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Rey-Velasco X, Lucena T, Belda A, Gasol JM, Sánchez O, Arahal DR, Pujalte MJ. Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean. Front Microbiol 2024; 15:1407904. [PMID: 38863746 PMCID: PMC11165706 DOI: 10.3389/fmicb.2024.1407904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.
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Affiliation(s)
| | - Teresa Lucena
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Ana Belda
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - María J. Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
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Brady C, Crampton B, Kaur S, Maddock D, Kile H, Arnold D, Denman S. Two novel Raoultella species associated with bleeding cankers of broadleaf hosts, Raoultella scottia sp. nov. and Raoultella lignicola sp. nov. Front Microbiol 2024; 15:1386923. [PMID: 38756725 PMCID: PMC11096500 DOI: 10.3389/fmicb.2024.1386923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Seventeen Gram-negative, facultatively anaerobic bacterial strains were isolated from bleeding cankers of various broadleaf hosts and oak rhizosphere soil in Great Britain. The strains were tentatively identified as belonging to the genus Raoultella based on 16S rRNA gene sequencing. Multilocus sequence analysis (MLSA), based on four protein-encoding genes (fusA, leuS, pyrG, and rpoB), separated the strains into three clusters within the Raoultella genus clade. The majority of strains clustered with the type strain of Raoultella terrigena, with the remaining strains divided into two clusters with no known type strain. Whole genome sequencing comparisons confirmed these two clusters of strains as belonging to two novel Raoultella species which can be differentiated phenotypically from their current closest phylogenetic relatives. Therefore, two novel species are proposed: Raoultella scottia sp. nov. (type strain = BAC 10a-01-01T = LMG 33072T = CCUG 77096T) and Raoultella lignicola sp. nov. (type strain = TW_WC1a.1T = LMG 33073T = CCUG 77094T).
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Affiliation(s)
- Carrie Brady
- Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Bridget Crampton
- Centre for Forest Protection, Forest Research, Farnham, United Kingdom
| | - Sundeep Kaur
- Centre for Forest Protection, Forest Research, Farnham, United Kingdom
| | - Daniel Maddock
- Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Helene Kile
- Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Dawn Arnold
- Harper Adams University, Newport, United Kingdom
| | - Sandra Denman
- Centre for Forest Protection, Forest Research, Farnham, United Kingdom
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Shi C, He M, Xue Q, Wang C, Liu A. Parasedimentitalea denitrificans sp. nov., a novel denitrifying bacteria isolated from the Yellow Sea and transfer of Zongyanglinia huanghaiensis and Zongyanglinia marina to the genus Parasedimentitalea as Parasedimentitalea huanghaiensis comb. nov. and Parasedimentitalea maritima nom. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38728208 DOI: 10.1099/ijsem.0.006377] [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: 05/12/2024] Open
Abstract
A Gram-stain-negative and rod-shaped bacterium, designated strain CY04T, was isolated from a sediment sample collected from the Yellow Sea. CY04T exhibited the highest 16S rRNA gene sequence similarity of 98.7 % to Zongyanglinia huanghaiensis CY05T, followed by the similarities of 98.6 %, 98.0 and 98.0 % to Zongyanglinia marina DSW4-44T, Parasedimentitalea marina W43T and Parasedimentitalea psychrophila QS115T respectively. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on genome sequences revealed that CY04T formed a robust cluster with Z. huanghaiensis CY05T, Z. marina DSW4-44T, P. marina W43T and P. psychrophila QS115T. Calculated digital DNA-DNA hybridisation and average nucleotide identity values between CY04T and its closely related species were 22.2-23.7 % and 79.0-81.2 % respectively. Cells of CY04T were strictly aerobic, non-motile and positive for catalase, oxidase and denitrification. CY04T harboured a set of genes encoding the enzymes involved in denitrification. Growth occurred at 10-30 °C (optimum, 20 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 1-6 % (w/v) (optimum, 2.5 %,) NaCl. The major component of the fatty acids was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The isoprenoid quinone was Q-10. Results of the phenotypic, chemotaxonomic and molecular study indicate that strain CY04T represents a novel species of the genus Parasedimentitalea, for which the name Parasedimentitalea denitrificans sp. nov. is proposed. The type strain is CY04T (=MCCC 1K08635T=KCTC 62199T). It is also proposed that Zongyanglinia huanghaiensis and Zongyanglinia marina should be reclassified as Parasedimentitalea huanghaiensis comb. nov. and Parasedimentitalea maritima nom. nov. An emended description of the genus Parasedimentitalea is also proposed.
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Affiliation(s)
- Caixing Shi
- College of Basic Medicine, Jining Medical University, Jining 272067, Shandong, PR China
- Jining Key Laboratory of Pharmacology, Jining Medical University, Jining 272067, Shandong, PR China
| | - Mengdan He
- College of Basic Medicine, Jining Medical University, Jining 272067, Shandong, PR China
- College of Basic Medicine, Weifang Medical University, Weifang 261042, Shandong, PR China
| | - Qingjie Xue
- College of Basic Medicine, Jining Medical University, Jining 272067, Shandong, PR China
| | - Chuangong Wang
- College of Basic Medicine, Jining Medical University, Jining 272067, Shandong, PR China
- Jining Key Laboratory of Pharmacology, Jining Medical University, Jining 272067, Shandong, PR China
| | - Ang Liu
- College of Basic Medicine, Jining Medical University, Jining 272067, Shandong, PR China
- Jining Key Laboratory of Pharmacology, Jining Medical University, Jining 272067, Shandong, PR China
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Jiang Z, Li X, Liang Z, Tan Z, Zhou N, Liu Y, Liu Z, Yin H, Luo K, Ingsriswang S, Liu S, Jiang C. Fodinisporobacter ferrooxydans gen. nov., sp. nov.-A Spore-Forming Ferrous-Oxidizing Bacterium Isolated from a Polymetallic Mine. Microorganisms 2024; 12:853. [PMID: 38792683 PMCID: PMC11123200 DOI: 10.3390/microorganisms12050853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/26/2024] Open
Abstract
A novel acidophilic, aerobic bacterium strain, MYW30-H2T, was isolated from a heap of polymetallic mine. Cells of strain MYW30-H2T were Gram-stain-positive, endospore-forming, motile, and rod-shaped. Strain MYW30-H2T grew at a temperature range of 30-45 °C (optimum 40 °C) and a pH range of 3.5-6.0 (optimum 4.0) in the presence of 0-0.5% (w/v) NaCl. Strain MYW30-H2T could grow heterotrophically on yeast extract and glucose, and grow mixotrophically using ferrous iron as an electron donor with yeast extract. Menaquinone-7 (MK-7) was the sole respiratory quinone of the strain. Iso-C15:0 and anteiso-C15:0 were the major cellular fatty acids. The 16S rRNA gene sequence analysis showed that MYW30-H2T was phylogenetically affiliated with the family Alicyclobacillaceae, and the sequence similarity with other Alicyclobacillaceae genera species was below 91.51%. The average amino acid identity value of the strain with its phylogenetically related species was 52.3-62.1%, which fell into the genus boundary range. The DNA G+C content of the strain was 44.2%. Based on physiological and phylogenetic analyses, strain MYW30-H2T represents a novel species of a new genus of the family Alicyclobacillaceae, for which the name Fodinisporobacter ferrooxydans gen. nov., sp. nov. is proposed. The type strain is MYW30-H2T (=CGMCC 1.17422T = KCTC 43278T).
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Affiliation(s)
- Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zonglin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zebao Tan
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenghua Liu
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Huaqun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Kun Luo
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Supawadee Ingsriswang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Xu X, He M, Xue Q, Li X, Liu A. Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation. BMC Genomics 2024; 25:389. [PMID: 38649849 PMCID: PMC11034169 DOI: 10.1186/s12864-024-10269-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation. RESULTS This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy. CONCLUSIONS Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.
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Affiliation(s)
- Xiaokun Xu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Mengdan He
- School of Basic Medical Sciences, Shandong Second Medical University, 261042, Weifang, Shandong, P. R. China
| | - Qingjie Xue
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Xiuzhen Li
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Ang Liu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China.
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Park Y, Min J, Kim W, Park W. Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38602466 DOI: 10.1099/ijsem.0.006338] [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: 04/12/2024] Open
Abstract
Strain Ran72T, a novel Gram-stain-negative, obligately aerobic, non-motile, and rod-shaped bacterium, was isolated from the faeces of the rhinoceros species Ceratotherium simum. The novel bacterial strain grew optimally in Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5, and 30 °C. Based on phylogenetic analysis using 16S rRNA gene sequencing, strain Ran72T was found to be most closely related to Chryseobacterium faecale F4T (98.4 %), Kaistella soli DKR-2T (98.0 %), and Kaistella haifensis H38T (97.4 %). A comprehensive genome-level comparison between strain Ran72T with C. faecale F4T, K. soli DKR-2T, and K. haifensis H38T revealed average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values of ≤74.9, ≤19.3, and ≤78.7 %, respectively. The major fatty acids were anteiso-C15 : 0 (22.3 %), with MK-6 being the predominant respiratory quinone. The major polar lipids of strain Ran72T were phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. Based on our chemotaxonomic, genotypic, and phenotype characterizations, strain Ran72T was identified as representing a novel species in the genus Kaistella, for which the name Kaistella rhinocerotis sp. nov. is proposed, with the type strain Ran72T (=KACC 23136T=JCM 36038T). Based on the outcomes of our phylogenomic study, Chryseobacterium faecale should be reclassified under the genus Kaistella as Kaistella faecalis comb. nov.
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Affiliation(s)
- Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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Tian M, Wu S, Zhang W, Zhang G, Yu X, Wu Y, Jia P, Zhang B, Chen T, Liu G. Saxibacter everestensis gen. nov., sp. nov., A Novel Member of the Family Brevibacteriaceae, Isolated from the North Slope of Mount Everest. J Microbiol 2024; 62:277-284. [PMID: 38446393 DOI: 10.1007/s12275-024-00108-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 03/07/2024]
Abstract
We isolated and analyzed a novel, Gram-stain-positive, aerobic, rod-shaped, non-motile actinobacterium, designated as strain ZFBP1038T, from rock sampled on the north slope of Mount Everest. The growth requirements of this strain were 10-37 °C, pH 4-10, and 0-6% (w/v) NaCl. The sole respiratory quinone was MK-9, and the major fatty acids were anteiso-C15:0 and iso-C17:0. Peptidoglycan containing meso-diaminopimelic acid, ribose, and glucose were the major cell wall sugars, while polar lipids included diphosphatidyl glycerol, phosphatidyl glycerol, an unidentified phospholipid, and an unidentified glycolipid. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFBP1038T has the highest similarity with Spelaeicoccus albus DSM 26341 T (96.02%). ZFBP1038T formed a distinct monophyletic clade within the family Brevibacteriaceae and was distantly related to the genus Spelaeicoccus. The G + C content of strain ZFBP1038T was 63.65 mol% and the genome size was 4.05 Mb. Digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between the genomes of strain ZFBP1038T and representative reference strains were 19.3-25.2, 68.0-71.0, and 52.8-60.1%, respectively. Phylogenetic, phenotypic, and chemotaxonomic characteristics as well as comparative genome analyses suggested that strain ZFBP1038T represents a novel species of a new genus, for which the name Saxibacter gen. nov., sp. nov. was assigned with the type strain Saxibacter everestensis ZFBP1038T (= EE 014 T = GDMCC 1.3024 T = JCM 35335 T).
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Affiliation(s)
- Mao Tian
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shiyu Wu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China.
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Xue Yu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Yujie Wu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Puchao Jia
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu Province, 730000, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
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Kim M, Kim W, Park Y, Jung J, Park W. Lineage-specific evolution of Aquibium, a close relative of Mesorhizobium, during habitat adaptation. Appl Environ Microbiol 2024; 90:e0209123. [PMID: 38412007 PMCID: PMC10952388 DOI: 10.1128/aem.02091-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. The genomes of Aquibium species isolated from water were smaller and had higher GC contents than those of Mesorhizobium species. Six Mesorhizobium species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 Mesorhizobium species. Therefore, they were classified as the non-N2-fixing Mesorhizobium lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific fur/mur indicated that Mesorhizobium species may have evolved from Aquibium species through an ecological transition. Halotolerant and alkali-resistant Aquibium and Mesorhizobium microcysteis belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (mrpABCDEFG). These genes were not present in the N2-fixing Mesorhizobium lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in Aquibium species, close relatives of Mesorhizobium species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.IMPORTANCEPhylogenetic analyses revealed that the Aquibium lineage (AL) and non-N2-fixing Mesorhizobium lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N2-fixing Mesorhizobium lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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Huang HJ, Zhang X, Sun XW, Chen B, Li XT, Zhou N, Abdugheni R, Cheng QY, Zhang TJ, Liu Y, Jiang Y, Deng Y, Liu SJ, Jiang CY. Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales. Arch Microbiol 2024; 206:141. [PMID: 38441685 DOI: 10.1007/s00203-024-03909-5] [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: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).
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Affiliation(s)
- Hao-Jie Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Biao Chen
- Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Yin Cheng
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Tie-Jun Zhang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Ye Deng
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512750 DOI: 10.1099/ijsem.0.006300] [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: 03/23/2024] Open
Abstract
The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding of microbial diversity and evolution. The introduction of molecular techniques, particularly DNA sequencing and genomics, has transformed our perception of prokaryotic diversity. In the past two decades, advancements in genome sequencing have transitioned from traditional methods to a genome-based taxonomic framework, not only to define species, but also higher taxonomic ranks. As technology and databases rapidly expand, maintaining updated standards is crucial. This work seeks to revise the 2018 guidelines for applying genome sequencing data in microbial taxonomy, adapting minimal standards and recommendations to reflect technological progress during this period.
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Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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11
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Miranda CD, Irgang R, Concha C, Rojas R, Avendaño-Herrera R. Phenotypic and genomic characterization of a non-pathogenic Epilithonimonas ginsengisoli isolated from diseased farmed rainbow trout (Oncorhynchus mykiss) in Chile. JOURNAL OF FISH DISEASES 2024; 47:e13897. [PMID: 38031399 DOI: 10.1111/jfd.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
Flavobacterial infection associated with diseased fish is caused by multiple bacterial species within the family Flavobacteriaceae. In the present study, the Chilean isolate FP99, from the gills of a diseased, farmed rainbow trout (Oncorhynchus mykiss), was characterized using phenotypic and genomic analyses. Additionally assessed was pathogenic activity. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that isolate FP99 belonged to the genus Epilithonimonas, an average nucleotide identity value of 100% was detected with the Chilean isolate identified as Epilithonimonas sp. FP211-J200. In silico genome analysis, mechanisms for toxins production, and superantigens, adhesion, or other genes associated with virulence were not detected. However, genes encoding proteins for antibiotic resistance were found, including the chrA gene and the nucleotide sequence that encodes for multiple antibiotic resistance MarC proteins. Furthermore, the blaESP-1 gene (87.85% aminoacidic sequence identity), encoding an extended-spectrum subclass B3 metallo-β-lactamase and conferring carbapenem-hydrolysing activity, and the tet(X) gene, which encodes a monooxygenase that catalyses the degradation of tetracycline-class antimicrobials were carried by this isolate. Phenotyping analyses also supported assignment as E. ginsengisoli. Challenge trials against healthy rainbow trout resulted in no observed pathogenic effect. Our findings identify for the first time the species E. ginsengisoli as associated with fish farming, suggesting that this isolate may be a component of the microbiota of the freshwater system. Notwithstanding, poor environmental conditions and any stressors associated with aquaculture situations or lesions caused by other pathogenic bacteria, such as F. psychrophilum, could favour the entry of E. ginsengisoli into rainbow trout.
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Affiliation(s)
- Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile
- Centro Tecnológico de Innovación Acuícola AquaPacífico, Coquimbo, Chile
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo, Chile
- Centro Tecnológico de Innovación Acuícola AquaPacífico, Coquimbo, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
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12
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Lee SD, Yang HL, Han JH, Kim IS. Speluncibacter jeojiensis gen. nov. sp. nov., a novel bacterium of the order Mycobacteriales isolated from a cave and a proposal of Speluncibacteraceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38345846 DOI: 10.1099/ijsem.0.006267] [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: 02/15/2024] Open
Abstract
Two Gram-stain-positive, aerobic, non-spore-forming, non-motile, irregular rod-shaped actinobacteria, designated as D2-41T and D3-21, were isolated from soil samples collected in a natural cave in Jeju, Republic of Korea. Both of the isolates were shown to share 100 % 16S rRNA sequence identity. The cell wall contained meso-diaminopimelic acid, arabinose and galactose. The predominant menaquinone was MK-8(H2). The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified aminoglycolipid, an unidentified phospholipid and two unidentified lipids. The predominant fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Mycolic acids of C30-C38 were present. The 16S rRNA gene trees showed that the organisms occupied a distinct position remotely located from recognized genera within the order Mycobacteriales, albeit with the 16S rRNA gene similarities of 97.0-97.1 % with Rhodococcus olei, Rhodococcus rhodnii and Rhodococcus triatomae. The genome sizes and DNA G+C contents of strains D2-41T and D3-21 were 4.77-4.88 Mbp and 69.8 mol%, respectively. Both of the isolates shared an average nucleotide identity of 99.4 % and digital DNA-DNA hybridization of 95.2 % to each other, revealing that strains D2-41T and D3-21 belonged to the same species. In the core genome-based phylogenomic tree, both of the isolates were found to be closely associated with members of the genus Tomitella. However, strains D2-41T and D3-21 revealed the highest amino acid identity values (mean 66.5 %, range 66.2-67.0 % with the genus Prescottella of the family Nocardiaceae, followed by the genus Tomitella (mean 64.1 %, range 63.6-64.7 %) of the family Tomitellaceae. Based on the combined data obtained here, the novel isolates belong to a new genus of the new family for which the name Speluncibacter jeojiensis gen. nov. sp. nov. is proposed, with Speluncibacteraceae fam. nov. The type strain is strain D2-41T (=KACC 17930T=DSM 101875T).
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| | - Hong-Lim Yang
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| | - Jong-Heon Han
- Bio Conversion Center, JTP Jeju Technopark, Jeju 63243, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
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13
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Ai J, He X, Ren M, Yu T, Liu X, Jiang Y, Li Z, Deng Z. Kaistella yananensis sp. nov., a Novel Indoleacetic Acid-Producing Bacterium Isolated from the Root Nodules of Sophora davidii (Franch.) Skeels. Curr Microbiol 2024; 81:60. [PMID: 38206520 DOI: 10.1007/s00284-023-03578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
A novel endophytic bacterium, designated strain BT6-1-3T, was isolated from the root nodules of a leguminous shrub named Sophora davidii (Franch.) Skeels, found growing wild in Yan'an, Shaanxi Province, China. Cells were Gram-staining-negative, non-motile, catalase-positive, oxidase-positive, and did not produce H2S. Strain BT6-1-3T grew at 15-40 °C (optimum 30 °C), at pH 6.0-10.0 (optimum pH 9.0), and with 0-1% (w/v) NaCl (optimum 0.5%). The quinone system was menaquinone 6. The major fatty acids present in BT6-1-3T were iso-C11:0, iso-C15:0, and C16:0. The G+C content of genomic DNA was 39.4 mol% by whole genome sequencing. According to the analysis of 16S rRNA gene sequence, the closest relative was Kaistella montana WG4 (nucleotide identity was 97.6%). The genome of strain BT6-1-3T was sequenced, and the genome similarity was calculated using average nucleotide identity and genome-to-genome distance analysis with the genomes of other strains of Kaistella. Both strongly supported that the strain BT6-1-3T belonged to the genus Kaistella as a representative of a new species. Based on phylogenetic analysis, chemotaxonomic data, and physiological and biochemical characteristics, strain BT6-1-3T represents a new species of the genus Kaistella and is named as Kaistella yananensis sp. nov. Type strain is BT6-1-3T (= NBRC 115452T = CGMCC 1.60032T).
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Affiliation(s)
- Jiamin Ai
- College of Life Science, Northwest A&F University, Yangling, 712100, China
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Xiaolong He
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Mingxia Ren
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Tianfei Yu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Xiaodong Liu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Yingying Jiang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
| | - Zhefei Li
- College of Life Science, Northwest A&F University, Yangling, 712100, China.
| | - Zhenshan Deng
- College of Life Sciences, Yan'an University, Yan'an, 716000, China.
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14
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Yang SH, Park MJ, Oh HM, Park YJ, Kwon KK. Flavivirga spongiicola sp. nov. and Flavivirga abyssicola sp. nov., Isolated from Marine Environments. J Microbiol 2024; 62:11-19. [PMID: 38319586 DOI: 10.1007/s12275-023-00102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 02/07/2024]
Abstract
Two novel Gram-stain-negative, strictly-aerobic, rod-shaped (1.2 ± 3.4 μm × 0.3 ± 0.7 μm), and non-motile marine bacterial species, designated MEBiC05379T and MEBiC07777T, were isolated from a marine sponge Pseudaxinella sp. in Gangneung City and deep-sea sediments of the Ulleung basin in the East Sea of Korea, respectively. The 16S rRNA gene sequence analysis revealed high levels of similarities between these strains and members of the genus Flavivirga (97.0-98.4% sequence identities). Both novel strains revealed as mesophilic, neutrophilic in pH and slightly halophilic. Similar to those of other Flavivirga members, the primary cellular fatty acids of both strains were iso-C15:0, iso-C15:1 G, iso-C15:03-OH, and iso-C17:0 3-OH, with MEBiC05379T and MEBiC07777T containing relatively higher proportions of C12:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). In both taxa, the major isoprenoid quinone was MK-6. The DNA G + C contents of MEBiC05379T and MEBiC07777T genomes were 32.62 and 32.46 mol%, respectively. Compared to other members of Flavivirga, both strains exhibited similar DNA G + C ratio and fatty acids pattern, yet enzyme expression and carbon sources utilization pattern were different. Genomes of the genus Flavivirga showed enzyme preferences to fucoidan and sulfated galactans. Considering the monophyly rule, AAI values delineate the genus Flavivirga from adjacent genera calculated to be 76.0-78.7%. Based on the phenotypic, genomic and biochemical data, strains for MEBiC05379T and MEBiC07777T thus represent two novel species in the genus Flavivirga, for which the names Flavivirga spongiicola sp. nov. (MEBiC05379T [= KCTC 92527 T = JCM 16662 T]), and Flavivirga abyssicola sp. nov. (MEBiC07777T [= KCTC 92563 T = JCM 36477 T]) are proposed.
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Affiliation(s)
- Sung-Hyun Yang
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
| | - Mi-Jeong Park
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
| | - Hyun-Myung Oh
- Institute of Liberal Arts Education, Pukyong National University, Busan, 48547, Republic of Korea
| | - Yeong-Jun Park
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology & Bioresource Research Department, Korea Institute of Ocean Science & Technology, Busan, 49111, Republic of Korea.
- KIOST School, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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15
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Lee SD, Yang HL, Kim IS. Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium. Front Microbiol 2023; 14:1299950. [PMID: 38164402 PMCID: PMC10757982 DOI: 10.3389/fmicb.2023.1299950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - Hong Lim Yang
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, Republic of Korea
- BioPS Co., Ltd., Daejeon, Republic of Korea
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16
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Wang YW, Wang XH, Zhang J, Du ZJ, Mu DS. Cerina litoralis gen. nov., sp. nov., a novel potential polysaccharide degrading bacterium of the family Flavobacteriaceae, isolated from marine sediment. Antonie Van Leeuwenhoek 2023; 116:1447-1455. [PMID: 37899393 DOI: 10.1007/s10482-023-01888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
The Gram-strain-negative, facultative anaerobic, chemoheterotrophic, short-rod-shaped, non-motile, forming yellow colonies strain, designated F89T, was isolated from marine sediment of Xiaoshi Island, Weihai. Strain F89T grew at 15-37 °C (optimally at 28 °C), at pH 6.0-8.5 (optimally at pH 7.0) and in the presence of 1-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain F89T was related to the family Flavobacteriaceae. F89T had highest 16S rRNA gene sequence similarity to Maribacter cobaltidurans MCCC 1K03318T (93.3%). The predominant cellular fatty acids of F89T were iso-C15:0, iso-C15:0 G and Summed Feature 3. The main respiratory quinone of F89T was menaquinone 6 (MK-6), consistent with that observed for all related strains. The polar lipid profile of strain F89T contained phosphatidylethanolamine, two aminolipids and three unidentified polar lipids. The genomic DNA G + C content of strain F89T was 42.7%. Strain F89T encoded 121 glycoside hydrolases and was a potential polysaccharide degrading bacterium. Differential phenotypic and genotypic characteristics of the strain showed that F89T should be classified as a novel genus in Flavobacteriaceae, for which the name Cerina litoralis is proposed. The type strain is F89T (= MCCC 1H00510T = KCTC 92203T).
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Affiliation(s)
- Ya-Wei Wang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Xin-Hui Wang
- ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, 264209, Shandong, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China
| | - Da-Shuai Mu
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, China.
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17
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Bowman JP, Hugo C, Nicholson A, Hahnke R, Lau EF, Holmes B, Sutcliffe I. International Committee on Systematics of Prokaryotes: Subcommittee on the taxonomy of aerobic Bacteroidota. Minutes of the online meeting 25 April 2023. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917547 DOI: 10.1099/ijsem.0.006144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Celia Hugo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Ainsley Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Richard Hahnke
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Ellen Frandsen Lau
- Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
| | - Barry Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle Upon Tyne, Tyne & Wear, UK
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18
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Val-Calvo J, Vázquez-Boland JA. Mycobacteriales taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation. mBio 2023; 14:e0220723. [PMID: 37796005 PMCID: PMC10653829 DOI: 10.1128/mbio.02207-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales. Formal descriptions of proposed taxonomic changes based on our study are included.
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Affiliation(s)
- Jorge Val-Calvo
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - José A. Vázquez-Boland
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
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19
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Zhao L, Yang C, Chen M, Zhang J, Kong M, Dong L, Gong J, Yang J, Pu J, Lu S, Jin D, Liu L, Wang S, Xu J. Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37906507 DOI: 10.1099/ijsem.0.006020] [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: 11/02/2023] Open
Abstract
Two Gram-stain-negative, non-spore-forming, rod-shaped, and obligately aerobic bacteria, designated strains CX-624T and cx-311, were isolated from soil samples in Qinghai Province, China. The two strains grew best at 28 °C on the plate with Tryptone soya agar (TSA). Cells formed circular, convex, translucent, smooth, and orange colonies with approximately 1.0 mm diameter after 2 days of incubation on TSA at 28 °C. The strains were oxidase-negative and catalase-positive. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and major polar lipids included phosphatidylethanolamine, an unidentified aminophospholipid, four unidentified lipids and an aminolipid. MK-6 was the sole menaquinone in strain CX-624T. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed strains CX-624T and cx-311 were member of the family Weeksellaceae, with the highest similarity to Kaistella haifensis H38T (96.66 %), Epilithonimonas pallida DSM 18015T (96.59 %), and Chryseobacterium gambrini DSM 18014T (96.53 %). Both phylogenetic analysis of the 16S rRNA gene and 177 core genes revealed that strains CX-624T and cx-311 formed an independent clade. Average nucleotide identity values (< 72.64 %), average amino-acid identity values (<72.61 %) and digital DNA-DNA hybridization (< 21.10 %) indicated that the strains CX-624T and cx-311 should constitute a novel genus. The DNA G+C contents of strains CX-624T and cx-311 were 43.0 mol% and 42.7 mol%. According to the data obtained in this study, strain CX-624T represents a novel species belonging to a novel genus of the Weeksellaceae, for which the name Marnyiella aurantia gen. nov., sp. nov. is proposed. The type strain is CX-624T (=GDMCC 1.1714T = JCM 33925T).
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Affiliation(s)
- Lijun Zhao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Mengshan Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, PR China
| | - Mimi Kong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lingzhi Dong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jian Gong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Suping Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Institute of Public Health, Nankai University, Tianjin 300350, PR China
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20
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Mo K, Huang H, Ye L, Wu Q, Hu YH. Polycladospora coralii gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae isolated from stony coral in the South China Sea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791652 DOI: 10.1099/ijsem.0.006055] [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: 10/05/2023] Open
Abstract
Two novel filamentous bacteria, designated as IB182353T and IB182357, were isolated from stony coral of the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains IB182353T and IB182357 were closely related to Hazenella coriacea DSM 45707T (with 93.4 and 93.5% similarity, respectively). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization results showed that the pairwise similarities between isolate IB182353T and the other recognized Thermoactinomycetaceae species were less than 68.9, 60.5 and 21.1 %, respectively. Both strains produced aerial and substrate mycelia, grew optimally at 25-30 °C, pH 8.0-9.0 and with 2-3 % (w/v) NaCl. The cell-wall peptidoglycan type was meso-DAP and the whole-cell hydrolysates contained ribose. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and three unidentified phospholipids. The genomic DNA G+C content was 39.5 mol%. Strain IB182353T was distinguishable from its related type strains by the contents of two fatty acids, iso-C15 : 0 and iso-C17 : 1 ω10c. Based on polyphasic taxonomic characterization, we propose that strains IB182353T and IB182357 represent a novel genus and species within the family Thermoactinomycetaceae, for which the name Polycladospora coralii gen. nov. sp. nov. is proposed. The type strain is IB182353T (=MCCC 1K04631T=JCM 34206T).
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Affiliation(s)
- Kunlian Mo
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, PR China
- Institute of Tropical Bioscience and Biotechnology, CATAS & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
| | - Huiqin Huang
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, PR China
- Institute of Tropical Bioscience and Biotechnology, CATAS & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
| | - Lin Ye
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, PR China
- Institute of Tropical Bioscience and Biotechnology, CATAS & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
| | - Qingjuan Wu
- Institute of Tropical Bioscience and Biotechnology, CATAS & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
| | - Yong Hua Hu
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, PR China
- Institute of Tropical Bioscience and Biotechnology, CATAS & Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, 571101, PR China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou 571101, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Shandong, PR China
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21
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Itoh H, Sugisawa Y, Mise K, Xu Z, Kuniyasu M, Ushijima N, Kawano K, Kobayashi E, Shiratori Y, Masuda Y, Senoo K. Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils. Int J Syst Evol Microbiol 2023; 73. [PMID: 37675765 DOI: 10.1099/ijsem.0.006073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79T, W786T, Red222T, Red802T, Red803T, and Red804T, were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222T, Red802T, Red803T, and Red804T formed a cluster with the type strains of Geothrix species, but strains W79T and W786T created an independent cluster from any other type strains. The former four strains shared 97.95-99.08% similarities of 16S rRNA gene sequence with the type strains of the genus Geothrix, whereas the latter two strains 94.86-95.49% similarities. The average amino acid identity of strains W79T and W786T were <63 % to any other type strains, which were below the genus delineation thresholds. Moreover, colonies of these two strains were white, while those of the other four isolated strains were reddish-yellow as well as the type strain Geothrix fermentans H-5T. Although the known type strains of Geothrix species have been reported to be non-motile, five strains (W79T, W786T, Red222T, Red803T, and Red804T) except for strain Red802T displayed motility. Furthermore, multiple genomic, phylogenetic, and phenotypic features supported the discrimination between these isolated strains. Based on the study evidence, we propose these six isolates as novel members within the Acidobacteriota/Holophagae/Holophagales/Holophagaceae, comprising two novel species of a novel genus, Mesoterricola silvestris gen. nov., sp. nov., and Mesoterricola sediminis sp. nov., and four novel species of the genus Geothrix: Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Yumi Sugisawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Kazumori Mise
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Present address: Marine College, Shandong University, Weihai, Shandong, PR China
| | - Miyu Kuniyasu
- Department of Biotechnology, Hokkaido High-technology College, Hokkaido 061-1396, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Keisuke Kawano
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
- Present address: Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Emiko Kobayashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata 940-0826, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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22
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Chhetri G, Kim I, Park S, Jung Y, Seo T. Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant. Arch Microbiol 2023; 205:324. [PMID: 37656250 DOI: 10.1007/s00203-023-03657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6 days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200 bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea.
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23
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Jerabkova M, Smrhova T, Lopez-Echartea E, Dresler J, Suman J, Kapinusova G, Cajthaml T, Skrob Z, Kyclt R, Fagerman J, Strejcek M, Uhlik O. Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden. Int J Syst Evol Microbiol 2023; 73. [PMID: 37768182 DOI: 10.1099/ijsem.0.006048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6T, was classified in the family Chromobacteriaceae, class Betaproteobacteria, and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum. On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6T (=DSM 115342T=CCM 9308T).
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Affiliation(s)
- Martina Jerabkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Tereza Smrhova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Eglantina Lopez-Echartea
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Jiri Dresler
- Military Health Institute, Ministry of Defence of the Czech Republic, Prague, Czechia
| | - Jachym Suman
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Gabriela Kapinusova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Zdena Skrob
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Michal Strejcek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
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24
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Yao B, Niu G, Wang Z, Mu H, Ren X, Jiao Y, Cai C, Li J. Kaistella polysaccharea sp. nov., isolated from Antarctic intertidal sediment produces a novel extracellular polymeric substance. Int J Syst Evol Microbiol 2023; 73. [PMID: 37725075 DOI: 10.1099/ijsem.0.006037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
An exopolysaccharide-producing bacterial strain GW4-15T, belonging to the genus Kaistella, was isolated from intertidal sediment from King George Island, Antarctic. The strain was Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow-pigmented. The strain was able to grow in the presence of 0-2 % (w/v) NaCl (optimum, 0 %), at 4-30 °C (optimum, 20-28 °C) and at pH 5.0-10.0 (optimum, pH 8.0). A phylogenetic tree based on 16S rRNA gene sequences showed that strain GW4-15T formed a lineage within the genus Kaistella with the closest phylogenetic neighbours Kaistella carnis NCTC 13525T (98.3 %), Kaistella gelatinilytica G5-32T (97.7 %), Kaistella antarctica LMG 24720T (97.4 %) and Kaistella yonginensis HMD1043T (96.9 %). Digital DNA-DNA hybridization values of strain GW4-15T with K. carnis NCTC 13525T, K. antarctica LMG 24720T, K. gelatinilytica G5-32T and K. yonginensis HMD1043T were 22.8, 22.0, 21.7 and 21.6 %, respectively. The average nucleotide identity values between strain GW4-15T and K. carnis NCTC 13525T , K. antarctica LMG 24720T, K. gelatinilytica G5-32T and K. yonginensis HMD1043T were 79.3, 78.6, 77.5 and 77.2 %, respectively. The G+C content of the genome was 36.2 mol%. The major phospholipids were phosphatidylethanolamine and aminophospholipid. The predominant menaquinone was MK-6. The major fatty acids were anteiso-C15 : 0 (28.7 %), iso-C16 : 0 3-OH (15.7 %), iso-C16 : 0 H (10.0 %), iso-C16 : 0 (5.4 %), summed feature 9 (comprising iso-C17 : 1 ω9c and/or 10-methyl C16 : 0; 5.2 %) and iso-C15 : 0 (5.1 %). The monosaccharide composition of the new type of extracellular polymeric of GW4-15T was Glc, GalN, GlcN, Rha, Man and Gal with a molar ratio of 3.14 : 3.83 : 8.38 : 5.16 : 1 : 2.82. Based on phenotypic, phylogenetic and genotypic data, a novel species, Kaistella polysaccharea sp. nov., is proposed with the type strain GW4-15T (=CGMCC 1.19368T=KCTC 92753T).
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Affiliation(s)
- Boqing Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Guojiang Niu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Zhe Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, 266003, PR China
| | - Hongmei Mu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Xingtao Ren
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Yabin Jiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Chao Cai
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, 266003, PR China
| | - Jing Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
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25
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Bowman JP. Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37589187 DOI: 10.1099/ijsem.0.005991] [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: 08/18/2023] Open
Abstract
Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta. This results in the transfer of 35 Massilia species to the genus Telluria. The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species 'Massilia antibiotica', 'Massilia aromaticivorans', 'Massilia cellulosiltytica' and 'Massilia humi' are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.
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Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Hobart, Tasmania, 7005, Australia
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26
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Ren T, Zhang C, Jin CZ, Jin FJ, Li T, Oh HM, Lee HG, Jin L. Description of Hymenobacter sediminicola sp. nov., isolated from contaminated sediment. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01846-9. [PMID: 37237242 DOI: 10.1007/s10482-023-01846-9] [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: 01/06/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
A polyphasic taxonomic study was conducted on two Gram-negative, non-sporulating, non-motile bacterial strains, S2-20-2T and S2-21-1, isolated from a contaminated freshwater sediment in China. Comparative 16S rRNA gene sequence studies revealed a clear affiliation of two strains with Bacteroidetes, which showed the highest pairwise sequence similarities with Hymenobacter duratus BT646T (99.3%), Hymenobacter psychrotolerans Tibet-IIU11T (99.3%), Hymenobacter kanuolensis T-3T (97.6%), Hymenobacter swuensis DY53T (96.9%), Hymenobacter tenuis POB6T (96.8%), Hymenobacter seoulensis 16F7GT (96.7%), and Hymenobacter rigui KCTC 12533T (96.5%). The phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Hymenobacter. Major fatty acids were identified as iso-C15:0, anteiso-C15:0, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c/t) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). Major cellular polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophosopholipid and an unidentified lipid. The respiratory quinone was detected as MK-7 and the genomic DNA G + C content was determined to be 57.9% (genome) for type strain S2-20-2T and 57.7 mol% (HPLC) for strain S2-21-1. The observed ANI and dDDH values between strain S2-20-2T and its closely related strains were 75.7-91.4% and 21.2-43.9%, respectively. Based on physiological, biochemical, genetic and genomic characteristics, we propose that strains S2-20-2T and S2-21-1 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter sediminicola sp. nov. is proposed. The type strain is S2-20-2T (= CGMCC 1.18734T = JCM 35801T).
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Affiliation(s)
- Tingting Ren
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Chengxiao Zhang
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Feng-Jie Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Taihua Li
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Long Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Sun JR, Mo KL, Li X, Hu YH, Liu ZY, Huang HQ. Neiella litorisoli sp. nov., an alginate lyase: producing bacterium from South China Sea, and proposal of Echinimonadaceae fam. nov. in the order Alteromonadales. Arch Microbiol 2023; 205:227. [PMID: 37160479 DOI: 10.1007/s00203-023-03573-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/16/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
A Gram-stain-negative, rod-shaped bacterium, designated HB171785T, was isolated from soil sample collected from Qishui Bay, Hainan, China. The strain grew optimally at pH 7-8, 37-40 °C and with NaCl 3-4%. The predominant isoprenoid quinone was found to be Q-8 and the major fatty acids were C16:0, C16:1 ω7c/C16:1 ω6c, C18:1 ω7c/C18:1 ω6c and C12:0 3OH. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The size of the draft genome was 4.32 Mbp with G + C content 49.7%. Phylogenetic analysis of 16S rRNA gene sequence indicated that the closest phylogenetically related species were Neiella marina j221T, "Neiella holothuriorum" 126 and Echinimonas agarilytica KMM 6351T with the similarities of 98.2, 96.0 and 95.0%, respectively. The phylogenetic tree based on 16S rRNA gene and phylogenomic tree based on core genome showed that strain HB171785T clustered together with N. marina j221T, with the highest values of average nucleotide identity (82.9%) and digital DNA-DNA hybridization (25.4%). The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB171785T represents a novel species of the genus Neiella, for which the name Neiella litorisoli sp. nov. is proposed. The type strain is HB171785T (= MCCC 1K04625T = KCTC 82319T). In addition, Echinimonadaceae fam. nov. in the order Alteromonadales was proposed.
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Affiliation(s)
- Jing-Ran Sun
- College of Marine Science, Hainan University, Haikou, 570228, China
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Kun-Lian Mo
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Xue Li
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163000, China
| | - Yong-Hua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China
| | - Zhi-Yuan Liu
- College of Marine Science, Hainan University, Haikou, 570228, China.
| | - Hui-Qin Huang
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, China.
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, China.
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Nguyen TV, Viver T, Smets I, Bernaerts K, Faust K, Lavigne R, Poughon L, Dussap CG, Springael D. Thermocaproicibacter melissae gen. nov., sp. nov., a thermophilic chain-elongating bacterium, producing n-caproate from polymeric carbohydrates. Int J Syst Evol Microbiol 2023; 73. [PMID: 37200213 DOI: 10.1099/ijsem.0.005893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Strain MDTJ8T is a chain-elongating thermophilic bacterium isolated from a thermophilic acidogenic anaerobic digestor treating human waste while producing the high commodity chemical n-caproate. The strain grows and produces formate, acetate, n-butyrate, n-caproate and lactate from mono-, di- and polymeric saccharides at 37-60 °C (optimum, 50-55 °C) and at pH 5.0-7.0 (optimum, pH 6.5). The organism is an obligate anaerobe, is motile and its cells form rods (0.3-0.5×1.0-3.0 µm) that stain Gram-positive and occur primarily as chains. Phylogenetic analysis of both the 16S rRNA gene and full genome sequence shows that strain MDTJ8T belongs to a group that consists of mesophylic chain-elongating bacteria within the family Oscillospiraceae, being nearest to Caproicibacter fermentans EA1T (94.8 %) and Caproiciproducens galactitolivorans BS-1T (93.7 %). Its genome (1.96 Mbp) with a G+C content of 49.6 mol% is remarkably smaller than those of other chain-elongating bacteria of the family Oscillospiraceae. Pairwise average nucleotide identity and DNA-DNA hybridization values between strain MDJT8T and its mesophilic family members are less than 70 and 35 %, respectively, while pairwise average amino acid identity values are less than 68 %. In addition, strain MDJT8T uses far less carbohydrate and non-carbohydrate substrates compared to its nearest family members. The predominant cellular fatty acids of strain MDTJ8T are C14 : 0, C14 : 0 DMA (dimethyl acetal) and C16 : 0, while its polar lipid profile shows three unidentified glycophospholipids, 11 glycolipids, 13 phospholipids and six unidentified lipids. No respiratory quinones and polyamines are detected. Based on its phylogenetic, genotypic, morphological, physiological, biochemical and chemotaxonomic characteristics, strain MDTJ8T represents a novel species and novel genus of the family Oscillospiraceae and Thermocaproicibacter melissae gen. nov., sp. nov. is proposed as its name. The type strain is MDTJ8T (=DSM 114174T=LMG 32615T=NCCB 100883T).
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Affiliation(s)
- Tinh Van Nguyen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Tomeu Viver
- Marine Microbiology Group, Mediterranean Institute of Advanced Studies (CSIC-UIB), C/Miquel Marquès 21, 07190 Esporles, Spain
| | - Ilse Smets
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Kristel Bernaerts
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium
| | - Laurent Poughon
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Claude-Gilles Dussap
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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Shelomi M, Han CJ, Chen WM, Chen HK, Liaw SJ, Mühle E, Clermont D. Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros, and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage. Int J Syst Evol Microbiol 2023; 73. [PMID: 37074162 DOI: 10.1099/ijsem.0.005813] [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: 04/20/2023] Open
Abstract
Two strains of Chryseobacterium identified from different experiments are proposed to represent new species. Strain WLa1L2M3T was isolated from the digestive tract of an Oryctes rhinoceros beetle larva. Strain 09-1422T was isolated from a cage housing the stick insect Eurycantha calcarata. Sequence analysis of the 16S rRNA and rpoB genes found both strains to be similar but not identical to other Chryseobacterium species. Whole-genome sequencing suggested the isolates represent new species, with average nucleotide identity values ranging from 74.6 to 80.5 %. Genome-to-genome distance calculations produced values below 25.3 %, and digital DNA-DNA hybridization values were 13.7-29.9 %, all suggesting they are distinct species. The genomic DNA G+C content of WLa1L2M3T is approximately 32.53 %, and of 09-1422T is approximately 35.89 %. The predominant cellular fatty acids of strain WLa1L2M3T are C15 : 0 iso, summed feature 9 (C16 : 0 10OH or C17 : 1 iso ω6c), C17 : 0 iso 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso 3OH, C15 : 0 anteiso and C13 : 0 iso, and those of strain 09-1422T are C15 : 0 iso, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 iso 3OH, C15 : 0 anteiso, C15 : 0 iso 3OH, C16 : 1 ω7c, C17 : 0 2OH and C18 : 0. In addition, physiological and biochemical tests revealed phenotypic differences from related Chryseobacterium type strains. These cumulative data indicate that the two strains represent novel species of the genus Chryseobacterium for which the names Chryseobacterium oryctis sp. nov. and Chryseobacterium kimseyorum sp. nov. are proposed with WLa1L2M3T (=BCRC 81350T=JCM 35215T=CIP 112035T) and 09-1422T (=UCDFST 09-1422T=BCRC 81359T=CIP 112165T), as type strains, respectively.
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Affiliation(s)
- Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chiao-Jung Han
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Wen-Ming Chen
- Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan, ROC
| | - Hsin-Kuang Chen
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan, ROC
| | - Shwu-Jen Liaw
- Department and Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC
| | - Estelle Mühle
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur, F-75015 Paris, France
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, Collection of Institut Pasteur, F-75015 Paris, France
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Ueki A, Tonouchi A, Kaku N, Ueki K. Anaeromicropila herbilytica gen. nov., sp. nov., a plant polysaccharide-decomposing anaerobic bacterium isolated from anoxic soil subjected to reductive soil disinfestation, and reclassification of Clostridium populeti as Anaeromicropila populeti comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748612 DOI: 10.1099/ijsem.0.005695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
An obligately anaerobic bacterial strain (TB5T) was isolated from a soil sample subjected to reductive or biological soil disinfestation. Cells of the strain were Gram-stain-positive, spore-forming and motile rods. The strain grew at 15–40 °C (optimum, 37 °C) and pH 5.4–7.5 (optimum, pH 7.3). Strain TB5Tutilized a wide variety of carbohydrates including polysaccharides (cellulose, xylan, starch, inulin, glucomannan and laminarin) and organic acids. Acetate, ethanol, H2 and CO2 were products from the substrates utilized. The major components of the cellular fatty acids were C16 : 1
ω7c DMA, C16 : 0 DMA and C18 : 1
ω7c DMA. The diagnostic amino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. The closest related species to strain TB5T based on 16S rRNA gene sequences was
Clostridium populeti
743AT (95.4 % sequence similarity). The genome size of strain TB5T was 5.09 Mb and the genomic DNA G+C content was 32.7 mol%. Strain TB5T had genes encoding polysaccharide-decomposing enzymes such as cellulase, xylanase, β-glucosidase and β-mannosidase in the genome. Based on the phylogenetic, genomic and phenotypic data, a novel species of a novel genus in the family
Lachnospiraceae
, Anaeromicropila herbilytica gen. nov., sp. nov., is proposed to accommodate the strain. The type species is Anaeromicropila herbilytica with strain TB5T (=NBRC 112093T=DSM 110037T) as the type strain. For the closest related species
C. populeti
, Anaeromicropila populeti comb. nov. is proposed with an emended description of the species.
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Affiliation(s)
- Atsuko Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
| | - Nobuo Kaku
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
| | - Katsuji Ueki
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
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Lopez Marin MA, Suman J, Jani K, Ulbrich P, Cajthaml T, Filipova A, Pajer P, Neumann-Schaal M, Strejcek M, Uhlik O. Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748542 DOI: 10.1099/ijsem.0.005678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
An actinobacterial strain, designated A5X3R13T, was isolated from a compost soil suspension supplemented with extracellular material from a Micrococcus luteus-culture supernatant. The strain was cultured on tenfold-diluted reasoner's 2A agar. The cells were ovoid-to-rod shaped, non-motile, Gram-stain-positive, oxidase-negative, catalase-positive and had a width of 0.5 µm and a length of 0.8-1.2 µm. The results of both 16S rRNA-based phylogenetic and whole-genome analyses indicate that A5X3R13T forms a distinct lineage within the family Nocardioidaceae (order Propionibacteriales). On the basis of the 16S rRNA gene sequence, A5X3R13T was closely related to Aeromicrobium terrae CC-CFT486T (96.2 %), Nocardioides iriomotensis IR27-S3T (96.2 %), Nocardioides guangzhouensis 130T (95.6 %), Marmoricola caldifontis YIM 730233T (95.5 %), Aeromicrobium alkaliterrae KSL-107T (95.4 %), Aeromicrobium choanae 9H-4T (95.4 %), Aeromicrobium panaciterrae Gsoil 161T (95.3 %), and Nocardioides jensenii NBRC 14755T (95.2 %). The genome had a length of 4 915 757 bp, and its DNA G+C content was 68.5 mol %. The main fatty acids were 10-methyl C17 : 0, C16 : 0, C15 : 0, C18 : 0, C17 : 0 and iso-C16 : 0. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. MK-9(H4) was the predominant respiratory quinone. The peptidoglycan type was A3γ (A41.1) and contained alanine, glycine, glutamic acid and ll-diaminopimelic acid in a molar ratio of 1.2 : 0.9 : 1.0 : 0.8. On the basis of the results of the phylogenetic and phenotypic analyses and comparisons with other members of the family Nocardioidaceae, strain A5X3R13T is proposed to represent a novel species within a novel genus, for which the name Solicola gregarius gen. nov., sp. nov. is proposed. The type strain is A5X3R13T (=DSM 112953T=NCCB 100840T).
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Affiliation(s)
- Marco A Lopez Marin
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Kunal Jani
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Pavel Ulbrich
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Alena Filipova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02, Prague, Czech Republic
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7 B, 38124, Braunschweig, Germany
| | - Michal Strejcek
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
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Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus. J Microbiol 2023; 61:175-187. [PMID: 36800167 DOI: 10.1007/s12275-023-00022-y] [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: 12/08/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023]
Abstract
Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5-9 (optimum, pH 7-7.5), and in 0-8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5-56.1 °C) and 44 °C (20.7-50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5-94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. (MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. (MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.
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33
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Lawson PA, Saavedra Perez L, Sankaranarayanan K. Reclassification of Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia as Thomasclavelia cocleata gen. nov., comb. nov., Thomasclavelia ramosa comb. nov., gen. nov., Thomasclavelia spiroformis comb. nov. and Thomasclavelia saccharogumia comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748617 DOI: 10.1099/ijsem.0.005694] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The genus Clostridium is phenotypically and genotypically diverse, with many species phylogenetically located outside Clostridium sensu stricto. One such group consists of the species Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia (formally clostridial rRNA cluster XVIII) [1]. Sequencing of the 16S rRNA and, more recently, the results of genomic analyses have demonstrated that these species represent a coherent cluster separated from other closely related genera located in the family Coprobacillaceae within the order Erysipelotrichales [2]. In addition to phenotypic, phylogenetic and genomic comparisons, chemotaxonomic features were consistent between all four species, the predominant fatty acids were C16 : 0 and C18 : 1ω9c, while glucose and ribose were the whole cell sugars present in the cell walls. Furthermore, he results of peptidoglycan analysis indicated that meso-2,6-diaminopimelic acid was present as the diagnostic diamino acid in all four species. Biochemical profiles were also concordant with them being closely related species. Therefore, on the basis of phylogenetic, genomic, phenotypic and chemotaxonomic information, a novel genus, Thomasclavelia gen. nov., is proposed. It is suggested that Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia be transferred to this genus as Thomasclavelia cocleata comb. nov., Thomasclavelia ramosa comb. nov., Thomasclavelia saccharogumia comb. nov. and Thomasclavelia spiroformis comb. nov. The type species of the genus is Thomasclavelia ramosa CCUG 24038T (=ATCC 25582T=DSM 1402T).
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Affiliation(s)
- Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Liz Saavedra Perez
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,Present address: Molecular & Biomedical Sciences, University of Maine, 5735 Hitchner Hall, Orono, Maine 04469-5735, USA
| | - Krithivasan Sankaranarayanan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
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34
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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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Kim M, Kim YS, Cha CJ. Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea. J Microbiol 2023; 61:37-47. [PMID: 36723793 DOI: 10.1007/s12275-022-00008-2] [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: 09/28/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 02/02/2023]
Abstract
Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rod-shaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).
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Affiliation(s)
- Miryung Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Maddock D, Arnold D, Denman S, Brady C. Description of a novel species of Leclercia, Leclercia tamurae sp. nov. and proposal of a novel genus Silvania gen. nov. containing two novel species Silvania hatchlandensis sp. nov. and Silvania confinis sp. nov. isolated from the rhizosphere of oak. BMC Microbiol 2022; 22:289. [PMID: 36460957 PMCID: PMC9716735 DOI: 10.1186/s12866-022-02711-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Acute Oak Decline (AOD) is a decline disease first reported on native oaks in the UK, but in recent years reports from further afield such as Europe and the Middle East, indicate that the distribution and host range is increasing at an alarming rate. The stem weeping symptoms of the disease partially develop due to polymicrobial-host interaction, caused by several members of the order Enterobacterales. While investigating the rhizosphere soil of AOD-unaffected trees, termed 'healthy' trees, and diseased oaks suffering from Acute Oak Decline (AOD), an enrichment method designed for enhanced recovery of Enterobacterales led to the recovery of several isolates that could not be classified as any existing species. These isolates showed a close relationship to the genus Leclercia, of which both species are of clinical importance, but the type species Leclercia adecarboxylata also displays plant growth-promoting properties in the rhizosphere. RESULTS Partial sequencing of four housekeeping genes revealed similarity to the genus Leclercia with varying degrees of relatedness. As such a complete polyphasic approach was used to determine the true taxonomic position of these isolates. This involved whole genome sequencing, phylogenomic analysis, phylogenetic analysis of both the 16S rRNA and four housekeeping gene sequences, combined with phenotypic testing and fatty acid analysis. Both the phylogenomic and phylogenetic analyses separated the isolates into four clusters, two of which were contained in the Leclercia clade. The remaining two clusters formed a separate lineage far removed from any currently defined species. Further investigation into the role of the isolates as plant growth-promoting bacteria as well as plant pathogens was investigated computationally, revealing a number of plant growth-promoting traits as well as virulence genes related to motility, adhesion and immune modulation. CONCLUSION Based on the genotypic and phenotypic data presented here, these isolates could be differentiated from each other and their closest neighbours. As such we propose the description of Leclercia tamurae sp. nov. (type strain H6S3T = LMG 32609T = CCUG 76176T), Silvania gen. nov., Silvania hatchlandensis sp. nov. (type strain H19S6T = LMG 32608T = CCUG 76185T) and Silvania confinis sp. nov. (type strain H4N4T = LMG 32607T = CCUG 76175T). Due to their interesting protein annotations and alignments, these species warrant further investigation for their role in relation to plant health.
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Affiliation(s)
- Daniel Maddock
- grid.6518.a0000 0001 2034 5266Centre for Research in Bioscience, School of Applied Sciences, University of the West of England, Bristol, BS16 1QY UK
| | - Dawn Arnold
- grid.417899.a0000 0001 2167 3798Harper Adams University, Shropshire, Newport, UK
| | - Sandra Denman
- grid.479676.d0000 0001 1271 4412Centre for Ecosystems, Society and Biosecurity, Forest Research, Farnham, UK
| | - Carrie Brady
- grid.6518.a0000 0001 2034 5266Centre for Research in Bioscience, School of Applied Sciences, University of the West of England, Bristol, BS16 1QY UK
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Urvashi, Gundawar K, Sharma S, Choksket S, Sharma M, Grover V, Patil PB, Korpole S. Lacrimispora defluvii PI-S10-B5AT sp. nov., an Obligate Anaerobe, Isolated from an Industrial Waste and Reclassification of Hungatella xylanolytica as Lacrimispora xylanolytica and Clostridium indicum as Lacrimispora indica Comb. nov. Curr Microbiol 2022; 79:397. [DOI: 10.1007/s00284-022-03096-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
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Brady C, Kaur S, Crampton B, Maddock D, Arnold D, Denman S. Transfer of Erwinia toletana and Erwinia iniecta to a novel genus Winslowiella gen. nov. as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov. and description of Winslowiella arboricola sp. nov., isolated from bleeding cankers on broadleaf hosts. Front Microbiol 2022; 13:1063107. [DOI: 10.3389/fmicb.2022.1063107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Following a screening campaign of bleeding cankers of broadleaf hosts in Great Britain, numerous bacterial strains were isolated, identified by 16S rRNA and protein-coding gene sequencing and ultimately classified. During the course of the study, several Gram-negative, facultatively anaerobic strains were isolated from bleeding Platanus x acerifolia (London plane) and Tilia x europaea (common lime) cankers that could not be assigned to an existing species. Partial 16S rRNA gene sequencing placed these strains in the genus Erwinia, as a close phylogenetic relative of Erwinia toletana. In an effort to determine the taxonomic position of the strains, a polyphasic approach was followed including genotypic, genomic, phenotypic, and chemotaxonomic assays. Multilocus sequence analysis based on four protein-coding genes (gyrB, rpoB, infB, and atpD) confirmed the phylogenetic position of the strains as a novel taxon of subgroup 3 of the genus Erwinia, along with E. toletana and E. iniecta, and furthermore, provided support for their reclassification in a novel genus. Whole genome comparisons allowed the delimitation of the novel species and also supported the proposed transfer of subgroup 3 species to a novel genus in the Erwiniaeae. Phenotypically the novel species could be differentiated from E. toletana and E. iniecta, and the novel genus could be differentiated from the closely related genera Erwinia and Mixta. Therefore, we propose (1) the reclassification of E. toletana and E. iniecta in a novel genus, Winslowiella gen. nov., as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov., with W. toletana comb. nov. as the type species (type strain A37T = CFBP 6631T = ATCC 700880T = CECT 5263T), and (2) classification of the novel strains as Winslowiella arboricola sp. nov. (type strain BAC 15a-03bT = LMG 32576T = NCPPB 4696T).
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Liu Q, Zheng H, Wang H, Zhou W, Zhao D, Qiao Z, Zheng J, Ren C, Xu Y. Proteiniphilum propionicum sp. nov., a novel member of the phylum Bacteroidota isolated from pit clay used to produce Chinese liquor. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748686 DOI: 10.1099/ijsem.0.005612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A novel, Gram-stain-negative, rod-shaped, strictly anaerobic bacterium of genus Proteiniphilum of the phylum Bacteroidota, named strain JNU-WLY501T, was isolated from pit clay used to produce strong aroma-type liquor in PR China. The genomic DNA G+C content and genome size of JNU-WLY501T were 41.4 % and 3.9 Mbp, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that JNU-WLY501T was closely related to Proteiniphilum acetatigenes DSM 18083T (95.7 %) and Proteiniphilum saccharofermentans M3/6T (94.9 %). The pairwise average nucleotide identity based on blast and average amino acid identity values of JNU-WLY501T compared with Proteiniphilum saccharofermentans M3/6T were 73.6 and 77.3 %, respectively, which both were lower than the threshold values for bacterial species delineation. The strain grew at 20-40 °C, with optimum growth at 37 °C. The pH range for growth was 5.4-9.1, with optimum growth at pH 7.5. The sodium chloride range for growth was 0.0-4.0 %, with optimum growth at 0 %. The strain did not use glucose, maltose, fructose or starch. Yeast extract, tryptone and peptone supported the growth of JNU-WLY501T, and the main fermentation products were acetate and propionate. The predominant cellular fatty acids (>5 %) of JNU-WLY501T were anteiso-C15 : 0 (30.6 %), anteiso-C17 : 0 (26.1 %), C16 : 0 (7.7 %), iso-C16 : 0 (5.0 %) and iso-C17 : 0 (5.0 %). The respiratory quinone of JNU-WLY501T was MK-5. On the basis of the morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, JNU-WLY501T represents a novel species of the genus Proteiniphilum, for which the name Proteiniphilum propionicum sp. nov. is proposed. The type strain is JNU-WLY501T (=GDMCC 1.2686T=JCM 34753T).
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Affiliation(s)
- Qiuju Liu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Huizhen Zheng
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Huilin Wang
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Weicheng Zhou
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China
| | - Dong Zhao
- Wuliangye Yibin Co., Ltd., No.150 Minjiang West Road, Yibin 644007, PR China.,Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Yibin 644007, PR China.,JNU-WLY Collaborative Innovation Laboratory of Microbiome and Ecological Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Zongwei Qiao
- Wuliangye Yibin Co., Ltd., No.150 Minjiang West Road, Yibin 644007, PR China.,Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Yibin 644007, PR China.,JNU-WLY Collaborative Innovation Laboratory of Microbiome and Ecological Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jia Zheng
- Wuliangye Yibin Co., Ltd., No.150 Minjiang West Road, Yibin 644007, PR China.,Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Yibin 644007, PR China.,JNU-WLY Collaborative Innovation Laboratory of Microbiome and Ecological Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Cong Ren
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China.,JNU-WLY Collaborative Innovation Laboratory of Microbiome and Ecological Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, PR China.,JNU-WLY Collaborative Innovation Laboratory of Microbiome and Ecological Fermentation Technology, Jiangnan University, Wuxi 214122, PR China
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Liu X, Wang D, Yin Z, Sun L, Pang S, Liu J, Li W, Cui S, Huang W, Du Y, Xie Z. Insights into Evolutionary, Genomic, and Biogeographic Characterizations of Chryseobacterium nepalense Represented by a Polyvinyl Alcohol-Degrading Bacterium, AC3. Microbiol Spectr 2022; 10:e0217922. [PMID: 36000867 PMCID: PMC9602593 DOI: 10.1128/spectrum.02179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 12/31/2022] Open
Abstract
Chryseobacterium spp. are Gram-negative rods found ubiquitously in the environment, with certain species being reported as having unusual degrading properties. Polyvinyl alcohol (PVA) is used widely in industry but causes serious global environmental pollution. Here, we report the complete genome sequence of a novel bacterium, AC3, that efficiently degrades PVA. As the representative genome of Chryseobacterium nepalense, key genomic characteristics (e.g., mobile genetic elements, horizontal genes, genome-scale metabolic network, secondary metabolite biosynthesis gene clusters, and carbohydrate-active enzymes) were comprehensively investigated to reveal the potential genetic features of this species. Core genome phylogenetic analysis in combination with average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values provided an accurate taxonomic position of C. nepalense in the genus Chryseobacterium. Comparative genomic analysis of AC3 with closely related species suggested evolutionary dynamics characterized by a species-specific genetic repertoire, dramatic rearrangements, and evolutionary constraints driven by selective pressure, which facilitated the speciation and adaptative evolution of C. nepalense. Biogeographic characterization indicated that this species is ubiquitously distributed not only in soil habitats but also in a variety of other source niches. Bioinformatic analysis revealed the potential genetic basis of PVA degradation in AC3, which included six putative genes associated with the synthesis of PVA dehydrogenase, cytochrome c, oxidized PVA hydrolase, and secondary alcohol dehydrogenase. Our study reports the first complete genome of C. nepalense with PVA-degrading properties, providing comprehensive insights into the genomic characteristics of this species and increasing our understanding of the microbial degradation of PVA. IMPORTANCE Although PVA is a biodegradable polymer, the widespread use of PVA in global industrialization has resulted in serious environmental problems. To date, knowledge of effective and applicable PVA-degrading bacteria is limited, and thus, the discovery of novel PVA biodegraders is pertinent. Here, we isolated a novel bacterial strain, AC3, which efficiently degraded PVA. The complete genome of AC3 was sequenced as the first genome sequence of the species C. nepalense. Comparative genomic analysis was performed to comprehensively investigate the phylogenetic relationships, genome-scale metabolic network, key genomic characteristics associated with genomic evolution, evolutionary dynamics between AC3 and its close relatives, and biogeographic characterization of C. nepalense, particularly regarding the potential genetic basis of PVA degradation. These findings could advance our understanding of the genomic characteristics of C. nepalense and PVA bioremediation.
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Affiliation(s)
- Xinbei Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Dandan Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Li Sun
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Shiqi Pang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Jianing Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Wei Li
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, People’s Republic of China
| | - Shiyu Cui
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Weiwei Huang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Yuhui Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
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Zhang YJ, Sun HN, Xu TT, Zhao DL, Yu CM, Zhang Y, Zhang XY, Chen XL, Zhang YQ, Zhao F. Gilvimarinus xylanilyticus sp. nov., a novel 1,3-xylanase-secreting bacterium isolated from a marine green alga. Front Microbiol 2022; 13:1006116. [PMID: 36353462 PMCID: PMC9638140 DOI: 10.3389/fmicb.2022.1006116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/07/2022] [Indexed: 12/02/2022] Open
Abstract
1,3-xylan, an important organic carbon in the ocean, is peculiar to marine algae. 1,3-xylanase-secreting bacteria and their extracellular 1,3-xylanases play pivotal roles in the degradation and biomass conversion of 1,3-xylan. However, only a few 1,3-xylanase-secreting bacteria and 1,3-xylanases have been reported. Here, we identified a novel marine bacterium capable of secreting 1,3-xylanases, designated as strain HB14T. Phylogenetic analysis revealed that strain HB14T clustered tightly with known species of the genus Gilvimarinus, showing the highest 16S rRNA gene sequence similarity (97.7%) with the type strain of Gilvimarinus chinensis. Based on phylogenetic, genomic, chemotaxonomic and phenotypic studies, strain HB14T was classified as a representative of a novel species in the genus Gilvimarinus, for which the name Gilvimarinus xylanilyticus sp. nov. was proposed. The type strain is HB14T (=CCTCC AB 2022109T = KCTC 92379T). Four 1,3-xylanases secreted by strain HB14T were identified based on genome and secretome analyses, and the two (Xyn65 and Xyn80) with relatively higher abundance in secretome were successfully expressed in Escherichia coli and biochemically characterized. They showed the highest activity at pH 6.0–7.0 and 40°C and released mainly 1,3-xylobiose and 1,3-xylotriose from 1,3-xylan. These data suggest that strain HB14T acts as a player in marine 1,3-xylan degradation and recycling and that its extracellular 1,3-xylanases may have a good potential in 1,3-xylooligosaccharides preparation.
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Affiliation(s)
- Yan-Jiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hai-Ning Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ting-Ting Xu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Dian-Li Zhao
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Chun-Mei Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yi Zhang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Yu-Qiang Zhang,
| | - Fang Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- *Correspondence: Fang Zhao,
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Madhaiyan M, Saravanan VS, See-Too WS, Volpiano CG, Sant’Anna FH, Faria da Mota F, Sutcliffe I, Sangal V, Passaglia LMP, Rosado AS. Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The family
Streptomycetaceae
is a large and diverse family within the phylum
Actinomycetota
. The members of the family are known for their ability to produce medically important secondary metabolites, notably antibiotics. In this study, 19 type strains showing low 16S rRNA gene similarity (<97.3 %) to other members of the family
Streptomycetaceae
were identified and their high genetic diversity was reflected in a phylogenomic analysis using conserved universal proteins. This analysis resulted in the identification of six distinct genus-level clades, with two separated from the genus
Streptacidiphilus
and four separated from the genus
Streptomyces
. Compared with members of the genera
Streptacidiphilus
and
Streptomyces
, average amino acid identity (AAI) analysis of the novel genera identified gave values within the range of 63.9–71.3 %, as has been previously observed for comparisons of related but distinct bacterial genera. The whole-genome phylogeny was reconstructed using PhyloPhlAn 3.0 based on an optimized subset of conserved universal proteins, the results of AAI and percentage of conserved proteins (POCP) analyses indicated that these phylogenetically distinct taxa may be assigned to six novel genera, namely Actinacidiphila gen. nov., Mangrovactinospora gen. nov., Peterkaempfera gen. nov., Phaeacidiphilus gen. nov., Streptantibioticus gen. nov. and Wenjunlia gen. nov.
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Affiliation(s)
- Munusamy Madhaiyan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
| | | | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Camila Gazolla Volpiano
- Department of Pediatrics (Genetics), Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Fábio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, 4365, Brasil Ave, Rio de Janeiro, RJ, Brazil
| | - Iain Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brasil
| | - Alexandre Soares Rosado
- BESE, Biological and Environmental Sciences and Engineering Division, KAUST, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Heo J, Won M, Lee D, Kim JS, Han BH, Kim SJ, Hong SB, Kwon SW. Chryseobacterium oryzae sp. nov. and Chryseobacterium suipulveris sp. nov., isolated from Andong sikhye and pigpen dust, respectively. Int J Syst Evol Microbiol 2022; 72. [PMID: 36201336 DOI: 10.1099/ijsem.0.005532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, mesophilic, rod-shaped bacteria, ADR-1T and SC2-2T, were isolated from Andong sikhye and dust in a pigpen, respectively. The phylogenetic tree on the basis of 16S rRNA gene sequences showed that strains ADR-1T and SC2-2T were members of the genus Chryseobacterium and revealed the highest sequence similarities to Chryseobacterium binzhouense LM2T (97.6 %) and Chryseobacterium koreense Chj707T (94.9 %), respectively. Phylogenomic treeing using 92 core genes clearly indicated that strain ADR-1T clustered with Chryseobacterium echinoideorum CC-CZW010T, Chryseobacterium binzhouense LM2T and Chryseobacterium taihuense CGMCC 1.10941T, and strain SC2-2T formed a compact cluster with Chryseobacterium koreense CCUG 49689T. The digital DNA-DNA hybridization (dDDH) and orthologous average nucleotide identity (ANI) values of strain ADR-1T with the closely related species of the genus Chryseobacterium were ≤24.4 % and ≤80.7 %, and those of strain SC2-2T were ≤24.0 % and ≤77.8 %, respectively, which are well below the cut-off values of species discrimination (>70 % dDDH and >95-96 % ANI). The only respiratory quinone in both strains was menaquinone 6. The polar lipid profile of strain ADR-1T comprised phosphatidylethanolamine, four unidentified aminolipids and three unidentified lipids, while strain SC2-2T contained phosphatidylethanolamine, two unidentified aminolipids, one unidentified aminophospholipid and five unidentified polar lipids. The major fatty acids (>10 %) of strain ADR-1T were iso-C15 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and those of strain SC2-2T were iso-C15 : 0 and anteiso-C15 : 0. On the basis of the results of phenotypic and phylogenetic analyses, strains ADR-1T and SC2-2T represent two distinct novel species in the genus Chryseobacterium, for which the names Chryseobacterium oryzae sp. nov. (type strain ADR-1T=KACC 19311T=NBRC 113104T) and Chryseobacterium suipulveris sp. nov. (type strain SC2-2T=KACC 19313T=NBRC 113106T) are proposed.
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Affiliation(s)
- Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
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Sangal V, Goodfellow M, Jones AL, Sutcliffe IC. A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named
Rhodococcus equi
, ‘Prescottella equi’ and
Rhodococcus hoagii
. As a consequence, we present here the genus name
Prescottella
and that of its nomenclatural type species,
Prescottella equi
comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus
Prescottella
. Nearly a century after the original description of the type strain of the type species as
Corynebacterium equi
, we provide a stable home for
Prescottella equi
and its relatives.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Amanda L. Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Iain C. Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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Sedimentimonas flavescens gen. nov., sp. nov., isolated from sediment of Clam Island, Liaoning Province. Antonie Van Leeuwenhoek 2022; 115:979-994. [PMID: 35672593 DOI: 10.1007/s10482-022-01754-4] [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: 02/16/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
A novel Gram-stain negative, aerobic and ovoid to short rod shaped bacterium with a single polar flagellum, named strain B57T, was isolated from sediment of Clam Island, Liaoning Province, China. The optimal growth of this strain was found to occur at 37 °C, pH 6-6.5, and in the presence of 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B57T forms a distinct lineage within the family Rhodobacteraceae, sharing high 16S rRNA gene sequence similarity with Sinirhodobacter populi sk2b1T (97.4%). The average amino acid identity of B57T and the closely related species were lower than the threshold level for genus delineation. The dominant respiratory quinone of strain B57T was identified as Q-10. The major fatty acids were found to be Summed Feature 8 (C18:1ω7c and/or C18:1ω6c), Summed Feature 3 (C16:1ω7c and/or C16:1ω6c) and C16: 0. The polar lipids were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, one unidentified glycolipid, and one unidentified lipid. The DNA G + C content of strain B57T was determined to be 64.1 mol%. Based on the biochemical, phylogenetic and chemotaxonomic analysis, strain B57T is concluded to represent a novel species of a novel genus, for which the name Sedimentimonas flavescens gen. nov., sp. nov.is proposed. The type strain is B57T (= CGMCC1.19488T = KCTC 92053T).
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Potekhina NV, Ariskina EV, Shashkov AS, Tul’skaya TM, Evtushenko LI. Cell Wall Glycopolymers as a Diagnostic Trait of Arthrobacter crystallopoietes. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Rhodoflexus caldus gen. nov., sp. nov., a new member of the phylum Bacteroidota isolated from a hot spring sediment. Antonie van Leeuwenhoek 2022; 115:889-898. [PMID: 35562517 DOI: 10.1007/s10482-022-01742-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/15/2022] [Indexed: 10/18/2022]
Abstract
A thermophilic bacterium, designated strain SYSU G04325T, was isolated from a hot spring sediment in Yunnan, China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G04325T shows high sequence similarity to Thermoflexibacter ruber NBRC 16677T (86.2%). The strain can be differentiated from other species of the family Thermoflexibacteraceae by its distinct phenotypic and genotypic characteristics. Cells of the strain SYSU G04325T were observed to be aerobic, Gram-stain negative and filamentous. Growth was found to occur optimally at 45 ºC and pH 7.0. In addition, the respiratory quinone was identified as menaquinone-7, while the major fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 and Summed Feature 9 (iso-C17:1ω9c). The polar lipids detected included phosphatidylethanolamine, three unidentified phospholipids, one unidentified glycolipid, five unidentified aminolipids and four unidentified polar lipids. The G + C content of the genomic DNA was determined to be 47.6% based on the draft genome sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G04325T is concluded to represent a novel species of a novel genus in the family Thermoflexibacteraceae, for which the name Rhodoflexus caldus gen. nov., sp. nov. is proposed. The type strain of Rhodoflexus caldus is SYSU G04325T (= MCCC 1K06127T = KCTC 82848T).
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Heidler von Heilborn D, Nover LL, Weber M, Hölzl G, Gisch N, Waldhans C, Mittler M, Kreyenschmidt J, Woehle C, Hüttel B, Lipski A. Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modified atmosphere (MA) packaging plays an important role in improving food quality and safety. By using different gas mixtures and packaging materials the shelf life of fresh produce can significantly be increased. A Gram-negative-staining, rod-shaped, orange-pigmented strain DH-B6T, has been isolated from MA packed raw pork sausage (20% CO2, 80% O2). The strain produced biofilms and showed growth at high CO2 levels of up to 40%. Complete 16S rRNA gene and whole-genome sequences revealed that strain DH-B6T belongs to the genus
Chryseobacterium
, being closely related to strain
Chryseobacterium indologenes
DSM 16777T (98.4%), followed by
Chryseobacterium gleum
NCTC11432T (98.3%) and
Chryseobacterium lactis
KC1864T (98.2%). Average nucleotide identity value between DH-B6T and
C. indologenes
DSM 16777T was 81.1% and digital DNA–DNA hybridisation was 24.9%, respectively. The DNA G+C content was 35.51 mol%. Chemotaxonomical analysis revealed the presence of the rare glycine lipid cytolipin, the serine-glycine lipid flavolipin and the sulfonolipid sulfobacin A, as well as phosphatidylethanolamine, monohexosyldiacylglycerol and ornithine lipid, including the hydroxylated forms. Major fatty acids were iC15 : 0 (50.7%) and iC17 : 1 cis 9 (28.7%), followed by iC15 : 0 2-OH (7.0%) and iC17 : 0 3-OH (6.2%). The isolated strain contained MK-6 as the only respiratory quinone and flexirubin-like pigments were detected as the major pigments. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, the strain DH-B6T (=DSM 110542T=LMG 31915T) represents a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium capnotolerans sp. nov. is proposed. Emended descriptions of the genus
Chryseobacterium
and eight species of this genus based on polar lipid characterisation are also proposed.
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Affiliation(s)
- David Heidler von Heilborn
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Lena-Luisa Nover
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Mareike Weber
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Georg Hölzl
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany
| | - Nicolas Gisch
- Bioanalytical Chemistry, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Claudia Waldhans
- Institute of Animal Sciences, Cold-Chain Management, University of Bonn, Katzenburgweg 7-9, 53115 Bonn, Germany
| | - Maureen Mittler
- Institute of Animal Sciences, Cold-Chain Management, University of Bonn, Katzenburgweg 7-9, 53115 Bonn, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, Cold-Chain Management, University of Bonn, Katzenburgweg 7-9, 53115 Bonn, Germany
| | - Christian Woehle
- Max Planck Institute for Plant Breeding Research, Max Planck-Genome-centre Cologne (MP-GC), Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Bruno Hüttel
- Max Planck Institute for Plant Breeding Research, Max Planck-Genome-centre Cologne (MP-GC), Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - André Lipski
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
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Lee SD, Kim SM, Byeon YS, Yang HL, Chang SH, Kim IS. Tenebrionicola larvae gen. nov., sp. nov., isolated from larvae of mealworm Tenebrio molitor L., and a proposal to transfer Erwinia teleogrylli Liu et al. 2016 to a new genus Entomohabitans as Entomohabitans teleogrylli comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005329] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Two enterobacterial strains, designated YMB-R21T and YMB-R22, were isolated from larvae of mealworm Tenebrio molitor L. and examined for their taxonomic characteristics. A 16S rRNA gene-based neighbour-joining tree showed that the two isolates formed two distinct sublineages within the family
Enterobacteriaceae
and were separated from other genera of the family. The isolates showed 16S rRNA gene sequence similarity of 98.9 % to each other and ≤96.5 % to members of the order
Enterobacteriales
. The phylogenomic analysis based on 92 singly-copy core genes showed that the two isolates belonged to the family
Enterobacteriaceae
and formed a distinct sublineage at a position located remotely from the genera of the family. The loosely associated members were the type strain of
Erwinia teleogrylli
and members of the genus
Shimwellia
. Average nucleotide identity and digital DNA–DNA hybridization values showed that the isolates represented members of a novel species in the family
Enterobacteriaceae
. The values of amino acid identity between the two isolates and the closest relatives were 74.5–75.0 % with the type strain of
E. teleogrylli
and 74.5–74.8 % with the type strains of two
Shimwellia
species, while
E. teleogrylli
showed the amino acid identity values of 76.3–76.5 % with two
Shimwellia
species. Based on the results obtained here, we propose a new genus Tenebrionicola with the description of Tenebrionicola larvae sp. nov. (type strain YMB-R21T=KCTC 82597T=CCM 9152T and strain YMB-R22=KCTC 82598=CCM 9153), with the transfer of
Erwinia teleogrylli
Liu et al. 2016 to a new genus Entomohabitans as Entomohabitans teleogrylli comb. nov. (type strain SCU-B244T=CGMCC 1.12772T=DSM 28222T=KCTC 42022T).
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| | - Seong-Min Kim
- Department Food Bioengineering, Jeju National University, Jeju 63243, Republic of Korea
| | - Yeong-Sik Byeon
- Department Food Bioengineering, Jeju National University, Jeju 63243, Republic of Korea
| | - Hong Lim Yang
- Institute of Hallasan Ecology and Culture, Jeju 63064, Republic of Korea
| | | | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
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Genome-based reclassification of the genus Meiothermus along with the proposal of a new genus Allomeiothermus gen. nov. Antonie van Leeuwenhoek 2022; 115:645-659. [PMID: 35348967 DOI: 10.1007/s10482-022-01723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
Phylogenomic analyses were performed on the nine species of the genus Meiothermus and four species of the genus Calidithermus. Phylogenetic analysis, low values of genomic relatedness indices and functional diversity analysis indicated that Meiothermus silvanus should not be classified within the clades for Meiothermus and Calidithermus but instead be reclassified as a new genus, for which we propose the name Allomeiothermus gen. nov., with Allomeiothermus silvanus comb. nov. as type species. In addition, the species Meiothermus cateniformans Zhang et al. (Int J Syst Evol Microbial 60:840-844, 2010) should also be reclassified as a later heterotypic synonym of Meiothermus taiwanensis Chen et al. (Int J Syst Evol Microbiol 52:1647-1654, 2002) emend. Raposo et al. (2019). This reclassification is based on the high genomic relatedness indices (98.8% ANI; 90.2% dDDH; 99% AAI) that are above the threshold values necessary for defining a new species, as well as on the observation of overlapping functions on Principal Coordinate Analysis plot generated from Clusters of Orthologous Genes.
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