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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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2
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Sun X, Zhao J, Luo X, Hou W, Xiang W, Song J, Wang X. Lentzea alba sp. nov. , a novel actinobacterium isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33502301 DOI: 10.1099/ijsem.0.004661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterium, designated strain NEAU-D13T, was isolated from soil collected from Aohan Banner, Chifeng, Inner Mongolia Autonomous Region, China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-D13T belonged to the genus Lentzea and shared the highest sequence similarity with Lentzea kentuckyensisJCM 14913T (99.17 %). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Lentzea. Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were ribose and mannose. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and phosphatidylinositol. The menaquinone was only MK-9(H4). The major fatty acids were iso-C16:0, C16:0, anteiso-C17:0, iso-C15:0 and anteiso-C15:0. DNA G+C content was 68.71 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a stable clade with L. kentuckyensisJCM 14913T in the genus Lentzea. Meanwhile, a combination of digital DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-D13T could be distinguished from its closely related strain. Therefore, it is concluded that strain NEAU-D13T represents a novel species of the genus Lentzea, for which the name Lentzea alba sp. nov. is proposed, with NEAU-D13T (=CCTCC AA 2019089T=JCM 33970T) as the type strain.
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Affiliation(s)
- Xiujun Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xianxian Luo
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wenyu Hou
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, PR China.,Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
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Ping M, Yun-Lin Z, Jun L, Jian G, Zheng-Gang X. Proposal of Lentzea deserti (Okoro et al. 2010) Nouioui et al. 2018 as a later heterotypic synonym of Lentzea atacamensis (Okoro et al. 2010) Nouioui et al. 2018 and an emended description of Lentzea atacamensis. PLoS One 2021; 16:e0246533. [PMID: 33539471 PMCID: PMC7861442 DOI: 10.1371/journal.pone.0246533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/20/2021] [Indexed: 11/19/2022] Open
Abstract
The taxonomic relationship of Lentzea atacamensis and Lentzea deserti were re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that the type strains of L. atacamensis and L. deserti shared 99.7% sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the genomes of two type strains were 88.6% and 98.8%, respectively, greater than the two recognized thresholds values of 70% dDDH and 95-96% ANI for bacterial species delineation. These results suggested that L. atacamensis and L. deserti should share the same taxonomic position. And this conclusion was further supported by similar phenotypic and chemotaxonomic features between them. Therefore, we propose that L. deserti is a later heterotypic synonym of L. atacamensis.
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Affiliation(s)
- Mo Ping
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Zhao Yun-Lin
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Liu Jun
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Gao Jian
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Xu Zheng-Gang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, Hunan, China
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, China
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Molina-Menor E, Gimeno-Valero H, Pascual J, Peretó J, Porcar M. High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert. Front Microbiol 2021; 11:583120. [PMID: 33488536 PMCID: PMC7821382 DOI: 10.3389/fmicb.2020.583120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.
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Affiliation(s)
- Esther Molina-Menor
- Institute for Integrative Systems Biology I2SysBio (University of València-CSIC), Paterna, Spain
| | - Helena Gimeno-Valero
- Darwin Bioprospecting Excellence S.L., Parc Científic Universitat de València, Paterna, Spain
| | - Javier Pascual
- Darwin Bioprospecting Excellence S.L., Parc Científic Universitat de València, Paterna, Spain
| | - Juli Peretó
- Institute for Integrative Systems Biology I2SysBio (University of València-CSIC), Paterna, Spain.,Darwin Bioprospecting Excellence S.L., Parc Científic Universitat de València, Paterna, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology I2SysBio (University of València-CSIC), Paterna, Spain.,Darwin Bioprospecting Excellence S.L., Parc Científic Universitat de València, Paterna, Spain
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Maiti PK, Mandal S. Lentzea indica sp. nov., a novel actinobacteria isolated from Indian Himalayan-soil. Antonie van Leeuwenhoek 2020; 113:1411-1423. [PMID: 32699968 DOI: 10.1007/s10482-020-01449-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/11/2020] [Indexed: 12/26/2022]
Abstract
A novel actinobacterium, strain PSKA42T was isolated from a soil sample of Kashmir Himalaya, India (latitude: 34°-01' N; longitude: 74°-47' E; altitude: 5328 ft). The morphological, biochemical and molecular characteristics predicted that PSKA42T belongs to the genera Lentzea. Using the Ezbiocloud server it has also been manifested that the 16S rRNA gene sequence of PSKA42 was 98.4% similar with Lentzea guizhouensis DHSC013T, Lentzea albidocapillata subsp. violacea IMSNU50388T; 98.26% similar with Lentzea aerocolonigenes NRRLB-3298T, Lentzea albidocapillata subsp. albidocapillata NRRLB-24057T and 98.19% similar with Lentzea californiensis DSM43393T. Whole-genome average nucleotide identity values between PSKA42T and L. guizhouensis DHSC013T, L. albidocapillata subsp. violaera IMSNU50388T, L. aerocolonigenes NRRLB-3298T, L. albidocapillata subsp. albidocapillata NRRLB-24057T, L. californiensis DSM43393T, L. flaviverucosa As40578T were 84.94%, 85.8%, 87.15%, 87.71%, 79.29, and 87.22%, respectively, suggesting that PSKA42T represented a new species. In-silco genome-to-genome distances analysis and MLSA with selected housekeeping genes also indicated that the isolate should be assigned to a new species under the genus Lentzea. Analysis of the whole-cell hydrolysate found mannose and ribose as major sugar while cell wall amino acid was identified as meso-diaminopimelic acid. Major fatty acids (> 5%) were observed as 15:0 iso (23.81%), and 16:0 iso (26.11%). PSKA42 contains polyketide synthase type-I genes but unable to show antimicrobial activity in laboratory conditions. The average GC content in its genome is 68.3%. Further, based on physicochemical, chemotaxonomic markers and molecular analysis, PSKA42T can be assigned as novel species of Lentzea, we proposed Lentzea indica sp nov. The type strain is PSKA42T (JCM 33729T, MTCC 12936T, MCC 4127T).
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Affiliation(s)
- Pulak Kumar Maiti
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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