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Deng A, Fu L, Mo P, Zheng Y, Tang T, Gao J. New insights into the relationship between the average nucleotide identity and the digital DNA-DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis. Front Microbiol 2024; 15:1359021. [PMID: 38686110 PMCID: PMC11056570 DOI: 10.3389/fmicb.2024.1359021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
At present, it is widely believed that a 95-96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA-DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95-96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis.
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Affiliation(s)
- Aihua Deng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Li Fu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Ping Mo
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Yaxi Zheng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Ting Tang
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, China
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Weeraphan T, Supong K, Sripreechasak P, Jutakanoke R, Kowinthanaphat S, Tanasupawat S, Pittayakhajonwut P, Phongsopitanun W. Streptomyces rugosispiralis sp. nov., a Novel Actinobacterium Isolated from Peat Swamp Forest Soil That Produces Ansamycin Derivatives and Nocardamines. Antibiotics (Basel) 2023; 12:1467. [PMID: 37760763 PMCID: PMC10525797 DOI: 10.3390/antibiotics12091467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/05/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Actinomycetes, especially the genus Streptomyces, are one of the most promising sources of bioactive natural products. In this study, a novel Streptomyces strain, RCU-064T, was isolated from a soil sample collected from a peat swamp forest in Thailand. Strain RCU-064T showed the highest 16S rRNA gene sequence similarity (99.06%) with Streptomyces malaysiensis NBRC 16446T. Based on a polyphasic approach, strain RCU-064T represents a novel species of the genus Streptomyces, for which the name Streptomyces rugosispiralis sp. nov. is proposed. The chemical isolation of the crude ethyl acetate extracts of the strain led to the isolation of six compounds: (1) geldanamycin, (2) 17-O-demethylgeldanamycin, (3) reblastatin, (4) 17-demethoxyreblastatin, (5) nocardamine, and (6) dehydroxynocardamine. These compounds were evaluated for their biological activities. All compounds showed no antimicrobial activity against tested microorganisms used in this study. Compounds (1)-(4) displayed cytotoxic activity against the NCI-H187 cell line, with IC50 values ranging from 0.045-4.250 µg/mL. Cytotoxicity against the MCF-7 cell line was found in compounds (1) and (3) with IC50 values of 3.51 and 1.27 µg/mL, respectively. Compounds (5) and (6) exhibited cytotoxicity only against Vero cells (IC50 of 16.57 µg/mL) and NCI-H187 cells (IC50 of 13.96 µg/mL), respectively. These results indicate that peat swamp forest soil remains a promising reservoir of novel actinomycetes capable of producing bioactive natural products.
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Affiliation(s)
- Trinset Weeraphan
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (T.W.); (S.K.); (S.T.)
| | - Khomsan Supong
- Department of Applied Science and Biotechnology, Faculty of Agro-Industrial Technology, Rajamangala University of Technology Tawan-ok, Chantaburi 22210, Thailand
| | - Paranee Sripreechasak
- Office of Educational Affairs, Faculty of Science, Burapha University, Chonburi 20131, Thailand;
| | - Rumpa Jutakanoke
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand;
| | - Supalerk Kowinthanaphat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (T.W.); (S.K.); (S.T.)
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (T.W.); (S.K.); (S.T.)
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani 12120, Thailand;
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (T.W.); (S.K.); (S.T.)
- Natural Products and Nanoparticles Research Units (NP2), Chulalongkorn University, Bangkok 10330, Thailand
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Kanchanasin P, Sripreechasak P, Suriyachadkun C, Supong K, Pittayakhajonwut P, Somphong A, Tanasupawat S, Phongsopitanun W. Streptomyces macrolidinus sp. nov., a novel soil actinobacterium with potential anticancer and antimalarial activity. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748587 DOI: 10.1099/ijsem.0.005682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A novel actinomycete, strain RY43-2T, belonging to the genus Streptomyces, was isolated from a peat swamp forest soil collected from Rayong Province, Thailand. The strain was characterized by using a polyphasic approach. The cell-wall peptidoglycan contained ll-diaminopimelic. Ribose and glucose were detected in its whole-cell hydrolysates. The strain contained anteiso-C15:0, iso-C14:0 and iso-C16:0 as the predominant fatty acids, and MK-9(H4), MK-9(H6) and MK-9(H8) as the major menaquinones. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified ninhydrin-positive phospholipids and two unidentified phospholipids. Strain RY43-2T showed the highest 16S rRNA gene similarity to Streptomyces misionensis JCM 4497T (98.9 %) and Streptomyces lichenis LCR6-01T (98.9 %). The draft genome of RY43-2T was 6.7 Mb with 6078 coding sequences with an average G+C content of 70.8 mol%. Genomic analysis revealed that the average nucleotide identity (ANI) values based on blast (ANIb) and MUMmer (ANIm) between strain RY43-2T and S. misionensis JCM 4497T were 80.1 and 86.1%, respectively. The ANIb and ANIm values between strain RY43-2T and S. lichenis LCR6-01T were 77.0 and 85.5%, respectively. The digital DNA-DNA hybridization values were 25.2 and 23.0% in comparison with the draft genomes of S. misionensis JCM 4497T and S. lichenis LCR6-01T, respectively. The results of taxonomic analysis suggested that strain RY43-2T represented a novel species of the genus Streptomyces for which the name Streptomyces macrolidinus sp. nov. is proposed. The type strain is RY43-2T (=TBRC 7286T=NBRC 115640T). Strain RY43-2T exhibited antimicrobial activity against Enterococcus faecium ATCC 51559, Colletotrichum capsici BMGC 106 and Colletotrichum gloeosporioides BMGC 107 with the minimum inhibitory concentration values of 25.0, 12.5, and 6.25 µg ml-1. It also exhibited potent antimalarial activity against Plasmodium falciparum K1 with IC50 of 0.0031 µg ml-1. In addition, it showed cytotoxicity against Vero, KB, MCF-7 and NCI-H187 with IC50 values of 0.0347, 6.15, 3.36 and 0.0352 µg ml-1, respectively.
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Affiliation(s)
- Pawina Kanchanasin
- Department of Microbiology, Faculty of Science, Burapha University, Chonburi 20131, Thailand
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Paranee Sripreechasak
- Department of Biotechnology, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathumthani 12120, Thailand
| | - Khomsan Supong
- Department of Applied Science and Biotechnology, Faculty of Agro-Industrial Technology, Rajamangala University of Technology Twan-ok Chanthaburi campus, Chantaburi 22210, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Achiraya Somphong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
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Teo WFA, Lipun K, Srisuk N, Duangmal K. Amycolatopsis acididurans sp. nov., isolated from peat swamp forest soil in Thailand. J Antibiot (Tokyo) 2020; 74:199-205. [PMID: 33128034 DOI: 10.1038/s41429-020-00382-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 12/22/2022]
Abstract
A polyphasic approach was used to describe strain K13G38T, a novel actinomycete isolated from peat swamp forest soil collected from Surat Thani Province, Thailand. The 16S rRNA gene phylogenetic analysis indicated that the strain belonged to the genus Amycolatopsis and showed the highest sequence similarities to both Amycolatopsis acidiphila JCM 30562T and Amycolatopsis bartoniae DSM 45807T (96.8% sequence similarity). Furthermore, strain K13G38T, which formed extensively branched substrate and aerial mycelia, exhibited chemotaxonomical characteristics of the genus Amycolatopsis which included phospholipid pattern type II and cell-wall chemotype IV. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, two unidentified phospholipids, and an unidentified aminolipid. MK-9(H4) was a predominant menaquinone of the organism. The major cellular fatty acids were iso-C16:0, anteiso-C17:0, and C16:0. The genomic DNA size of strain K13G38T was 8.5 Mbp with 69.5 mol% G+C content. On the basis of phenotypic characteristics, overall genomic relatedness index and phylogenetic distinctiveness, strain K13G38T represents a novel species of the genus Amycolatopsis, for which the name A. acididurans sp. nov. is proposed. The type strain is K13G38T (=TBRC 12507T = NBRC 114553T).
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Affiliation(s)
- Wee Fei Aaron Teo
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kenika Lipun
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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