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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: 394] [Impact Index Per Article: 65.7] [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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Hamada M, Shibata C, Nurkanto A, Ratnakomala S, Lisdiyanti P, Tamura T, Suzuki KI. Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae. Antonie van Leeuwenhoek 2015; 107:1299-306. [PMID: 25761861 DOI: 10.1007/s10482-015-0424-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Two novel Gram-stain positive actinobacteria, designated PS-14-16(T) and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4α. Their predominant menaquinone was identified as MK-9(H4) and the major fatty acid as anteiso-C(15:0). The DNA G+C content was determined to be 68.4-68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16(T) and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94%. However, strains PS-14-16(T) and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA-DNA hybridization experiments indicated that strains PS-14-16(T) and RS-7-1 belong to the same species. Strains PS-14-16(T) and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16(T) (=NBRC 110109(T) = IanCC A 516(T)). [corrected].
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Affiliation(s)
- Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan,
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3
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Schumann P, Kampfer P, Busse HJ, Evtushenko LI. Proposed minimal standards for describing new genera and species of the suborder Micrococcineae. Int J Syst Evol Microbiol 2009; 59:1823-49. [DOI: 10.1099/ijs.0.012971-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589-608. [PMID: 19244447 DOI: 10.1099/ijs.0.65780-0] [Citation(s) in RCA: 385] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.
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Affiliation(s)
- Xiao-Yang Zhi
- The Key Laboratory for Microbial Resources of the 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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Mayilraj S, Saha P, Suresh K, Saini HS. Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 2006; 56:1657-1661. [PMID: 16825645 DOI: 10.1099/ijs.0.64138-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A buff-yellow-pigmented bacterium, strain K22-20T, which was isolated from a cold desert of the Indian Himalayas, was subjected to a polyphasic taxonomic study. Phenotypic and chemical properties of strain K22-20T were consistent with its classification in the genus Ornithinimicrobium. The major fatty acids of the strain were iso-C17 : 1
ω9c (cis-15-methyl 7-hexadecenoic acid), iso-C15 : 0 (13-methyl tetradecanoic acid), iso-C16 : 0 (14-methyl pentadecanoic acid) and iso-C17 : 0 (15-methyl hexadecanoic acid). The G+C content of the genomic DNA was 71 mol%. According to 16S rRNA gene sequence analysis, strain K22-20T was closely related to Ornithinimicrobium humiphilum HKI 0124T (97.7 %). However, genomic relatedness between strain K22-20T and O. humiphilum MTCC 6406T, as revealed by DNA–DNA hybridization, was 64.5 %. Based on the polyphasic data, strain K22-20T (=MTCC 6545T=DSM 17687T=JCM 12763T) represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium kibberense sp. nov. is proposed.
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MESH Headings
- Actinomycetales/classification
- Actinomycetales/genetics
- Actinomycetales/isolation & purification
- Actinomycetales/physiology
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA
- India
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
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Affiliation(s)
- S Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector 39-A, Chandigarh, 160 036, India
| | - P Saha
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector 39-A, Chandigarh, 160 036, India
| | - K Suresh
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector 39-A, Chandigarh, 160 036, India
| | - H S Saini
- Department of Microbiology, Guru Nanak Dev University (GNDU), Amritsar, 144 005, India
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Kitagaki H, Shimoi H, Itoh K. Identification and analysis of a static culture-specific cell wall protein, Tir1p/Srp1p in Saccharomyces cerevisiae. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:343-9. [PMID: 9363789 DOI: 10.1111/j.1432-1033.1997.t01-1-00343.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A 100-kDa protein was found to be a major cell wall protein in Saccharomyces cerevisiae cells cultured without shaking, but was not present in cells cultured with shaking. The amino acid sequence of this protein was identical to the sequence of Tir1p/Srp1p. TIR1/SRP1 has previously been identified as a gene induced by glucose, cold shock or anaerobiosis and was believed to be a cell membrane protein but not a cell wall protein. However, we found that beta-1,3-glucanase solubilized Tir1p/Srp1p from the cell wall and the purified Tir1p/Srp1p reacted with antiserum to beta-1,6-glucan and contained glucose. These results suggest that Tir1p/Srp1p is a major structural cell wall protein in the static-cultured yeast cells and is bound to the cell wall through beta-1,6-glucan. TIR1/SRP1 mRNA was transcribed only in the static culture and its transcription was regulated by the ROX1 repressor.
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Affiliation(s)
- H Kitagaki
- National Research Institute of Brewing, Higashihiroshima, Japan
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Molecular structure of Rarobacter faecitabidus protease I. A yeast-lytic serine protease having mannose-binding activity. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)74023-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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8
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Suzuki KI, Collins MD, Iijima E, Komagata K. Chemotaxonomic characterization of a radiotolerant bacterium,Arthrobacter radiotolerans: Description ofRubrobacter radiotoleransgen. nov., comb. nov. FEMS Microbiol Lett 1988. [DOI: 10.1111/j.1574-6968.1988.tb02568.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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Ruddon R, Bryan A, Hanson C, Perini F, Ceccorulli L, Peters B. Characterization of the intracellular and secreted forms of the glycoprotein hormone chorionic gonadotropin produced by human malignant cells. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69385-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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