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Geng Y, Zhao JY, Yuan HR, Li LL, Wen ML, Li MG, Tang SK. Aestuariimicrobium ganziense sp. nov., a new Gram-positive bacterium isolated from soil in the Ganzi Tibetan autonomous prefecture, China. Arch Microbiol 2021; 203:2653-2658. [PMID: 33710378 DOI: 10.1007/s00203-021-02261-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
A novel Gram-stain positive, oval-shaped, and non-flagellated bacterium, designated YIM S02566T, was isolated from alpine soil in Shadui Towns, Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, PR China. Growth occurred at 23-35 °C (optimum, 30 °C) in the presence of 0.5-4% (w/v) NaCl (optimum, 1%) and at pH 7.0-8.0 (optimum, pH 7.0). The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain YIM S02566T was most closely related to the genus Aestuariimicrobium, with Aestuariimicrobium kwangyangense R27T and Aestuariimicrobium soli D6T as its closest relative (sequence similarities were 96.3% and 95.4%, respectively). YIM S02566T contained LL-diaminopimelic acid in the cell wall. MK-9(H4) was the predominant menaquinone. The major fatty acid patterns were anteiso-C15:0 (60.0%). The major polar lipid was DPG. The genome size of strain YIM S02566T was 3.1 Mb, comprising 3078 predicted genes with a DNA G + C content of 69.0 mol%. Based on these genotypic, chemotaxonomic and phenotypic evidences, strain YIM S02566T was identified as a novel species in the genus Aestuariimicrobium, for which the name Aestuariimicrobium ganziense sp. nov. is proposed. The type strain is YIM S02566T (= CGMCC 1.18751 T = KCTC 49,477 T).
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Affiliation(s)
- Yu Geng
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jiang-Yuan Zhao
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Hui-Ren Yuan
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Le-Le Li
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Liang Wen
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ming-Gang Li
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shu-Kun Tang
- Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
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Diop K, Cadoret F, Nguyen TT, Baudoin JP, Armstrong N, Raoult D, Bretelle F, Fournier PE, Fenollar F. Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge. Int J Syst Evol Microbiol 2020; 70:4091-4097. [PMID: 32628103 DOI: 10.1099/ijsem.0.004106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C16 : 0 (29 %), C18:1ω9 (18 %), and iso-C15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275T was related to members of the family Propionibacteriaceae (between 90.32-92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275T (=CSUR P3275T=CECT 9677T).
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Affiliation(s)
- Khoudia Diop
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Frederic Cadoret
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Thi Tien Nguyen
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Florence Bretelle
- Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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Leung MHY, Tong X, Bastien P, Guinot F, Tenenhaus A, Appenzeller BMR, Betts RJ, Mezzache S, Li J, Bourokba N, Breton L, Clavaud C, Lee PKH. Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants. MICROBIOME 2020; 8:100. [PMID: 32591010 PMCID: PMC7320578 DOI: 10.1186/s40168-020-00874-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/20/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing. RESULTS Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds. CONCLUSIONS The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | | | - Florent Guinot
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Arthur Tenenhaus
- CentraleSupelec-L2S-Laboratoire des signaux et systèmes, Brain and Spine Institute, Université Paris-Sud, Orsay, France
| | | | | | | | - Jing Li
- L’Oréal Research and Innovation, Pudong, China
| | | | - Lionel Breton
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Cécile Clavaud
- L’Oréal Research and Innovation, Aulnay-sous-Bois, France
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
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Chen LL, Chen F, Zhao HZ, Feng ZZ, Zhang H, Huang X. Aestuariimicrobium soli sp. nov., isolated from farmland soil, and emended description of the genus Aestuariimicrobium. Int J Syst Evol Microbiol 2018; 68:3296-3300. [PMID: 30141771 DOI: 10.1099/ijsem.0.002986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-positive, catalase-positive, non-spore-forming and short rod- or oval-shaped bacterial strain, designated D6T, was isolated from farmland soil in Xuancheng, Anhui Province, China. Growth occurred at 4-37 °C (optimum, 30 °C), at pH 6.5-8.5 (optimum, 7.0) and with 0-7 % (w/v) NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D6T was most closely related to Aestuariimicrobium kwangyangense DSM 21549T (98.47 %), followed by Tessaracoccus rhinocerotis YIM 101269T (94.46 %). Strain D6T had a cell-wall peptidoglycan based on ll-diaminopimelic acid. MK-9(H4) was the predominant menaquinone. The major fatty acids of strain D6T were anteiso-C15 : 0, iso-C15 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The major polar lipids were a lipid, glycolipid and phospholipid. The DNA G+C content was 69.2 mol% and strain D6T showed low DNA-DNA relatedness to A. kwangyangense DSM 21549T (36.45±0.42 %). Based on these genotypic and phenotypic data, strain D6T represents a novel species in the genus Aestuariimicrobium, for which the name Aestuariimicrobium soli sp. nov. is proposed. The type strain is D6T (=KCTC 39995T=DSM 105824T). An emended description of the genus Aestuariimicrobium is presented.
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Affiliation(s)
- Ling-Ling Chen
- 1College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Feng Chen
- 1College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hua-Zhu Zhao
- 1College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhao-Zhong Feng
- 2School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Hao Zhang
- 1College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xing Huang
- 1College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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Sun Y, Chen HH, Sun HM, Ai MJ, Su J, Yu LY, Zhang YQ. Naumannella huperziae sp. nov., an endophytic actinobacterium isolated from Huperzia serrata (Thunb.). Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ye Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hua-Hong Chen
- Department of Chemistry, Chuxiong Normal College, Chuxiong, Yunnan 675000, PR China
| | - Hong-Min Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Meng-Jie Ai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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Bae KS, Kim MS, Lee JH, Kang JW, Kim DI, Lee JH, Seong CN. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria. J Microbiol 2016; 54:789-795. [PMID: 27888457 DOI: 10.1007/s12275-016-6446-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/26/2022]
Abstract
To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju, Gyeonggi, Jeonnam, Daejeon, and Chungnam. A large number of novel actinobacterial species continue to be discovered since the Korean government is encouraging the search for new bacterial species and researchers are endeavoring to find out novel strains from extreme or untapped environments.
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Affiliation(s)
- Kyung Sook Bae
- Biological Resource Center, KRIBB, Jeongeup, 56212, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, Republic of Korea.
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Claverías FP, Undabarrena A, González M, Seeger M, Cámara B. Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile. Front Microbiol 2015; 6:737. [PMID: 26284034 PMCID: PMC4516979 DOI: 10.3389/fmicb.2015.00737] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Marine-derived Actinobacteria are a source of a broad variety of secondary metabolites with diverse biological activities, such as antibiotics and antitumorals; many of which have been developed for clinical use. Rare Actinobacteria represent an untapped source of new bioactive compounds that have been scarcely recognized. In this study, rare Actinobacteria from marine sediments were isolated from the Valparaíso bay, Chile, and their potential to produce antibacterial compounds was evaluated. Different culture conditions and selective media that select the growth of Actinobacteria were used leading to the isolation of 68 bacterial strains. Comparative analysis of the 16S rRNA gene sequences led to identifying isolates that belong to the phylum Actinobacteria with genetic affiliations to 17 genera: Aeromicrobium, Agrococcus, Arthrobacter, Brachybacterium, Corynebacterium, Dietzia, Flaviflexus, Gordonia, Isoptericola, Janibacter, Microbacterium, Mycobacterium, Ornithinimicrobium, Pseudonocardia, Rhodococcus, Streptomyces, and Tessaracoccus. Also, one isolate could not be consistently classified and formed a novel phylogenetic branch related to the Nocardiopsaceae family. The antimicrobial activity of these isolates was evaluated, demonstrating the capability of specific novel isolates to inhibit the growth of Gram-positive and Gram-negative bacteria. In conclusion, this study shows a rich biodiversity of culturable Actinobacteria, associated to marine sediments from Valparaíso bay, highlighting novel rare Actinobacteria, and their potential for the production of biologically active compounds.
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Affiliation(s)
| | | | | | | | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
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8
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Enhancement of sludge granulation in anaerobic acetogenesis by addition of nitrate and microbial community analysis. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Subramani R, Aalbersberg W. Culturable rare Actinomycetes: diversity, isolation and marine natural product discovery. Appl Microbiol Biotechnol 2013; 97:9291-321. [DOI: 10.1007/s00253-013-5229-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
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10
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Rieser G, Scherer S, Wenning M. Naumannella halotolerans gen. nov., sp. nov., a Gram-positive coccus of the family
Propionibacteriaceae
isolated from a pharmaceutical clean room and from food. Int J Syst Evol Microbiol 2012; 62:3042-3048. [DOI: 10.1099/ijs.0.037218-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-stain-positive, aerobic bacterial strains isolated from a pharmaceutical clean room (strain WS4616T), a dessert milk product (strain WS4617) and from raw milk (strains WS4623 and WS4624) were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences showed that they formed a distinct lineage within the family
Propionibacteriaceae
. Similarity values between 16S rRNA gene sequences of the four novel strains and the type species of all genera belonging to the family
Propionibacteriaceae
were 89.2–94.1 %. The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were MK-8(H4) and MK-9(H4). The cell-wall peptidoglycan of type A3γ contained ll-diaminopimelic acid, alanine, glycine and glutamic acid. The G+C content of the genomic DNA of strain WS4616T was 67.7 mol%. The whole-cell sugar pattern contained ribose, mannose, arabinose, glucose and galactose. On the basis of phenotypic and genetic data, strains WS4616T, WS4617, WS4623 and WS4624 are classified as members of a novel species in a new genus of the family
Propionibacteriaceae
, for which the name Naumannella halotolerans gen. nov., sp. nov. is proposed. The type strain is WS4616T ( = DSM 24323T = LMG 26184T) and three additional strains are WS4617, WS4623 and WS4624.
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Affiliation(s)
- Gernot Rieser
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, D-85350 Freising, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, D-85350 Freising, Germany
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, D-85350 Freising, Germany
| | - Mareike Wenning
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, D-85350 Freising, Germany
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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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12
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Lee DW, Lee SD. Ponticoccus gilvus gen. nov., sp. nov., a novel member of the family Propionibacteriaceae from seawater. J Microbiol 2008; 46:508-12. [PMID: 18974950 DOI: 10.1007/s12275-008-0096-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 08/01/2008] [Indexed: 11/28/2022]
Abstract
A novel actinobacterium, designated strain MSW-19(T), was isolated from a seawater sample in Republic of Korea. Cells were aerobic, Gram-positive, non-endospore-forming, and non-motile cocci. Colonies were circular, convex, opaque, and vivid yellow in colour. A phylogenetic tree based on 16S rRNA gene sequences exhibited that the organism formed a distinct clade within the radius encompassing representatives of the family Propionibacteriaceae. The phylogenetic neighbors were the type strains of the genera Friedmanniella, Microlunatus, Micropruina, Propionicicella, and Propionicimonas. Levels of 16S rRNA gene sequence similarity between the isolate and members of the family were less than 95.3%. The cell wall peptidoglycan of the organism contained LL-diaminopimelic acid as the diagnostic diamino acid. The isolate contained MK-9(H(4)) as the predominant menaquinone, ai-C(15:0) as the major fatty acid and polar lipids including phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. The G+C content of the DNA was 69.6 mol%. On the basis of the phenotypic and phylogenetic data presented here, the isolate is considered to represent a novel genus and species in the family Propionibacteriaceae, for which the name Ponticoccus gilvus gen. nov., sp. nov. is proposed. The type strain is strain MSW-19(T) (= KCTC 19476(T)= DSM 21351(T)).
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Affiliation(s)
- Dong Wan Lee
- Department of Science Education, Cheju National University, Jeju 690-756, Republic of Korea
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