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Kaale SE, Machangu RS, Lyimo TJ. Molecular characterization and phylogenetic diversity of actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania. Microbiol Res 2024; 278:127543. [PMID: 37950928 DOI: 10.1016/j.micres.2023.127543] [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] [Received: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023]
Abstract
Soda lakes are naturally occurring ecosystems characterized by extreme environmental conditions especially high pH and salinity levels but harboring valuable microbial communities with medical and biotechnological potentials. Lake Natron is one of the soda lakes situated in eastern branch of the East African Gregory Rift valley, Tanzania. In this study, the taxonomy and phylogenetic diversity of Actinomycetota species were explored in Lake Natron using molecular techniques. The sequencing of their 16S rRNA gene resulted into 13 genera of phylum Actinomycetota namely Streptomyces, Microbacterium, Nocardiopsis, Gordonia, Dietzia, Micromonospora, Microcella, Pseudarthrobacter, Nocardioides, Actinotalea, Cellulomonas, Isoptericola, and Glutamicibacter. We describe for the first time, the isolation of Streptomyces lasalocidi, S. harbinensis, S. anthocyanicus, Microbacterium aureliae, Pseudarthrobacter sp., Nocardioides sp. and Glutamicibacter mishrai from soda lake habitats. It also reports for the first time, the isolation of Gordonia spp., Microcella sp. and Actinotalea sp. from an East African Soda Lake as well as isolation of S. pseudogriseolus, S. calidiresistens and Micromonospora spp. from a Tanzania soda lake. Furthermore, two putative novel species of the phylum Actinomycetota were identified. Given that Actinomycetota are known potential sources of important biotechnological compounds, we recommend the broadening of the scope of bioprospection in future to include the novel species from Lake Natron.
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Affiliation(s)
- Sadikiel E Kaale
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania; Department of Biochemistry and Molecular Biology, Saint Francis University College of Health and Allied Sciences, Ifakara-Morogoro, Tanzania
| | - Robert S Machangu
- Department of Microbiology, Saint Francis University College of Health and Allied Sciences, Ifakara-Morogoro, Tanzania
| | - Thomas J Lyimo
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania.
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Molina Ayala KM, Kim SB. Description of Microcella humidisoli sp. nov. and Microcella daejeonensis sp. nov., isolated from riverside soil, reclassification of Marinisubtilis pacificus as Microcella pacifica comb. nov., and emended description of the genus Microcella. Int J Syst Evol Microbiol 2023; 73. [PMID: 37930354 DOI: 10.1099/ijsem.0.006150] [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: 11/07/2023] Open
Abstract
Three Gram-positive, aerobic and rod shaped actinobacteria, designated strains MMS21-STM10T, MMS21-STM12T and MMS21-STM26, were isolated from riverside soil and subjected to polyphasic taxonomic analysis. The strains grew optimally at mesophilic temperatures (25-30 °C) and neutral to slightly alkaline pH (7-8), and NaCl was not required for growth. Best growth was observed on nutrient agar or marine agar media. The strains contained diphosphatidylglycerol, phosphatidylglycerol and a series of unidentified phospholipids, glycolipids and aminolipids, and anteiso-C15 : 0 and iso-C16 : 0 as the main fatty acids in common. The genome sizes ranged between 2.65 and 2.78 Mbp, and the DNA G+C contents between 70.4 and 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS21-STM10T showed highest sequence similarity of 98.3 % to Microcella putealis CV-2T, and MMS21-STM12T and MMS21-STM26 of 99.2-99.3 % to Microcella flavibacter WY83T, respectively. In the whole genome-based comparison using the orthologous average nucleotide identity and digital DNA-DNA hybridization, each of strains MMS21-STM10T and MMS21-STM12T could be separated from other species of Microcella. The genome analysis also indicated that both strains contained gene clusters involved in the biosynthesis of alkylresorcinol, microansamycin and carotenoids. The phenotypic characteristics again differentiated the strains from related species, and two new species of Microcella, Microcella humidisoli sp. nov. (type strain, MMS21-STM10T=KCTC 49773T=LMG 32522T) and Microcella daejeonensis sp. nov. (type strain, MMS21-STM12T=KCTC 49750T=LMG 32523T) are proposed accordingly. It was also evident that Marinisubtilis pacificus KN1116T should be reclassified as a new species of Microcella, and Microcella pacifica comb. nov. (type strain, KN1116T=CGMCC 1.17143T=KCTC 49299T) is proposed. In addition, an emended description of Microcella is proposed based on this study.
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Affiliation(s)
- Katya Michelle Molina Ayala
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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3
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Pan YM, Ren QQ, Chen LY, Jiang YX, Wu JG, Zhang GX. Microcella aerolata sp. nov., isolated from electronic waste-associated bioaerosols. Arch Microbiol 2022; 204:538. [PMID: 35916974 DOI: 10.1007/s00203-022-03094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/02/2022]
Abstract
A Gram-positive, non-motile, non-spore-forming and short rod-shaped actinomycete strain, designated GA224T, was isolated from electronic waste-associated bioaerosols. The optimal growth conditions for this isolate, a facultatively anaerobic bacterium, were 37 °C and pH 8.0. The cell-wall peptidoglycan type was B2γ, with 2,4-diaminobutyric acid (DAB) as the diamino acids, while the major menaquinone was MK-12. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and an unidentified lipid. The major cellular fatty acids were anteiso-C15:0 and iso-C16:0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GA224T fell within the genus Microcella. The draft genome of strain GA224T comprised 2,495,189 bp with a G + C content of 72.2 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain GA224T and the type strain of the type species of Microcella species were lower than 95% and 70%, respectively. Based on the phenotypic, chemotaxonomic and genomic data, strain GA224T represents a novel species, for which the name Microcella aerolata sp. nov. is proposed, with GA224T as the type strain (= GDMCC 1.2165 T = JCM 34462 T).
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Affiliation(s)
- Yi-Min Pan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Qiao-Qiao Ren
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China.,Sichuan Provincial Center for Disease Control and Prevention, No. 6, Zhongxue Road, Wuhou District, Chengdu, 610041, People's Republic of China
| | - Ling-Yun Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Yun-Xia Jiang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ji-Guo Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Guo-Xia Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China. .,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, 510006, People's Republic of China.
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Xie F, Pei S, Huang X, Wang L, Kou J, Zhang G. Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov. Antonie van Leeuwenhoek 2021; 114:2133-2145. [PMID: 34628559 DOI: 10.1007/s10482-021-01668-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
A novel Gram-staining positive, aerobic, rod-shaped, non-motile and yellow-pigmented actinobacterium, designated strain WY83T, was isolated from a marine sediment of Indian Ocean. Strain WY83T grew optimally at 30-35 °C, pH 7-8 and with 0-3% (w/v) NaCl. The predominant menaquinones were MK-10, MK-11 and MK-12, and the major fatty acids were C19:1 ω9c/C19:1 ω11c, anteiso-C15:0, C17:0 3OH, and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The cell-wall peptidoglycan contained lysine as a diamino acid. The DNA G + C content was 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and ninety-two bacterial core genes indicated that strain WY83T formed an evolutionary lineage with Chryseoglobus frigidaquae JCM 14730T, Chryseoglobus indicus CTD02-10-2T, Yonghaparkia alkaliphila JCM 15138T, Microcella alkaliphila DSM 18851T and Microcella putealis DSM 19627T within the radiation enclosing members of the family Microbacteriaceae. All pairwise percentage of conserved proteins between strain WY83T and the closely related phylogenetic neighbors were greater than 65%. The average nucleotide identity and in silico DNA-DNA hybridization values were both below the thresholds used for the delineation of a new species. On the basis of the evidence presented, strains WY83T, Y. alkaliphila JCM 15138T, C. frigidaquae JCM 14730T, M. alkaliphila DSM 18851T and M. putealis DSM 19627T should belong to different species of the same genus. Strain WY83T represents a novel species of the genus Microcella, for which the name Microcella flavibacter sp. nov. is proposed. The type strain is WY83T (= KCTC 39637T = MCCC 1A07099T). Furthermore, Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila were reclassified as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov., respectively.
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Affiliation(s)
- Fuquan Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Shengxiang Pei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Xiaoyun Huang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Lina Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Jinyan Kou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China
| | - Gaiyun Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, People's Republic of China.
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Hahn MW, Pitt A, Koll U, Schmidt J, Maresca JA, Neumann-Schaal M. Aurantimicrobium photophilum sp. nov., a non-photosynthetic bacterium adjusting its metabolism to the diurnal light cycle and reclassification of Cryobacterium mesophilum as Terrimesophilobacter mesophilus gen. nov., comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34431766 DOI: 10.1099/ijsem.0.004975] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aerobic primarily chemoorganotrophic actinobacterial strain MWH-Mo1T was isolated from a freshwater lake and is characterized by small cell lengths of less than 1 µm, small cell volumes of 0.05-0.06 µm3 (ultramicrobacterium), a small genome size of 1.75 Mbp and, at least for an actinobacterium, a low DNA G+C content of 54.6 mol%. Phylogenetic analyses based on concatenated amino acid sequences of 116 housekeeping genes suggested the type strain of Aurantimicrobium minutum affiliated with the family Microbacteriaceae as its closest described relative. Strain MWH-Mo1T shares with the type strain of that species a 16S rRNA gene sequence similarity of 99.6 % but the genomes of the two strains share an average nucleotide identity of only 79.3 %. Strain MWH-Mo1T is in many genomic, phenotypic and chemotaxonomic characteristics quite similar to the type strain of A. minutum. Previous intensive investigations revealed two unusual traits of strain MWH-Mo1T. Although the strain is not known to be phototrophic, the metabolism is adjusted to the diurnal light cycle by up- and down-regulation of genes in light and darkness. This results in faster growth in the presence of light. Additionally, a cell size-independent protection against predation by bacterivorous flagellates, most likely mediated by a proteinaceous cell surface structure, was demonstrated. For the previously intensively investigated aerobic chemoorganotrophic actinobacterial strain MWH-Mo1T (=CCUG 56426T=DSM 107758T), the establishment of the new species Aurantimicrobium photophilum sp. nov. is proposed.
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Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Salzburg, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Julia A Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Meina Neumann-Schaal
- Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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6
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A rapid and efficient method for the extraction and identification of menaquinones from Actinomycetes in wet biomass. BMC Microbiol 2021; 21:175. [PMID: 34103006 PMCID: PMC8188722 DOI: 10.1186/s12866-021-02240-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Menaquinones are constituents of prokaryote cell membranes where they play important functions during electron transport. Menaquinone profiles are strongly recommended for species classification when proposing a new Actinomycetes taxon. Presently, the most widely used methods to determine menaquinones are based on freeze-dried cells. Taxonomic research in our lab has revealed that menaquinone concentrations are low for some species of the genus Microbacterium, leading to difficulties in identifying menaquinones. Results Menaquinones extracted using the novel lysozyme-chloroform-methanol (LCM) method were comparable in quality to those obtained using the Collins method, the most widely used method. All tested strains extracted via the LCM method showed higher concentrations of menaquinones than those extracted via the Collins method. For some Microbacterium strains, the LCM method exhibited higher sensitivity than the Collins method, and more trace menaquinones were detected with the LCM method than the Collins method. In addition, LCM method is faster than the Collins method because it uses wet cells. Conclusion The LCM method is a simple, rapid and efficient technique for the extraction and identification of menaquinones from Actinomycetes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02240-z.
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Qin F, He WX, Zhang DC. Marinisubtilis pacificus gen. nov., sp. nov., a Member of the Family Microbacteriaceae Isolated From a Deep-Sea Seamount. Curr Microbiol 2021; 78:2136-2142. [PMID: 33811267 DOI: 10.1007/s00284-021-02468-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/16/2021] [Indexed: 11/30/2022]
Abstract
A Gram-stain-positive, yellow, aerobic, slender rod-shaped bacterial strain, designated KN1116T, was isolated from a deep-sea seamount. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain KN1116T was related to the genus Chryseoglobus and had highest 16S rRNA gene sequence identity with Chryseoglobus frigidaquae CW1T (98.5%). The predominant cellular fatty acids were anteiso-C15:0 and iso-C16:0. The quinone system for strain KN1116T comprised menaquinone MK-12, MK-11, MK-10 and MK-13. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, six unknown glycolipids, two unidentified phospholipids and one unknown polar lipid. The cell-wall peptidoglycan of strain KN1116T was of the type B1β, containing 2,4-diaminobutyric acid as the diamino acid. Genome sequencing revealed the strain KN1116T has a genome size of 2.7 Mbp and a G+C content of 69.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strain KN1116T represents a novel species of a novel genus of the family Microbacteriaceae, for which the name Marinisubtilis pacificus gen. nov., sp. nov. is proposed. The type strain of Marinisubtilis pacificus is KN1116T (=CGMCC 1.17143T =KCTC 49299T).
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Affiliation(s)
- Fang Qin
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Xuan He
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Chao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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Sheu SY, Liu LP, Chen WM. Puzihella rosea gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from freshwater. Int J Syst Evol Microbiol 2017; 67:2383-2389. [PMID: 28714844 DOI: 10.1099/ijsem.0.001967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, aerobic, pink, curved, rod-shaped, non-motile bacterial strains, designated MI-28T and SKY-11, were isolated from freshwater samples taken from a river and fish pond, respectively. Based on characterization using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic profiles. They demonstrated 99.9 % 16S rRNA gene sequence similarity and a 93-95 % DNA-DNA relatedness value, suggesting that they represent a single genomic species. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strains MI-28T and SKY-11 form a distinct lineage with respect to closely related genera within the family Microbacteriaceae of the class Actinobacteria, which is most closely related to Rhodoluna and Pontimonas, and levels of 16S rRNA gene sequence similarity with the type species of related genera were less than 95 %. Cell-wall analysis showed that the peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized glycolipid and an uncharacterized aminophospholipid. The major polyamine was putrescine. The major isoprenoid quinone was MK-10. The G+C content of DNA was between 62.6 and 62.9 mol%. On the basis of the genotypic and phenotypic data, strains MI-28T and SKY-11 represent a novel genus and species of the family Microbacteriaceae, for which the name Puzihella rosea gen. nov., sp. nov. is proposed. The type strain of the type species is MI-28T (=BCRC 80688T=LMG 27848T=KCTC 29239T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Li-Ping Liu
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Zhang L, Chen XL, Hu Q, Ruan ZP, Chen K, Li SP, Jiang JD. Huakuichenia soli gen. nov., sp. nov., a new member of the family Microbacteriaceae, isolated from contaminated soil. Int J Syst Evol Microbiol 2016; 66:5399-5405. [DOI: 10.1099/ijsem.0.001531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Xiao-Long Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Qiang Hu
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Zhe-Pu Ruan
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Kai Chen
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Shun-Peng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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11
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Jang YH, Kim SJ, Tamura T, Hamada M, Weon HY, Suzuki KI, Kwon SW, Kim WG. Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of
Leifsonia kribbensis
Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov. Int J Syst Evol Microbiol 2013; 63:1403-1410. [DOI: 10.1099/ijs.0.042945-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family
Microbacteriaceae
. The nearest phylogenetic neighbour was
Leifsonia kribbensis
MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and
Leifsonia kribbensis
MSL-13T formed a distinct cluster within the family
Microbacteriaceae
. Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that
Leifsonia kribbensis
be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).
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Affiliation(s)
- Yun-Hee Jang
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Wan-Gyu Kim
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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Jang GI, Cho Y, Cho BC. Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern. Int J Syst Evol Microbiol 2012; 63:2124-2131. [PMID: 23104361 DOI: 10.1099/ijs.0.043661-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, non-motile, strictly aerobic, non-spore-forming, vibrio-shaped bacterial strain, CL-TW6(T), was isolated from a reservoir seawater sample from a solar saltern in Korea. Analysis of the 16S rRNA gene sequence of strain CL-TW6(T) revealed a clear affiliation with the family Microbacteriaceae. Strain CL-TW6(T) showed the closest phylogenetic relationships with the genera Yonghaparkia and Microcella, with 16S rRNA gene sequence similarity of 94.8-95.3%. The strain grew in the presence of 1-9% sea salts, at 15-35 °C and at pH 7.0-9.0. The major cellular fatty acids of strain CL-TW6(T) were anteiso-C15:0 (32.6%), iso-C16:0 (20.4%), iso-C15:0 (13.2%) and iso-C14:0 (11.8%) and the major menaquinones were MK-9 and MK-10. Cell-wall analysis showed that the peptidoglycan of strain CL-TW6(T) contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain CL-TW6(T) was 60.0 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed clearly that strain CL-TW6(T) could be distinguished from members of the family Microbacteriaceae with validly published names. Thus, strain CL-TW6(T) should be classified as representing a novel genus and species in the family Microbacteriaceae, for which the name Pontimonas salivibrio gen. nov., sp. nov. is proposed. The type strain of Pontimonas salivibrio is CL-TW6(T) (=KCCM 90105(T) =JCM 18206(T)).
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Affiliation(s)
- Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Yirang Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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13
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Kim SJ, Tamura T, Hamada M, Ahn JH, Weon HY, Park IC, Suzuki KI, Kwon SW. Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost. Int J Syst Evol Microbiol 2012; 62:2410-2416. [DOI: 10.1099/ijs.0.036343-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, non-motile, short rod, designated SMC46T, was isolated from a spent mushroom compost sample collected in the Suwon region, South Korea. 16S rRNA gene sequence analysis revealed that strain SMC46T was a member of the family
Microbacteriaceae
; however, the isolate formed a branch separate from other genera within the family. Sequence similarity between strain SMC46T and other members of the family
Microbacteriaceae
was ≤97 %, the highest sequence similarity being with
Frigoribacterium faeni
801T and
Frondihabitans australicus
E1HC-02T (both 97.0 %). Some chemotaxonomic properties of strain SMC46T were consistent with those of the family
Microbacteriaceae
: MK-11 and MK-12 as the predominant menaquinones, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid as the polar lipids. However, strain SMC46T contained a B-type peptidoglycan not previously found in the family
Microbacteriaceae
. The DNA G+C content was 68 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain SMC46T was considered to represent a novel genus and species in the family
Microbacteriaceae
, for which the name Compostimonas suwonensis gen. nov., sp. nov. is proposed. The type strain of the type species is SMC46T ( = KACC 13354T = NBRC 106304T).
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Affiliation(s)
- Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Jae-Hyung Ahn
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - In-Cheol Park
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
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14
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Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Weon HY, Suzuki KI, Kwon SW. Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 2012; 50:673-9. [DOI: 10.1007/s12275-012-2096-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/23/2012] [Indexed: 11/24/2022]
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15
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The Extraction and Identification of Respiratory Lipoquinones of Prokaryotes and Their Use in Taxonomy. J Microbiol Methods 2011. [DOI: 10.1016/b978-0-12-387730-7.00009-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Li HR, Yu Y, Luo W, Zeng YX. Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic. Int J Syst Evol Microbiol 2010; 60:2535-2539. [DOI: 10.1099/ijs.0.018754-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain ZS314T was isolated from a sandy intertidal sediment sample collected from the coastal area off the Chinese Antarctic Zhongshan Station, east Antarctica (6 ° 22′ 13″ S 7 ° 21′ 41″ E). The cells were Gram-positive, motile, short rods. The temperature range for growth was 0–26 °C and the pH for growth ranged from 5 to 10, with optimum growth occurring within the temperature range 18–23 °C and pH range 6.0–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl, with optimum growth occurring in the presence of 2–4 % (w/v) NaCl. Strain ZS314T had MK-10 as the major menaquinone and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids. The cell-wall peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content was approximately 67 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain ZS314T represents a new lineage in the family Microbacteriaceae. On the basis of the phylogenetic analyses and phenotypic characteristics, a new genus, namely Marisediminicola gen. nov., is proposed, harbouring the novel species Marisediminicola antarctica sp. nov. with the type strain ZS314T (=DSM 22350T =CCTCC AB 209077T).
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Affiliation(s)
- Hui-Rong Li
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Wei Luo
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Yin-Xin Zeng
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
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17
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Behrendt U, Schumann P, Hamada M, Suzuki KI, Spröer C, Ulrich A. Reclassification of Leifsonia ginsengi (Qiu et al. 2007) as Herbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiux solani sp. nov., an actinobacterium associated with the phyllosphere of Solanum tuberosum L. Int J Syst Evol Microbiol 2010; 61:1039-1047. [PMID: 20511458 DOI: 10.1099/ijs.0.021352-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the context of studying the effects of transgenic fructan-producing potatoes on the community structure of phyllosphere bacteria, a group of strains closely related to the species Leifsonia ginsengi was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the new isolates and L. ginsengi DSM 19088(T) formed a lineage at the genus level and this finding was supported by chemotaxonomic characterization. The peptidoglycan type of the representative isolate, K134/01(T), and L. ginsengi DSM 19088(T) was B2γ, with d- and l-diaminobutyric acid as the diagnostic diamino acid and glycine, alanine and threo-3-hydroxyglutamic acid. The almost-complete substitution of glutamic acid by threo-3-hydroxyglutamic acid supported the differentiation of the new strains from recognized species of the genus Leifsonia. Furthermore, the detection of substantial amounts of the fatty acid cyclohexyl-C(17 : 0) in the new isolates and L. ginsengi DSM 19088(T) was a prominent chemotaxonomic feature for a clear demarcation of these strains from all genera of the family Microbacteriaceae that display the B2γ cell-wall type. Comparative phylogenetic and phenotypic analyses of the isolates and L. ginsengi DSM 19088(T) revealed the separate species status of the isolates. On the basis of these results, it is proposed that L. ginsengi should be classified as the type species of a novel genus, Herbiconiux gen. nov., with the name Herbiconiux ginsengi gen. nov., comb. nov. (type strain wged11(T) = CGMCC 4.3491(T) = JCM 13908(T) = DSM 19088(T) = NBRC 104580(T)). The phyllosphere isolates are assigned to a novel species, Herbiconiux solani sp. nov. (type strain K134/01(T) = DSM 19813(T) = LMG 24387(T) = NBRC 106740(T)).
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Affiliation(s)
- Undine Behrendt
- Leibniz-Centre for Agricultural Landscape Research (ZALF), Institute of Landscape Matter Dynamics, Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Peter Schumann
- DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Ken-Ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Cathrin Spröer
- DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Andreas Ulrich
- Leibniz-Centre for Agricultural Landscape Research (ZALF), Institute of Landscape Matter Dynamics, Eberswalder Str. 84, D-15374 Müncheberg, Germany
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18
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Pires C, Carvalho MF, De Marco P, Magan N, Castro PML. Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. Int J Syst Evol Microbiol 2010; 60:402-407. [DOI: 10.1099/ijs.0.010348-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-staining-negative bacterial strains, designated 3A10T and ECP37T, were isolated from sediment samples collected from an industrially contaminated site in northern Portugal. These two organisms were rod-shaped, non-motile, aerobic, catalase- and oxidase-positive and formed yellow colonies. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1
ω9c and iso-C17 : 0 3-OH. The G+C content of the DNA of strains 3A10T and ECP37T was 43 and 34 mol%, respectively. The major isoprenoid quinone of the two strains was MK-6. 16S rRNA gene sequence analysis revealed that strains 3A10T and ECP37T were members of the family Flavobacteriaceae and were related phylogenetically to the genus Chryseobacterium. Strain 3A10T showed 16S rRNA gene sequence similarity values of 97.2 and 96.6 % to the type strains of Chryseobacterium antarcticum and Chryseobacterium jeonii, respectively; strain ECP37T showed 97.3 % similarity to the type strain of Chryseobacterium marinum. DNA–DNA hybridization experiments revealed levels of genomic relatedness of <70 % between strains 3A10T and ECP37T and between these two strains and the type strains of C. marinum, C. antarcticum and C. jeonii, justifying their classification as representing two novel species of the genus Chryseobacterium. The names proposed for these organisms are Chryseobacterium palustre sp. nov. (type strain 3A10T =LMG 24685T =NBRC 104928T) and Chryseobacterium humi sp. nov. (type strain ECP37T =LMG 24684T =NBRC 104927T).
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Affiliation(s)
- Carlos Pires
- Cranfield Health, Cranfield University, Building 52A, Cranfield, Bedford MK43 0AL, UK
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Maria F. Carvalho
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Paolo De Marco
- CICS – Centro de Investigação em Ciências da Saúde, Institudo Superior de Ciências da Saúde – Norte, CESPU, 4585-116 Gandra PRD, Portugal
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Naresh Magan
- Cranfield Health, Cranfield University, Building 52A, Cranfield, Bedford MK43 0AL, UK
| | - Paula M. L. Castro
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Dr António Bernardino de Almeida, 4200-072 Porto, Portugal
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19
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Baik KS, Park SC, Kim HJ, Lee KH, Seong CN. Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae. Int J Syst Evol Microbiol 2009; 60:1311-1316. [PMID: 19667371 DOI: 10.1099/ijs.0.016212-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A motile, rod-shaped, yellow-pigmented bacterium, designated strain CW1(T), was isolated from a water-cooling system in the Republic of Korea. Cells were Gram-stain-positive, aerobic, catalase-positive and oxidase-negative. Strain CW1(T) formed slender rods with unusual bulbous protuberances. The major fatty acids were iso-C(16 : 1) (33.7 %), anteiso-C(15 : 0) (27.2 %), iso-C(14 : 0) (13.3 %) and C(16 : 0) (10.8 %). The cell-wall peptidoglycan was of type B2beta, containing lysine as the diamino acid. The respiratory quinones were menaquinones with 12, 13 and 14 isoprene units. A phylogenetic tree based on 16S rRNA gene sequences showed that strain CW1(T) formed an evolutionary lineage within the radiation enclosing members of the family Microbacteriaceae and was related to, but distant from, members of the genera Microcella and Yonghaparkia. On the basis of the evidence presented, strain CW1(T) is considered to represent a novel species of a new genus in the family Microbacteriaceae, for which the name Chryseoglobus frigidaquae gen. nov., sp. nov. is proposed. The type strain of Chryseoglobus frigidaquae is CW1(T) (=KCTC 13142(T) =JCM 14730(T)).
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Affiliation(s)
- Keun Sik Baik
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Seong Chan Park
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Ho Jun Kim
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Kang Hyun Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 52 Oun-dong, Yuseong, Daejeon 305-333, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
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20
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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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21
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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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22
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Greene AC, Euzeby JP, Tindall BJ, Patel BKC. Proposal of Frondihabitans gen. nov. to replace the illegitimate genus name Frondicola Zhang et al. 2007. Int J Syst Evol Microbiol 2009; 59:447-8. [DOI: 10.1099/ijs.0.010934-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Bora N, Vancanneyt M, Gelsomino R, Snauwaert C, Swings J, Jones AL, Ward AC, Chamba JF, Kroppenstedt RM, Schumann P, Goodfellow M. Mycetocola reblochoni sp. nov., isolated from the surface microbial flora of Reblochon cheese. Int J Syst Evol Microbiol 2008; 58:2687-93. [DOI: 10.1099/ijs.0.64201-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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24
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Cook DM, Henriksen ED, Rogers TE, Peterson JD. Klugiella xanthotipulae gen. nov., sp. nov., a novel member of the family Microbacteriaceae. Int J Syst Evol Microbiol 2008; 58:2779-82. [DOI: 10.1099/ijs.0.65748-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Lee DW, Lee JM, Seo JP, Schumann P, Kim SJ, Lee SD. Phycicola gilvus gen. nov., sp. nov., an actinobacterium isolated from living seaweed. Int J Syst Evol Microbiol 2008; 58:1318-23. [DOI: 10.1099/ijs.0.65283-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Matsumoto A, Yamada M, Omura S, Takahashi Y. Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae. Int J Syst Evol Microbiol 2008; 58:1019-23. [DOI: 10.1099/ijs.0.65070-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Lee SD. Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae. Int J Syst Evol Microbiol 2007; 57:2498-2502. [DOI: 10.1099/ijs.0.64591-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, non-motile, non-mycelium-forming, rod-shaped actinomycete, designated KSW2-17T, was isolated from dried seaweed collected from beach sand along the coast of Jeju, Republic of Korea. The organism had ornithine as the diagnostic cell-wall diamino acid, MK-10 and MK-11 as the major menaquinones, and phosphatidylglycerol and diphosphatidylglycerol as polar lipids. The fatty acid profile included predominantly iso- and anteiso-branched acids and a minor amount of tuberculostearic acid (10-methyl C18 : 0). The DNA G+C content was 68.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the seaweed isolate formed a distinct clade within the radiation of the family Microbacteriaceae and had highest sequence similarity (96.1–96.3 %) to members of the genera Cryobacterium, Frigoribacterium and Rathayibacter. On the basis of phenotypic and genotypic evidence, strain KSW2-17T is considered to represent a novel species of a new genus, for which the name Labedella gwakjiensis gen. nov., sp. nov. is proposed. The type strain is KSW2-17T (=JCM 14008T=KCTC 19176T).
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Affiliation(s)
- Soon Dong Lee
- Department of Science Education, Cheju National University, Jeju 690-756, Republic of Korea
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28
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Tiago I, Pires C, Mendes V, Morais PV, da Costa MS, Veríssimo A. Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater. Int J Syst Evol Microbiol 2006; 56:2571-2574. [PMID: 17082392 DOI: 10.1099/ijs.0.64281-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A low-G+C-content Gram-positive bacterium, designated CV53T, phylogenetically related to species of the genus Bacillus, was isolated from a highly alkaline non-saline groundwater environment (pH 11.4). This organism comprised rod-shaped cells, was aerobic, did not display spore formation, was catalase- and oxidase-negative, had an optimum growth temperature of 40 °C and had an optimum pH of approximately 7.0–8.5. Optimal growth was observed in the absence of NaCl, but growth did occur at NaCl concentrations up to 3.0 %. The strain possessed an A1γ-type peptidoglycan cell wall and the major respiratory quinone was MK-7. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The G+C content of the DNA was 43.1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that the novel isolate is closely related to the type strain of Bacillus jeotgali, forming a coherent cluster supported by bootstrap analysis at a confidence level of 90 %. The pairwise similarity of the 16S rRNA gene sequences of the two strains is 97.7 %. On the basis of the phylogenetic analyses and the distinct phenotypic characteristics, strain CV53T represents a novel species within the genus Bacillus, for which we propose the name Bacillus foraminis sp. nov. The type strain is CV53T (=LMG 23174T=CIP 108889T).
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Affiliation(s)
- Igor Tiago
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Carlos Pires
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Vítor Mendes
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Paula V Morais
- Instituto do Ambiente e Vida, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Bioquímica, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Milton S da Costa
- Departamento de Bioquímica, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - António Veríssimo
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
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Nunes I, Tiago I, Pires AL, da Costa MS, Veríssimo A. Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil. Int J Syst Evol Microbiol 2006; 56:1841-1845. [PMID: 16902018 DOI: 10.1099/ijs.0.64261-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive bacterium, designated B22(T), was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 degrees C and pH 8.0-8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0-8 % NaCl. The cell wall peptidoglycan is of the A4alpha type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22(T) formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22(T) exhibited 16S rRNA gene pairwise sequence similarity values of 94.7-94.3 % with members of the genus Salinibacillus, 95.1-92.8 % with members of the genus Virgibacillus, 94.7-93.2 % with members of the genus Oceanobacillus and 93.1-92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22(T) represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22(T) (=LMG 23148(T)=CIP 108857(T)) is the type strain of Paucisalibacillus globulus.
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Affiliation(s)
- Inês Nunes
- Departamento de Zoologia and Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Igor Tiago
- Departamento de Zoologia and Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Ana Luísa Pires
- Departamento de Zoologia and Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Milton S da Costa
- Departamento de Bioquímica and Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - António Veríssimo
- Departamento de Zoologia and Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
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Yoon JH, Kang SJ, Schumann P, Oh TK. Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil. Int J Syst Evol Microbiol 2006; 56:2415-2420. [PMID: 17012572 DOI: 10.1099/ijs.0.64258-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-positive, non-motile, non-spore-forming and rod-shaped actinomycete strains, KSL-113T and KSL-133, were isolated from an alkaline soil in Korea, and their taxonomic positions were investigated by using a polyphasic approach. The strains grew optimally at 30 °C and pH 9.0. Phenotypic, phylogenetic and genetic similarities indicated that strains KSL-113T and KSL-133 represent the same species. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KSL-113T and KSL-133 fell within the family Microbacteriaceae of the suborder Micrococcineae, the highest 16S rRNA gene sequence similarity values (98.2 %) being obtained with respect to Microcella putealis CV-2T. The 16S rRNA gene sequence similarities between strains KSL-113T and KSL-133 and the other members of the family Microbacteriaceae used in the phylogenetic analysis were less than 96.0 %. Strains KSL-113T and KSL-133 could be clearly distinguished from members of the family Microbacteriaceae on the basis of differences in chemotaxonomic properties, including the predominant menaquinone type, the cell-wall peptidoglycan type and the fatty acid profile. Accordingly, on the basis of the combined phenotypic, chemotaxonomic and phylogenetic data, strains KSL-113T and KSL-133 constitute a novel genus and species of the family Microbacteriaceae, for which the name Yonghaparkia alkaliphila gen. nov., sp. nov. is proposed. The type strain of Yonghaparkia alkaliphila is KSL-113T (=KCTC 19126T=CIP 108920T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Tiago I, Morais PV, da Costa MS, Veríssimo A. Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella. Int J Syst Evol Microbiol 2006; 56:2313-2316. [PMID: 17012553 DOI: 10.1099/ijs.0.64320-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A high-G+C-content Gram-positive bacterium, designated as strain AC4rT, was isolated from a highly alkaline, non-saline groundwater environment (pH 11.4). This organism formed small rod-shaped cells, was aerobic, heterotrophic, catalase-positive and oxidase-negative and had an optimum growth temperature of 35 °C and an optimum pH of 9.5. The strain possessed a B2β-type cell-wall peptidoglycan, with d-Orn as the diagnostic diamino acid. The major respiratory quinones were unsaturated menaquinones with 13 and 14 isoprene units. The predominant fatty acids were anteiso-15 : 0, iso-16 : 0, iso-14 : 0 and iso-15 : 0. The G+C content of the DNA was 67.1 mol%. In a 16S rRNA gene sequence analysis, strain AC4rT showed the highest level of similarity (99.2 %) to the type strain of Microcella putealis; however, the DNA–DNA reassociation value between these two organisms was low (38.3 %). On the basis of phylogenetic analysis, the DNA–DNA reassociation value and distinct phenotypic characteristics, strain AC4rT represents a novel species within the genus Microcella, for which the name Microcella alkaliphila sp. nov. is proposed. The type strain is AC4rT (=LMG 22690T=CIP 108473T).
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Affiliation(s)
- Igor Tiago
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Paula V Morais
- Instituto do Ambiente e Vida, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Bioquímica, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Milton S da Costa
- Departamento de Bioquímica, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - António Veríssimo
- Centro de Neurociências de Biologia Celular, Universidade de Coimbra, 3004-517 Coimbra, Portugal
- Departamento de Zoologia, Universidade de Coimbra, 3004-517 Coimbra, Portugal
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2005; 55:1743-1745. [PMID: 16166658 DOI: 10.1099/ijs.0.63996-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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