungonsiri Intra Bungonsiri Intra |
| author_facet | Chananan Ngamcharungchit Chananan Ngamcharungchit Atsuko Matsumoto Atsuko Matsumoto Chanwit Suriyachadkun Watanalai Panbangred Yuki Inahashi Yuki Inahashi Bungonsiri Intra Bungonsiri Intra |
| author_sort | Chananan Ngamcharungchit |
| collection | DOAJ |
| description | A novel marine actinomycete, designated strain MCN248T, was isolated from the coastal sediment in Songkhla Province, Thailand. Based on the 16S rRNA gene sequences, the new isolate was closely related to Nonomuraea harbinensis DSM45887T (99.2%) and Nonomuraea ferruginea DSM43553T (98.6%). Phylogenetic analyzes based on the 16S rRNA gene sequences showed that strain MCN248T was clustered with Nonomuraea harbinensis DSM45887T and Nonomuraea ferruginea DSM43553T. However, the digital DNA–DNA hybridization analyzes presented a low relatedness of 40.2% between strain MCN248T and the above closely related strains. This strain contained meso-diaminopimelic acid. The acyl type of the peptidoglycan was acetyl, and mycolic acids were absent. The major menaquinones were MK-9(H2) and MK-9(H4). The whole cell sugars consisted of madurose, ribose, mannose, and glucose. Diphosphatidylglycerol, hydroxyl-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol, and phosphatidylglycerol were detected as the major phospholipids. The predominant cellular fatty acids were iso-C16:0 (40.4%), 10-methyl-C17:0 (22.1%), and C17:1ω8c (10.9%). The DNA G + C content of the genomic DNA was 71.7%. With in silico analyzes, the antiSMASH platform uncovered a diverse 29 secondary metabolite biosynthesis arsenal, including non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) of strain MCN248T, with a high prevalence of gene cluster encoding pathways for the production of anticancer and cytotoxic compounds. Consistently, the crude extract could inhibit colorectal HCT-116 cancer cells at a final concentration of 50 μg/mL. Based on the polyphasic approach, strain MCN248 was designated as a novel species of the genus Nonomuraea, for which the name Nonomuraea corallina sp. nov. is proposed. The type strain of the type species is MCN248T (=NBRC115966T = TBRC17110T). |
| first_indexed | 2024-03-10T18:46:28Z |
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| id | doaj.art-688ab2220cbb42edaab6e915fd49e170 |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-10T18:46:28Z |
| publishDate | 2023-11-01 |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-688ab2220cbb42edaab6e915fd49e1702023-11-20T05:30:24ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-11-011410.3389/fmicb.2023.12269451226945Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potentialChananan Ngamcharungchit0Chananan Ngamcharungchit1Atsuko Matsumoto2Atsuko Matsumoto3Chanwit Suriyachadkun4Watanalai Panbangred5Yuki Inahashi6Yuki Inahashi7Bungonsiri Intra8Bungonsiri Intra9Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, ThailandMahidol University and Osaka Collaborative Research Center on Bioscience and Biotechnology, Bangkok, ThailandGraduate School of Infection Control Sciences, Kitasato University, Tokyo, JapanKitasato Institute for Life Sciences (O̅mura Satoshi Memorial Institute), Kitasato University, Tokyo, JapanThailand Bioresource Research Center (TBRC), National Science and Technology Development Agency, Pathumthani, ThailandResearch, Innovation and Partnerships Office – RIPO (Office of the President), King Mongkut’s University of Technology Thonburi, Bangkok, ThailandGraduate School of Infection Control Sciences, Kitasato University, Tokyo, JapanKitasato Institute for Life Sciences (O̅mura Satoshi Memorial Institute), Kitasato University, Tokyo, JapanDepartment of Biotechnology, Faculty of Science, Mahidol University, Bangkok, ThailandMahidol University and Osaka Collaborative Research Center on Bioscience and Biotechnology, Bangkok, ThailandA novel marine actinomycete, designated strain MCN248T, was isolated from the coastal sediment in Songkhla Province, Thailand. Based on the 16S rRNA gene sequences, the new isolate was closely related to Nonomuraea harbinensis DSM45887T (99.2%) and Nonomuraea ferruginea DSM43553T (98.6%). Phylogenetic analyzes based on the 16S rRNA gene sequences showed that strain MCN248T was clustered with Nonomuraea harbinensis DSM45887T and Nonomuraea ferruginea DSM43553T. However, the digital DNA–DNA hybridization analyzes presented a low relatedness of 40.2% between strain MCN248T and the above closely related strains. This strain contained meso-diaminopimelic acid. The acyl type of the peptidoglycan was acetyl, and mycolic acids were absent. The major menaquinones were MK-9(H2) and MK-9(H4). The whole cell sugars consisted of madurose, ribose, mannose, and glucose. Diphosphatidylglycerol, hydroxyl-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol, and phosphatidylglycerol were detected as the major phospholipids. The predominant cellular fatty acids were iso-C16:0 (40.4%), 10-methyl-C17:0 (22.1%), and C17:1ω8c (10.9%). The DNA G + C content of the genomic DNA was 71.7%. With in silico analyzes, the antiSMASH platform uncovered a diverse 29 secondary metabolite biosynthesis arsenal, including non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) of strain MCN248T, with a high prevalence of gene cluster encoding pathways for the production of anticancer and cytotoxic compounds. Consistently, the crude extract could inhibit colorectal HCT-116 cancer cells at a final concentration of 50 μg/mL. Based on the polyphasic approach, strain MCN248 was designated as a novel species of the genus Nonomuraea, for which the name Nonomuraea corallina sp. nov. is proposed. The type strain of the type species is MCN248T (=NBRC115966T = TBRC17110T).https://www.frontiersin.org/articles/10.3389/fmicb.2023.1226945/fullactinomycetesnovel marine taxaphylogenetic analysisNonomuraeaanti-colorectal cancer |
| spellingShingle | Chananan Ngamcharungchit Chananan Ngamcharungchit Atsuko Matsumoto Atsuko Matsumoto Chanwit Suriyachadkun Watanalai Panbangred Yuki Inahashi Yuki Inahashi Bungonsiri Intra Bungonsiri Intra Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential Frontiers in Microbiology actinomycetes novel marine taxa phylogenetic analysis Nonomuraea anti-colorectal cancer |
| title | Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential |
| title_full | Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential |
| title_fullStr | Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential |
| title_full_unstemmed | Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential |
| title_short | Nonomuraea corallina sp. nov., isolated from coastal sediment in Samila Beach, Thailand: insights into secondary metabolite synthesis as anticancer potential |
| title_sort | nonomuraea corallina sp nov isolated from coastal sediment in samila beach thailand insights into secondary metabolite synthesis as anticancer potential |
| topic | actinomycetes novel marine taxa phylogenetic analysis Nonomuraea anti-colorectal cancer |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1226945/full |
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