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Girão M, Lequint Z, Rego A, Costa I, Proença DN, Morais PV, Carvalho MF. Nocardiopsis codii sp. nov., and Rhodococcus chondri sp. nov., two novel actinomycetal species isolated from macroalgae collected in the northern Portuguese coast. Int J Syst Evol Microbiol 2024; 74. [PMID: 39255017 DOI: 10.1099/ijsem.0.006483] [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: 09/11/2024] Open
Abstract
Two novel actinomycetal strains, designated CC-R113T and CC-R104T, were isolated from the tissues of two macroalgae collected on the northern Portuguese coast. Phylogenetic analyses based on the 16S rRNA gene showed that strain CT-R113T belongs to the genus Nocardiopsis, being closely related to Nocardiopsis umidischolae 66/93T and Nocardiopsis tropica VKM Ac-1457T, with 98.65 and 98.39 % sequence similarity, respectively. The clade formed between the three type strains was confirmed by phylogenomic analysis. The genome of strain CT-R113T was 7.27 Mb in size with a G+C content of 71.3 mol %, with average nucleotide identity (ANI) values of 89.59 and 90.14 % with strains 66/93T and VKM Ac-1457T, respectively. The major cellular fatty acids were identified as C18 : 1 ω9c, iso-C16 : 0 and anteiso-C17 : 0. Menaquinone 10 (MK-10) was the major respiratory quinone. Comparative analysis of 16S rRNA gene sequences showed that strain CC-R104T belongs to the genus Rhodococcus and is most closely related to Rhodococcus pyridinivorans DSM 44555T, with 98.24 % sequence similarity. However, phylogenomic analysis revealed that strain CC-R104T establishes a clade with Rhodococcus artemisae DSM 45380T, being more distant from Rhodococcus pyridinivorans DSM 44555T. The genome of strain CC-R104T was 5.34 Mb in size with a G+C content of 67.01 mol%. The ANI value between strains CC-R104T and DSM 45380T was 81.2 % and between strains CC-R104T and DSM 44555T was 81.5 %. The major cellular fatty acids were identified as C18 : 1 ω9c, C16 : 0 and summed feature 3. Menaquinone 8 (MK-8) was the only respiratory quinone. For both CC-R113T and CC-R104T, optimum growth was observed at pH 7.0, 28 °C and 0-5 % NaCl and whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid. On the basis of phenotypic, molecular and chemotaxonomic characteristics, strains CT-R113T and CC-R104T are considered to represent novel species, for which the names Nocardiopsis codii sp. nov. (type strain CT-R113T=LMG33234T=UCCCB172T) and Rhodococcus chondri sp. nov. (type strain CC-R104T=LMG33233T=UCCCB171T) are proposed.
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Affiliation(s)
- Mariana Girão
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Zoé Lequint
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Polytech Clermont, University Clermont Auvergne, Clermont-Ferrand, France
| | - Adriana Rego
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Isabel Costa
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Diogo Neves Proença
- Department of Life Sciences, University of Coimbra, CEMMPRE, ARISE, Coimbra, Portugal
| | - Paula V Morais
- Department of Life Sciences, University of Coimbra, CEMMPRE, ARISE, Coimbra, Portugal
| | - Maria F Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
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Li C, Cao P, Jiang M, Hou Y, Du C, Xiang W, Zhao J, Wang X. Rhodococcus oryzae sp. nov., a novel actinobacterium isolated from rhizosphere soil of rice ( Oryza sativa L.). Int J Syst Evol Microbiol 2020; 70:3300-3308. [PMID: 32375931 DOI: 10.1099/ijsem.0.004171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67T, belonged to the genus Rhodococcus and formed a cluster with Rhodococcus maanshanensis DSM 44675T, Rhodococcus kronopolitis NEAU-ML12T and Rhodococcus tukisamuensis JCM 11308T (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C16 : 0, 10-methyl C18 : 0, C18 : 1 ω9c and C16 : 1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H2). Whole-cell hydrolysates contained meso-diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67T was 64.6 mol%. Strain NEAU-CX67T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with R. maanshanensis DSM 44675T (92.1 and 45.4 %) and R. tukisamuensis JCM 11308T (81.9 and 24.4 %). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67T is considered to represent a novel species of the genus Rhodococcus for which the name Rhodococcus oryzae sp. nov. is proposed. The type strain is NEAU-CX67T (=DSM 107701T=CCTCC AB 2018233T).
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Affiliation(s)
- Chenxu Li
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Peng Cao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Mengqi Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Yifan Hou
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin 150030, PR China
| | - Chuanjiao Du
- 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
| | - Junwei Zhao
- 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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Ma Q, Gao X, Bi X, Tu L, Xia M, Shen Y, Wang M. Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase. Sci Rep 2020; 10:4329. [PMID: 32152368 PMCID: PMC7062688 DOI: 10.1038/s41598-020-61349-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/24/2020] [Indexed: 11/19/2022] Open
Abstract
Chitin deacetylase (CDA) can hydrolyse the acetamido group of chitin polymers to produce chitosans, which are used in various fields including the biomedical and pharmaceutical industries, food production, agriculture, and water treatment. CDA represents a more environmentally-friendly and easier to control alternative to the chemical methods currently utilised to produce chitosans from chitin; however, the majority of identified CDAs display activity toward low-molecular-weight oligomers and are essentially inactive toward polymeric chitin or chitosans. Therefore, it is important to identify novel CDAs with activity toward polymeric chitin and chitosans. In this study, we isolated the bacterium Rhodococcus equi F6 from a soil sample and showed that it expresses a novel CDA (ReCDA), whose activity toward 4-nitroacetanilide reached 19.20 U/mL/h during fermentation and was able to deacetylate polymeric chitin, colloidal chitin, glycol-chitin, and chitosan. Whole genome sequencing revealed that ReCDA is unique to the R. equi F6 genome, while phylogenetic analysis indicated that ReCDA is evolutionarily distant from other CDAs. In conclusion, ReCDA isolated from the R. equi F6 strain expands the known repertoire of CDAs and could be used to deacetylate polymeric chitosans and chitin in industrial applications.
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Affiliation(s)
- Qinyuan Ma
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Xiuzhen Gao
- School of Life Science, Shandong University of Technology, Zibo, 255049, China
| | - Xinyu Bi
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Linna Tu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Menglei Xia
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China
| | - Yanbing Shen
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China.
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P.R. China.
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Current taxonomy of Rhodococcus species and their role in infections. Eur J Clin Microbiol Infect Dis 2018; 37:2045-2062. [PMID: 30159693 DOI: 10.1007/s10096-018-3364-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium
hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755-761. [DOI: 10.1099/ijs.0.053322-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-endospore-forming rod-shaped bacterium, strain Ca11T, was isolated from a bioreactor with extensive phosphorus removal and was studied in detail for its taxonomic allocation. 16S rRNA gene sequence analysis revealed closest sequence similarity of the strain to type strains of [
Corynebacterium hoagii
] and
Rhodococcus equi
(98.9 %),
Rhodococcus koreensis
and
Rhodococcus wratislaviensis
(both 98.4 %),
Rhodococcus opacus
and
Rhodococcus canchipurensis
(both 98.0 %) followed by
Rhodococcus kunmingensis
and
Rhodococcus imtechensis
(97.7 %). Phylogenetic trees showed a distinct clustering of strain Ca11T with the type strains of [
C. hoagii
],
R. equi
, and
R. kunmingensis
separate to all other species of the genus
Rhodococcus
. The quinone system of strain Ca11T was composed of dihydrogenated menaquinones with 8 (major amount) as well as 7 and 6 isoprenoid units [MK-8(H2), MK-7(H2), MK-6(H2)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phospholipid and an unidentified glycolipid. The fatty acid profile was similar to that reported for
R. equi
and contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, supporting the allocation of the strain to the genus
Rhodococcus
. Physiological and biochemical characterization and DNA–DNA hybridization with type strains of the most closely related species allowed clear phenotypic and genotypic differentiation of the isolate. On the basis of these results, strain Ca11T ( = DSM 45893T = LMG 27563T) represents a novel species of the genus
Rhodococcus
, with the proposed name Rhodococcus defluvii sp. nov. In addition, a polyphasic taxonomic analysis of [
Corynebacterium hoagii
] DSM 20295T and
Rhodococcus equi
DSM 20307T indicated that the two strains belong to the same species, for which the name Rhodococcus hoagii comb. nov. takes priority, according to the Rules of the Bacteriological Code.
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Affiliation(s)
- P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - W. Dott
- Institut für Hygiene und Umweltmedizin, RWTH Aachen, Germany
| | - K. Martin
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V., Hans-Knöll-Institut, D-07745 Jena, Germany
| | - S. P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Li J, Zhao GZ, Long LJ, Wang FZ, Tian XP, Zhang S, Li WJ. Rhodococcus nanhaiensis sp. nov., an actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 2011; 62:2517-2521. [PMID: 22180608 DOI: 10.1099/ijs.0.038067-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, two strains (SCSIO 10187(T) and SCSIO 10197) were isolated from a sediment sample collected from the South China Sea and characterized by using a polyphasic approach. Growth was observed at 15-35 °C (optimum 28 °C) and pH 5.0-8.0 (optimum pH 6.0). Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Rhodococcus. Phylogenetic analysis showed that the two strains clustered together and the 16S rRNA gene sequence similarities between them and other members of the genus Rhodococcus were 93.2-97.7 %. The menaquinone type was MK-8(H(2)). Major cellular fatty acids were C(16 : 0), C(18 : 1)ω9c, C(17 : 0), 10-methyl C(18 : 0), C(18 : 0), C(19 : 0) and C(17 : 1)ω8c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C contents of strains SCSIO 10187(T) and SCSIO 10197 were 63.7 and 63.2 mol%, respectively. The combined genotypic and phenotypic data showed that the two strains represent a novel species of the genus Rhodococcus, for which the name Rhodococcus nanhaiensis is proposed; the type strain is SCSIO 10187(T) ( = DSM 45608(T) = CCTCC AB 2011024(T)), with SCSIO 10197 ( = DSM 45609 = CCTCC AB 2011025) as a reference strain.
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Affiliation(s)
- Jie Li
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Guo-Zhen Zhao
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Li-Juan Long
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Fa-Zuo Wang
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Xin-Peng Tian
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Si Zhang
- Key Laboratory of Marine Bio-resources Sustainable Utilization CAS, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Letek M, González P, MacArthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R, Hapeshi A, Holdstock J, Leadon D, Navas J, Ocampo A, Quail MA, Sanders M, Scortti MM, Prescott JF, Fogarty U, Meijer WG, Parkhill J, Bentley SD, Vázquez-Boland JA. The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet 2010; 6:e1001145. [PMID: 20941392 PMCID: PMC2947987 DOI: 10.1371/journal.pgen.1001145] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 08/31/2010] [Indexed: 11/29/2022] Open
Abstract
We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid–rich intestine and manure of herbivores—two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche–adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT–acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi. Rhodococcus is a prototypic genus within the Actinobacteria, one of the largest microbial groups on Earth. Many of the ubiquitous rhodococcal species are biotechnologically useful due to their metabolic versatility and biodegradative properties. We have deciphered the genome of a facultatively parasitic Rhodococcus, the animal and human pathogen R. equi. Comparative genomic analyses of related species provide a unique opportunity to increase our understanding of niche-adaptive genome evolution and specialization. The environmental rhodococci have much larger genomes, richer in metabolic and degradative pathways, due to gene duplication and acquisition, not genome contraction in R. equi. This probably reflects that the host-associated R. equi habitat is more stable and favorable than the chemically diverse but nutrient-poor environmental niches of nonpathogenic rhodococci, necessitating metabolically more complex, expanded genomes. Our work also highlights that the recruitment or cooption of core microbial traits, following the horizontal acquistion of a few critical genes that provide access to the host niche, is an important mechanism in actinobacterial virulence evolution. Gene cooption is a key evolutionary mechanism allowing rapid adaptive change and novel trait acquisition. Recognizing the contribution of cooption to virulence provides a rational framework for understanding and interpreting the emergence and evolution of microbial pathogenicity.
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Affiliation(s)
- Michal Letek
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Patricia González
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Iain MacArthur
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Héctor Rodríguez
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Tom C. Freeman
- Division of Genetics and Genomics, Roslin BioCentre, University of Edinburgh, Edinburgh, United Kingdom
| | - Ana Valero-Rello
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Mónica Blanco
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Tom Buckley
- Irish Equine Centre, Johnstown, Naas, Ireland
| | - Inna Cherevach
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Ruth Fahey
- School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
| | - Alexia Hapeshi
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Jolyon Holdstock
- Oxford Gene Technology, Begbroke Science Park, Oxford, United Kingdom
| | | | - Jesús Navas
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | | | - Michael A. Quail
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Mandy Sanders
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Mariela M. Scortti
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Departamento de Bioquímica y Biología Molecular IV, Universidad Complutense, Madrid, Spain
| | - John F. Prescott
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | | | - Wim G. Meijer
- School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin, Ireland
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - José A. Vázquez-Boland
- Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Grupo de Patogenómica Bacteriana, Universidad de León, León, Spain
- * E-mail:
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Zhang YQ, Li WJ, Kroppenstedt RM, Kim CJ, Chen GZ, Park DJ, Xu LH, Jiang CL. Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil. Int J Syst Evol Microbiol 2005; 55:1133-1137. [PMID: 15879245 DOI: 10.1099/ijs.0.63390-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, non-motile, mesophilic strain, designated YIM 70056T, was isolated from a forest soil sample in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this isolate had less than 97·0 % similarity to any Rhodococcus species with validly published names, with the exception of Rhodococcus fascians (DSM 20669T), which was found to be its closest neighbour (98·9 % similarity). Chemotaxonomic data, including peptidoglycan type, diagnostic sugar compositions, fatty acid profiles, menaquinones, polar lipids and mycolic acids, were determined for this isolate; the results supported the affiliation of strain YIM 70056T to the genus Rhodococcus. The DNA G+C content was 63·5 mol%. The results of DNA–DNA hybridization with R. fascians DSM 20669T, in combination with chemotaxonomic and physiological data, demonstrated that isolate YIM 70056T represents a novel Rhodococcus species, for which the name Rhodococcus yunnanensis sp. nov. is proposed, with YIM 70056T (=CCTCC AA 204007T=KCTC 19021T=DSM 44837T) as the type strain.
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Affiliation(s)
- Yu-Qin Zhang
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Wen-Jun Li
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Reiner M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - Chang-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Guo-Zhong Chen
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Dong-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, 52 Oeundong, Yusong, Daejeon 305-333, Republic of Korea
| | - Li-Hua Xu
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
| | - Cheng-Lin Jiang
- The Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P. R. China
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