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Guzman J, Ortúzar M, Poehlein A, Daniel R, Trujillo ME, Vilcinskas A. Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus
Agromyces
. The type strain with the highest pairwise similarity was
Agromyces marinus
H23-8T (97.3%). The genome of G127ATT was sequenced by a combination of Illumina and Nanopore methods and consisted of a single circular DNA molecule with a size of 3.45 Mb. The DNA G+C content was 71.3 mol%. A phylogenomic tree based on conserved single copy housekeeping genes, placed G127ATT among the ancestral species of the genus
Agromyces
, and only
Agromyces atrinae
P27T was found to diverge earlier than G127ATT. Genome distance metrics average nucleotide identity (ANI) (76–78 %) and digital DNA–DNA hybridization (dDDH) (20.2–21.5 %) of the isolate against available genomes of several type strains of species of the genus
Agromyces
indicated that G127ATT represented a previously undescribed species of the genus
Agromyces
. Morphological, physiological and biochemical characteristics, including lipid profile, cellular fatty acids and peptidoglycan type were in accordance with usual attributes of members of the genus
Agromyces
. The novel isolate could be differentiated from the most closely related species by extracellular expression of acid and alkaline phosphatases, trypsin and α-chymotrypsin, and utilization of l-arabinose and salicin as sole carbon sources. On the basis of the combined genomic and phenotypic features, isolate G127ATT (=DSM 111850T=LMG 32099T) is considered to represent a novel species of the genus
Agromyces
, for which we propose the name Agromyces archimandritae sp. nov.
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Maite Ortúzar
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Martha E. Trujillo
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
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Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaíso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005207] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alkaliphilic actinobacterium, designated VN6-2T, was isolated from marine sediment collected from Valparaíso Bay, Chile. Strain VN6-2T formed yellowish-white branched substrate mycelium without fragmentation. Aerial mycelium was well developed, forming wavy or spiral spore chains. Strain VN6-2T exhibited a 16S rRNA gene sequence similarity of 93.9 % to
Salinactinospora qingdaonensis
CXB832T, 93.7 % to
Murinocardiopsis flavida
14-Be-013T, and 93.7 % to
Lipingzhangella halophila
14-Be-013T. Genome sequencing revealed a genome size of 5.9 Mb and an in silico G+C content of 69.3 mol%. Both of the phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core gene sequences revealed that strain VN6-2T formed a distinct monophyletic clade within the family
Nocardiopsaceae
. Chemotaxonomic assessment of strain VN6-2T showed that the major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0, and the predominant respiratory quinones were MK-9, MK-9(H2) and MK-9(H4). Whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid, and ribose and xylose as the diagnostic sugars. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, aminophospholipids, glycolipid and phospholipid. Based on the results of this polyphasic study, a novel genus, Spiractinospora gen. nov., is proposed within the family
Nocardiopsaceae
and the type species Spiractinospora alimapuensis gen. nov., sp. nov. The type strain is VN6-2T (CECT 30026T, CCUG 66258T). On the basis of the phylogenetic results herein, we also propose that Nocardiopsis arvandica and Nocardiopsis litoralis are later heterotypic synonyms of
Nocardiopsis sinuspersici
and
Nocardiopsis kunsanensis
, respectively, for which emended descriptions are given.
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Riahi HS, Heidarieh P, Fatahi-Bafghi M. Genus Pseudonocardia: What we know about its biological properties, abilities and current application in biotechnology. J Appl Microbiol 2021; 132:890-906. [PMID: 34469043 DOI: 10.1111/jam.15271] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.
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Affiliation(s)
- Hanieh Sadat Riahi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Parvin Heidarieh
- Department of Bacteriology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM, Bull AT, Goodfellow M. Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock. Int J Syst Evol Microbiol 2017; 67:2980-2985. [PMID: 28820114 DOI: 10.1099/ijsem.0.002063] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eleven actinobacterial strains were isolated from a rock sample collected in the Atacama Desert. Molecular typing by BOX-PCR divided the strains into three clusters and showed that, although very similar, they were not clones. Three strains, ATK01, ATK03T and ATK17, each representing one of the defined BOX clusters, were chosen for further characterization. Phylogenetic analysis indicated that the strains were related to the genus Pseudonocardia and were recovered in a cluster together with Pseudonocardia bannensis YIM 63101T and Pseudonocardia xinjiangensis AS 4.1538T. Chemotaxonomic analyses confirmed their affiliation to the genus Pseudonocardia but differences were found between the new strains and their closest phylogenetic relatives. Physiological and fatty acid analyses also revealed differences between these strains and their phylogenetic neighbours supporting their status as a distinct species. Based on the overall data, it is proposed that strains ATK01, ATK03T and ATK17 represent a novel species of the genus Pseudonocardia for which the name Pseudonocardia nigra sp. nov. is proposed (type strain ATK03T=DSM 104088T=CECT 9183T).
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Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Hamidah Idris
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - José M Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca (CSIC), Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Mingma R, Duangmal K, Ōmura S, Takahashi Y, Matsumoto A. Three novel species of the genus Kibdelosporangium; Kibdelosporangium kanagawaense sp. nov., Kibdelosporangiumrhizosphaerae sp. nov. and Kibdelosporangium rhizovicinum sp. nov. Int J Syst Evol Microbiol 2017; 67:1758-1765. [PMID: 28598312 DOI: 10.1099/ijsem.0.001861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of three actinomycete isolates, K08-0175T, K10-0543T and K12-0791T, which were isolated from plant root and rhizospheric soil samples were subjected to a polyphasic taxonomic study. On the basis of the results of phylogenetic analysis and morphological and chemotaxonomic characteristics, these three strains were classified as representing members of the genus Kibdelosporangium. These strains were observed to produce both long chains of rod-shaped spores and sporangium-like structures with well-defined walls on aerial hyphae. Phylogenetic position, DNA-DNA hybridization and comparison of the phylogenetically closest relatives revealed that these three strains were clearly distinguishable from each other and from their closest phylogenetic relatives. Therefore, three novel species are proposed as Kibdelosporangium kanagawaense sp. nov. [type strain K08-0175T (=NBRC 112388T=TBRC 6786T)], Kibdelosporangiumrhizosphaerae sp. nov. [type strain K10-0543T (=NBRC 112389T=TBRC 6787T)] and Kibdelosporangium rhizovicinum sp. nov. [type strain K12-0791T (=NBRC 112390T=TBRC 6788T)].
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Affiliation(s)
- Ratchanee Mingma
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand.,Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yōko Takahashi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.,Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Cao YR, Yang WQ, Dao Y, Hu B, He ZK, Liang LM. Kibdelosporangium metalli sp. nov., isolated from a rare earth mine. Int J Syst Evol Microbiol 2016; 67:101-107. [PMID: 27902300 DOI: 10.1099/ijsem.0.001578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, oxidase-negative, catalase-positive isolate forming sporangium-like globular bodies, isolated from the rare earth mine of Bayan Obo in China and designated strain KC 266T, was subjected to a comprehensive taxonomic study. Comparative 16S rRNA gene sequence analysis revealed that strain KC 266T represented a novel lineage within the genus Kibdelosporangium and showed highest 16S rRNA gene similarities to Kibdelosporangiumphilippinense (98.5 %), Kibdelosporangiumaridum subsp. largum (98.2 %), Kibdelosporangiumaridum subsp. aridum (98.2 %) and Kibdelosporangiumphytohabitans (98.0 %). The DNA-DNA relatedness between strain KC 266T and the four species of the genus Kibdelosporangium was less than 60 %. The DNA G+C content of strain KC 266T was 67.9 mol%. The quinone system consisted of major amounts of MK-9(H4) and MK-9(H2), minor amounts of MK-8(H2) and traces of MK-10(H4). The diamino acid of the peptidoglycan was meso-diaminopimelic acid. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, two unknown phospholipids and one unidentified aminophospholipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1 ω6c, iso-C15 : 0 and iso-C14 : 0. Physiological traits as well as unique traits of the polar lipid profile and the fatty acid pattern distinguished strain KC 266T from the most closely related species. All these results indicate that strain KC 266T represents a novel species of the genus Kibdelosporangium, for which the name Kibdelosporangium metalli sp. nov. is proposed. The type strain is KC 266T (=KCTC 39719T=CCTCC AA 2016002T).
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Affiliation(s)
- Yan-Ru Cao
- Key laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan province, Department of Life Science and Technology, Kunming University, Kunming, Yunnan, PR China
| | - Wen-Qing Yang
- Key laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan province, Department of Life Science and Technology, Kunming University, Kunming, Yunnan, PR China
| | - Ya Dao
- Key laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan province, Department of Life Science and Technology, Kunming University, Kunming, Yunnan, PR China
| | - Bin Hu
- Key laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan province, Department of Life Science and Technology, Kunming University, Kunming, Yunnan, PR China
| | - Zhong-Kan He
- Key laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan province, Department of Life Science and Technology, Kunming University, Kunming, Yunnan, PR China
| | - Lian-Ming Liang
- State Key laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, PR China
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016; 66:2463-2466. [DOI: 10.1099/ijsem.0.001149] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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