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Li X, Yao Y, Xia Z, Luo X, Zhang L. Myceligenerans pegani sp. nov., an endophytic actinomycete isolated from Peganum harmala L. in Xinjiang, PR China. Int J Syst Evol Microbiol 2024; 74. [PMID: 38315520 DOI: 10.1099/ijsem.0.006179] [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: 02/07/2024] Open
Abstract
An endophytic actinomycete designated TRM65318T, was isolated from the root of Peganum harmala L. Its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis indicated that strain TRM65318T is phylogenetically most closely related to Myceligenerans salitolerans XHU 5031T (98.15 %) and Myceligenerans xiligouense DSM 15700T (97.78 %). The peptidoglycan belonged to type A4α. The polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, two unknown lipids and three glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6) and the whole-cell sugars contained glucose, mannose and galactose. Major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Strain TRM65318T had a genome size of 5881012 bp with a genome G+C content of 71.79 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain TRM65318T and the most closely related species were much lower than the thresholds commonly used to define species. At the same time, differences in phenotypic and genotypic data showed that strain TRM65318T could be clearly distinguished from M. salitolerans XHU 5031T. Therefore, it is concluded that strain TRM65318T represents a novel species of the genus of Myceligenerans. The proposed name for this organism is Myceligenerans pegani sp. nov., with type strain TRM65318T (=CCTCC AA 2019057T=LMG 31679T).
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Affiliation(s)
- Xin Li
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - YuXiang Yao
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - Zhanfeng Xia
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - XiaoXia Luo
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
| | - LiLi Zhang
- Key Laboratory of Conservation and Utilisation of Biological Resources in the Tarim Basin of the Xinjiang Production and Construction Corps/College of Life Sciences and Technology, Tarim University, Alar 843300, PR China
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González-Salazar LA, Quezada M, Rodríguez-Orduña L, Ramos-Aboites H, Capon RJ, Souza-Saldívar V, Barona-Gomez F, Licona-Cassani C. Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments. Microb Genom 2023; 9:mgen000921. [PMID: 36748531 PMCID: PMC9973853 DOI: 10.1099/mgen.0.000921] [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] [Indexed: 01/21/2023] Open
Abstract
Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of 'rare actinobacteria' has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora. These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.
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Affiliation(s)
- Luz A González-Salazar
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Michelle Quezada
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorena Rodríguez-Orduña
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Hilda Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Valeria Souza-Saldívar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico.,Present address: Microbial Diversity and Specialized Metabolism Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Cuauhtémoc Licona-Cassani
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico.,Division of Integrative Biology, Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, Mexico
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Wang Y, Shi J, Liu T, Zhang Y, Zhang L, Zhang X. Actinokineospora xionganensis sp. nov., a filamentous actinomycete isolated from the lakeside soil of Baiyangdian. Antonie van Leeuwenhoek 2021; 114:487-496. [PMID: 33674994 DOI: 10.1007/s10482-021-01532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
A novel actinomycete, strain HBU206404T, belonging to the genus Actinokineospora, was isolated from the lakeside soil of Baiyangdian, in China. Cells grew at 9-37 °C (optimum temperature, 28 °C) and pH 6-9 (optimum, pH 7). Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan, and sugars present in whole-cell hydrolysates were arabinose, mannose, glucose and galactose. The predominant menaquinone was MK-9(H4). The predominant cellular fatty acids (> 5%) of the strain HBU206404T were iso-C16:0 (21.5%), iso-C15:0 (20.3%), C16:1ω7c/C16:1ω6c and/or C16:1ω6c/C16:1ω7c (15.0%), iso-C17:0 (8.6%), C16:0 (7.0%) and C17:1ω8c (6.9%). The major polar lipids of the strain HBU206404T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, six unknown aminolipids, two unknown aminolipids and an unidentified lipid. The 16S rRNA gene sequence analysis indicated that the strain HBU206404T was most closely related to Actinokineospora alba KCTC 19294T (99.58%), but whole-genome comparisons, using average nucleotide identity (ANI) value (91.77%) and digital DNA-DNA hybridization (dDDH) value (60%), confirmed low genome relatedness. Nitrogen metabolism pathway was found in the genome of strain HBU206404T which haboured nitrate reductase and nitrite reductase. Other phenotypic characteristics, such as ability to hydrolyze substances, enzyme activity, acid production from carbon source, etc., could also distinguish strain HBU206404T from Actinokineospora alba KCTC 19294T. On the basis of genetic and phenotypic evidence, strain HBU206404T represents a novel species of the genus Actinokineospora, for which the name Actinokineospora xionganensis sp. nov. is proposed. The type strain is HBU206404T (= MCCC 1K04412T = KCTC 49404T).
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Affiliation(s)
- Yuhui Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Jiangli Shi
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Tongtong Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Yufan Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Liping Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China
| | - Xiumin Zhang
- College of Life Science, Institute of Life Science and Green Development, Hebei University; Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Baoding, 071002, PR China.
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