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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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Oyuntsetseg B, Lee HB, Kim SB. Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia. Int J Syst Evol Microbiol 2024; 74. [PMID: 38359091 DOI: 10.1099/ijsem.0.006266] [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: 02/17/2024] Open
Abstract
A novel filamentous actinobacterium designated strain 4-36T showing broad-spectrum antifungal activity was isolated from a coal mining site in Mongolia, and its taxonomic position was determined using polyphasic approach. Optimum growth occurred at 30 °C, pH 7.5 and in the absence of NaCl. Aerial and substrate mycelia were abundantly formed on agar media. The colour of aerial mycelium was white and diffusible pigments were not formed. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain 4-36T formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity showed that the strain was mostly related to Amycolatopsis lexingtonensis DSM 44544T and Amycolatopsis rifamycinica DSM 46095T with 99.3 % sequence similarity. However, the highest digital DNA-DNA hybridization value to closest species was 44.1 %, and the highest average nucleotide identity value was 90.2 %, both of which were well below the species delineation thresholds. Chemotaxonomic properties were typical of the genus Amycolatopsis, as the major fatty acids were C15 : 0, iso-C16 : 0 and C16 : 0, the cell-wall diamino acid was meso-diaminopimelic acid, the quinone was MK-9(H4), and the main polar lipids were diphosphatidylglycerol, phosphatidylmethanolamine and phosphatidylethanolamine. The in silico prediction of chemotaxonomic markers was also carried out by phylogenetic analysis. The genome mining for biosynthetic gene clusters of secondary metabolites in strain 4-36T revealed the presence of 34 gene clusters involved in the production of polyketide synthase, nonribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, lanthipeptide, terpenes, siderophore and many other unknown clusters. Strain 4-36T showed broad antifungal activity against several filamentous fungi. The phenotypic, biochemical and chemotaxonomic properties indicated that the strain could be clearly distinguished from other species of Amycolatopsis, and thus the name Amycolatopsis mongoliensis sp. nov. is proposed accordingly (type strain, 4-36T=KCTC 39526T=JCM 30565T).
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Affiliation(s)
- Bilguun Oyuntsetseg
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyang Burm Lee
- Department of Agricultural Biological Chemistry, College of Agriculture & Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
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3
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Efimenko TA, Yakushev AV, Karabanova AA, Glukhova AA, Demiankova MV, Vasilieva BF, Boykova YV, Malkina ND, Terekhova LP, Efremenkova OV. Antimicrobial Activity of Bacteria Isolated from the Millipedes Nedyopus dawydoffiae and Orthomorpha sp. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722700023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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4
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Wang HF, Li XY, Gao R, Xie YG, Xiao M, Li QL, Li WJ. Amycolatopsis anabasis sp. nov., a novel endophytic actinobacterium isolated from roots of Anabasis elatior. Int J Syst Evol Microbiol 2020; 70:3391-3398. [DOI: 10.1099/ijsem.0.004184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15–40 °C, pH 6.0–8.0 and in the presence of 0–6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus
Amycolatopsis
and shared the highest sequence similarities with
Amycolatopsis nigrescens
JCM 14717T (97.1 %) and
Amycolatopsis sacchari
DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus
Amycolatopsis
were less than 97.0 %. The average nucleotide identity and DNA–DNA hybridization values between strain EGI 650086T and the reference strains were 78.1–79.8 % and 22.1–23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus
Amycolatopsis
, for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).
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Affiliation(s)
- Hong-Fei Wang
- School of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Xin-Yang Li
- School of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong 118000, PR China
| | - Yuan-Guo Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qiu-Li Li
- School of Life Science, Liaoning Normal University, Dalian 116029, PR China
| | - Wen-Jun Li
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, 830011, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, PR China
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5
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Chaiya L, Matsumoto A, Wink J, Inahashi Y, Risdian C, Pathom-Aree W, Lumyong S. Amycolatopsis eburnea sp. nov., an actinomycete associated with arbuscular mycorrhizal fungal spores. Int J Syst Evol Microbiol 2019; 69:3603-3608. [PMID: 31433288 DOI: 10.1099/ijsem.0.003669] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, designated strain GLM-1T, was isolated from arbuscular mycorrhizal fungal spores from Funneliformis mosseae RYA08, collected from Aquilaria crassna Pierre ex Lec. rhizosphere soil in Klaeng, Rayong Province, Thailand. Morphological characteristics of this strain included long chains of rod-like cells and squarish elements. The cell-wall composition of this novel isolate contained meso-diaminopimelic acid. The whole-cell diagnostic sugars were arabinose and galactose. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and iso-C15 : 0. Only phosphatidylethanolamine was detected as a polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GLM-1T was closely related to Amycolatopsis rhabdoformis SB026T (99.11 %) with a low DNA-DNA hybridization value of 22.6-34.7 %. Genome sequencing revealed a genome size of 10 Mbp. There were obvious distinctions in the average nucleotide identity values between stain GLM-1T and its closely related strains at around 86-93 % (ANIb) and 89-94 % (ANIm). The digital DNA-DNA hybridization values between strain GLM-1T and type strains of phylogenetically related species were 34-55 %. The G+C content of the genomic DNA was 71.8 mol%. Based on these data, strain GLM-1T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsiseburnea sp. nov. is proposed. The type strain is GLM-1T (=TBRC 9315T=NBRC 113658T).
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Affiliation(s)
- Leardwiriyakool Chaiya
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Atsuko Matsumoto
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.,Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.,Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Chandra Risdian
- Research Unit for Clean Technology, Indonesian Institute of Sciences (LIPI), Bandung 40135, Indonesia.,Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Wasu Pathom-Aree
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Science and Technology Research Institute, Chiang Mai University, Chiang Mai 50200, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- The Royal Society of Thailand, Academy of Science, Bangkok 10300, Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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7
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Bauermeister A, Calil FA, das C L Pinto F, Medeiros TCT, Almeida LC, Silva LJ, de Melo IS, Zucchi TD, Costa-Lotufo LV, Moraes LAB. Pradimicin-IRD from Amycolatopsis sp. IRD-009 and its antimicrobial and cytotoxic activities. Nat Prod Res 2018; 33:1713-1720. [PMID: 29451013 DOI: 10.1080/14786419.2018.1434639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new polycyclic antibiotic, pradimicin-IRD, was isolated from actinobacteria Amycolatopsis sp. IRD-009 recovered from soil of Brazilian rainforest undergoing restoration area. This molecule is the major compound produced in solid culture media. The new compound was detected by a focused method of precursor ion (high-performance liquid chromatography coupled to tandem mass spectrometer) developed previously to identify unusual aminoglycosyl sugar moieties. The compound was isolated and its structure was, therefore, elucidated by high-resolution mass spectrometry, and 1D and 2D nuclear magnetic resonance experiments. Pradimicin-IRD displayed potential antimicrobial activity against Streptococcus agalactiae (MIC 3.1 μg/mL), Pseudomonas aeruginosa (MIC 3.1 μg/mL) and Staphylococcus aureus (MIC 3.1 μg/mL), and also cytotoxicity against tumour and non-tumour cell lines with IC50 values ranging from 0.8 μM in HCT-116 colon carcinoma cells to 2.7 μM in MM 200 melanoma cells. Particularly, these biological properties are described for the first time for this chemical class.
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Affiliation(s)
- Anelize Bauermeister
- a Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Felipe A Calil
- a Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Francisco das C L Pinto
- b Departamento de Química Orgânica e Inorgânica , Universidade Federal do Ceará , Fortaleza , Brazil
| | - Talita C T Medeiros
- a Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Larissa C Almeida
- c Departamento de Farmacologia , Instituto de Ciências Biomédicas, Universidade de São Paulo , São Paulo , Brazil
| | - Leonardo J Silva
- d College of Agriculture "Luiz de Queiroz" , Universidade de São Paulo , Piracicaba , Brazil
| | - Itamar S de Melo
- e Laboratory of Environmental Microbiology , National Brazilian Research Corporation - EMBRAPA ENVIRONMENT , Jaguariuna , Brazil
| | - Tiago D Zucchi
- f Departamento de Pesquisa & Desenvolvimento , AGRIVALLE , Salto , Brazil
| | - Letícia V Costa-Lotufo
- c Departamento de Farmacologia , Instituto de Ciências Biomédicas, Universidade de São Paulo , São Paulo , Brazil
| | - Luiz A B Moraes
- a Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , Brazil
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8
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Ceresino EB, de Melo RR, Kuktaite R, Hedenqvist MS, Zucchi TD, Johansson E, Sato HH. Transglutaminase from newly isolated Streptomyces sp. CBMAI 1617: Production optimization, characterization and evaluation in wheat protein and dough systems. Food Chem 2017; 241:403-410. [PMID: 28958547 DOI: 10.1016/j.foodchem.2017.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/25/2017] [Accepted: 09/04/2017] [Indexed: 11/30/2022]
Abstract
The popularity of transglutaminase (TG) by the food industry and the variation in functionality of this enzyme from different origins, prompted us to isolate and evaluate a high-yielding TG strain. Through the statistical approaches, Plackett-Burman and response surface methodology, a low cost fermentation media was obtained to produce 6.074±0.019UmL-1 of TG from a novel source; Streptomyces sp. CBMAI 1617 (SB6). Its potential exploitation was compared to commonly used TG, from Streptomyces mobaraensis. Biochemical and FT-IR studies indicated differences between SB6 and commercial TG (Biobond™ TG-M). Additions of TG to wheat protein and flour based doughs revealed that the dough stretching depended on the wheat protein fraction, TG amount and its origin. A higher degree of cross-linking of glutenins and of inclusion of gliadin in the polymers was seen for SB6 as compared to commercial TG. Thus, our results support the potential of SB6 to tailor wheat protein properties within various food applications.
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Affiliation(s)
- Elaine B Ceresino
- Department of Food Science, School of Food Engineering, University of Campinas, Box 6121, 13083-862 Sao Paulo, SP, Brazil.
| | - Ricardo R de Melo
- Department of Food Science, School of Food Engineering, University of Campinas, Box 6121, 13083-862 Sao Paulo, SP, Brazil.
| | - Ramune Kuktaite
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Box 104, SE-23053 Alnarp, Sweden.
| | - Mikael S Hedenqvist
- KTH Royal Institute of Technology, School of Chemical and Engineering, Fibre and Polymer Technology, SE-10044 Stockholm, Sweden.
| | - Tiago D Zucchi
- Department of Research & Development, Agrivalle, 13329-600 Salto, SP, Brazil.
| | - Eva Johansson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Box 104, SE-23053 Alnarp, Sweden.
| | - Helia H Sato
- Department of Food Science, School of Food Engineering, University of Campinas, Box 6121, 13083-862 Sao Paulo, SP, Brazil.
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Oyuntsetseg B, Cho SH, Jeon SJ, Lee HB, Shin KS, Kim IS, Kim SB. Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil. Int J Syst Evol Microbiol 2017; 67:3387-3392. [DOI: 10.1099/ijsem.0.002126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bilguun Oyuntsetseg
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Sung-Heun Cho
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Sun Jeong Jeon
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Kee-Sun Shin
- Industrial Bio-materials Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong, Daejeon 34141, Republic of Korea
| | - In-Seop Kim
- Department of Biological Sciences and Biotechnology, College of Life Science and Nano Technology, Hannam University, 70 Hannam-ro, Daedeok, Daejeon 34430, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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10
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Tang B, Xie F, Zhao W, Wang J, Dai S, Zheng H, Ding X, Cen X, Liu H, Yu Y, Zhou H, Zhou Y, Zhang L, Goodfellow M, Zhao GP. A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239 T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus. Synth Syst Biotechnol 2016; 1:169-186. [PMID: 29062941 PMCID: PMC5640789 DOI: 10.1016/j.synbio.2016.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 04/01/2016] [Accepted: 05/18/2016] [Indexed: 12/31/2022] Open
Abstract
The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.
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Affiliation(s)
- Biao Tang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.,CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Feng Xie
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Wei Zhao
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jian Wang
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Shengwang Dai
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Xiaoming Ding
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Xufeng Cen
- CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haican Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yucong Yu
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Haokui Zhou
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China
| | - Lixin Zhang
- CAS-Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK
| | - Guo-Ping Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200438, China.,CAS-Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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Busarakam K, Brown R, Bull AT, Tan GYA, Zucchi TD, da Silva LJ, de Souza WR, Goodfellow M. Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov. Antonie van Leeuwenhoek 2016; 109:319-34. [PMID: 26809280 DOI: 10.1007/s10482-015-0635-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/09/2015] [Indexed: 11/25/2022]
Abstract
The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).
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Affiliation(s)
- Kanungnid Busarakam
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Department of Agricultural Technology, Thailand Institute of Scientific and Technological Research, Pathum Thani, 12120, Thailand
| | - Ros Brown
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tiago D Zucchi
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
- Agrivalle, Av. Tranquillo Giannini, 1050, Salto, 13329-600, Brazil
| | - Leonardo José da Silva
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
| | - Wallace Rafael de Souza
- Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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Souza WR, Silva RE, Goodfellow M, Busarakam K, Figueiro FS, Ferreira D, Rodrigues-Filho E, Moraes LAB, Zucchi TD. Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil. Int J Syst Evol Microbiol 2015; 65:1786-1793. [DOI: 10.1099/ijs.0.000176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus
Amycolatopsis
and formed a branch in the
Amycolatopsis
16S rRNA gene tree together with
Amycolatopsis bullii
NRRL B-24847T,
Amycolatopsis plumensis
NRRL B-24324T,
Amycolatopsis tolypomycina
DSM 44544T and
Amycolatopsis vancoresmycina
NRRL B-24208T. It was related most closely to
A. bullii
NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus
Amycolatopsis
as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).
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Affiliation(s)
- Wallace Rafael Souza
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
| | - Rafael Eduardo Silva
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | | | - Fernanda Sales Figueiro
- Laboratório de Espectrometria de Massa Aplicado à Química de Produtos Naturais, Faculdade de Filosofia, Ciencias e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, 14040-901, Ribeirão Preto, Brazil
| | - Douglas Ferreira
- Laboratório de Bioquímica Micromolecular de Microorganismos, Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, Caixa Postal 676, 13565-905, São Carlos, Brazil
| | - Edson Rodrigues-Filho
- Laboratório de Bioquímica Micromolecular de Microorganismos, Departamento de Química, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, Caixa Postal 676, 13565-905, São Carlos, Brazil
| | - Luiz Alberto Beraldo Moraes
- Laboratório de Espectrometria de Massa Aplicado à Química de Produtos Naturais, Faculdade de Filosofia, Ciencias e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes, 3900, 14040-901, Ribeirão Preto, Brazil
| | - Tiago Domingues Zucchi
- Laboratório de Microbiologia Ambiental, Rod SP 340-Km 127, 5, Caixa Postal 69, EMBRAPA Meio Ambiente, 13820-000 Jaguariúna, Brazil
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Everest GJ, le Roes-Hill M, Omorogie C, Cheung SK, Cook AE, Goodwin CM, Meyers PR. Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa. Antonie van Leeuwenhoek 2012. [PMID: 23180373 DOI: 10.1007/s10482-012-9851-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16(T), grouped with the type strains of Amycolatopsis alba, Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16(T) and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridisation experiments confirmed that strain UM16(T) represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A. alba, A. coloradensis and A. thailandensis, respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16(T) as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272(T) = NRRL B-24724(T)).
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Affiliation(s)
- Gareth J Everest
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012. [DOI: 10.1099/ijs.0.048033-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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