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Ahn S, Choi DHS, Weerawongwiwat V, Kim JH, Sukhoom A, Kim W. Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand. Int J Syst Evol Microbiol 2024; 74. [PMID: 38995165 DOI: 10.1099/ijsem.0.006458] [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: 07/13/2024] Open
Abstract
A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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Wang Q, Zhan PC, Han XL, Lu T. Metagenomic and culture-dependent analysis of Rhinopithecius bieti gut microbiota and characterization of a novel genus of Sphingobacteriaceae. Sci Rep 2024; 14:13819. [PMID: 38879636 PMCID: PMC11180105 DOI: 10.1038/s41598-024-64727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/12/2024] [Indexed: 06/19/2024] Open
Abstract
Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009T, formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009T and its most closely related strains S. kitahiroshimense 10CT, S. pakistanense NCCP-246T and S. faecium DSM 11690T were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009T represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009T = CCTCC AA 2021153T = KCTC 82941T) are proposed.
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Affiliation(s)
- Qiong Wang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
- Center for Pharmaceutical Sciences, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, PR China
| | - Peng-Chao Zhan
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
| | - Xiu-Lin Han
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
| | - Tao Lu
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
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Thite S, Godbole D, Debnath M, Bhatt A, Yadav A, Lodha T, Joseph N, Kirdat K, Boruah D, Sharma R, Joshi A. Alkalimonas mucilaginosa sp. nov. and Alkalimonas cellulosilytica sp. nov. isolated from alkaline Lonar lake, India. Antonie Van Leeuwenhoek 2024; 117:88. [PMID: 38850314 DOI: 10.1007/s10482-024-01986-6] [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: 02/05/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
Two alkaliphilic, Gram-stain-negative bacterial strains (MEB004T and MEB108T) were isolated from water samples collected from Lonar lake, India. The phylogenetic analysis of their 16S rRNA gene sequences showed the highest similarity to A. delamerensis DSM 18314T (98.4%), followed by A. amylolytica DSM 18337T and A. collagenimarina JCM 14267T (97.9%). The genome sizes of strains MEB004T and MEB108T were determined to be 3,858,702 and 4,029,814 bp, respectively, with genomic DNA G + C contents of 51.4 and 51.9%. Average Nucleotide Identity, DNA-DNA Hybridization and Amino Acid Identity values between strains (MEB004T and MEB108T) and A. amylolytica DSM 18337T were (82.3 and 85.5), (25.0 and 29.2) and (86.7 and 90.2%). Both novel strains produced industrially important enzymes, such as amylase, lipase, cellulase, caseinase, and chitinase at pH 10 evidenced by the genomic presence of carbohydrate-active enzymes encoding genes. Genomic analyses further identified pH tolerance genes, affirming their adaptation to alkaline Lonar Lake. Dominant fatty acids were Summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, Summed feature 3, Sum In Feature 2 and C12:0 3OH. The prevalent polar lipids included phosphatidyl ethanolamine, phosphatidyl glycerol, and diphosphatidyl glycerol. The major respiratory quinone was ubiquinone-8. Based on the polyphasic data, we propose the classification of strains MEB004T and MEB108T as novel species within the genus Alkalimonas assigning the names Alkalimonas mucilaginosa sp. nov. and Alkalimonas cellulosilytica sp. nov., respectively. The type strains are MEB004T (= MCC 5208T = JCM 35954T = NCIMB 15460T) and MEB108T (= MCC 5330T = JCM 35955T = NCIMB 15461T).
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Affiliation(s)
- Sonia Thite
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Devika Godbole
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Mahima Debnath
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Agrima Bhatt
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Amit Yadav
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Tushar Lodha
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, Maharashtra, India
| | - Neetha Joseph
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Kiran Kirdat
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India
| | - Dibyajyoti Boruah
- Department of Pathology, Armed Forces Medical College, Pune, 411040, India
| | - Roohani Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Amaraja Joshi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra State, India.
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Yadav A, Teware R, Bhatt A, Bhavsar Y, Maurya A, Thorat V, Vemuluri VR, Kirdat K. Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov. Arch Microbiol 2024; 206:242. [PMID: 38698177 DOI: 10.1007/s00203-024-03970-0] [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: 12/06/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024]
Abstract
A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).
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Affiliation(s)
- Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India.
| | - Ruchi Teware
- Department of Microbiology, Fergusson College, Shivajinagar, Pune, 411 004, India
| | - Agrima Bhatt
- Department of Biosciences and Technology, School of Science and Environmental Studies, Dr. Vishwanath Karad MIT World Peace University, Pune, 411 038, India
| | - Yash Bhavsar
- Department of Microbiology, Fergusson College, Shivajinagar, Pune, 411 004, India
| | - Akanksha Maurya
- Khwaja Moinuddin Chishti Language University, Sitapur Hardoi Road, Lucknow, 226 013, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India
| | - Venkata Ramana Vemuluri
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, 160 003, India
| | - Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune, 411 007, India.
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Ahn S, Weerawongwiwat V, Lee Y, Choi DHS, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Description of Roseibium sediminicola sp. nov. Isolated from Sediment of a Tidal Flat on the Yellow Sea Coast. Curr Microbiol 2024; 81:150. [PMID: 38647555 DOI: 10.1007/s00284-024-03681-1] [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: 10/17/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024]
Abstract
A Gram-stain-negative, aerobic, rod-shaped, motile, flagellated bacterial strain, designated as CAU 1639T, was isolated from the tidal flat sediment on the Yellow Sea in the Republic of Korea. Growth of the isolate was observed at 20-37 °C, at pH 5.0-10.5 and with 0-7% (w/v) NaCl. The genomic DNA G + C content was 60.8%. Phylogenetic analysis, grounded on 16S rRNA gene sequencing, revealed that strain CAU 1639T was closely related to species within the genus Roseibium. It shared the highest similarity with Roseibium album CECT 5095T, followed by Roseibium aggregatum IAM 12614T and Roseibium salinum Cs25T, with 16S rRNA gene sequence similarity ranging from 98.0-98.4%. It was observed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values ranged between 72.5-79.5 and 20.0-22.9%, respectively. The polyphasic taxonomic analysis reveals that strain CAU 1639T represents a novel species in the genus Roseibium with the proposed name Roseibium sediminicola sp. nov. The type strain is CAU 1639T (= KCTC 82430T = MCCC 1K06081T).
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Affiliation(s)
- Soyeon Ahn
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Yunjeong Lee
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - David Hyung-Sun Choi
- Faculty of Arts and Science, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jung-Hoon Yoon
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jung-Sook Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea.
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Chen B, Zhang M, Lin D, Ye J, Tang K. Roseihalotalea indica gen. nov., sp. nov., a halophilic Bacteroidetes from mesopelagic Southwest Indian Ocean with higher carbohydrate metabolic potential. Antonie Van Leeuwenhoek 2024; 117:66. [PMID: 38607563 DOI: 10.1007/s10482-024-01965-x] [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: 02/07/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
The pink-colored and strictly aerobic bacterium strain, designated as TK19036T, was isolated from mesopelagic layer of the Southwest Indian Ocean. This novel isolate can grow at 10-45 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0), and 2-14% NaCl concentrations (w/v) (optimum, 6%). The predominant respiratory quinone was Menaquinone-7. Major polar lipid profiles contained two aminolipids, aminophospholipid, two glycolipids, phosphatidylethanolamine, and three unknown polar lipids. The preponderant cellular fatty acids were iso-C15:0, C16:1 ω5c and iso-C17:0 3-OH. Phylogenetic analyses based on 16S rRNA gene sequence uncovered that the strain TK19036T pertained to the family Catalinimonadaceae under phylum Bacteroidota, and formed a distinct lineage with the closed species Tunicatimonas pelagia NBRC 107804T. The up-to-bacteria-core gene phylogenetic trees also demonstrated a deep and novel branch formed by the strain TK19036T within the family Catalinimonadaceae. Based on chemotaxonomic, phylogenetic and genomic features presented above, strain TK19036T represents a novel species from a novel genus of the family Catalinimonadaceae, for which the name Roseihalotalea indica gen. nov. sp. nov. is proposed. The type strain is TK19036T (= CGMCC 1.18940T = NBRC 116371T).
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Mingzhe Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Dan Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
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Ran Q, Du X, Han L, Wang J, Li YZ. Three novel species of the genus Flavobacterium, Flavobacterium odoriferum sp. nov., Flavobacterium fragile sp. nov. and Flavobacterium luminosum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2024; 74. [PMID: 38305772 DOI: 10.1099/ijsem.0.006258] [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: 02/03/2024] Open
Abstract
Three Gram-stain-negative, rod-shaped, non-spore-forming bacteria were isolated from activated sludge samples. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that the three strains, designated HXWNR29T, HXWNR69T and HXWNR70T, had the highest sequence similarity to the type strains Flavobacterium cheniae NJ-26T, Flavobacterium channae KSM-R2A30T and Flavobacterium amniphilum KYPY10T with similarities of 97.66 %, 98.66 and 98.14 %, respectively. The draft genomes of these three strains were 2.93 Mbp (HXWNR29T), 2.69 Mbp (HXWNR69T) and 2.65 Mbp (HXWNR70T) long with DNA G+C contents of 31.84 %, 32.83 % and 34.66 %, respectively. These genomes contained many genes responsible for carbohydrate degradation and antibiotic resistance. The major fatty acids (>5 %) included iso-C15 : 0, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. The major menaquinone was MK-6 for all the three strains. The average nucleotide identity (ANI; 72.7-88.5 %) and digital DNA-DNA hybridization (dDDH; 19.6-35.3 %) results further indicated that these three strains represented three novel species within the genus Flavobacterium, for which the names Flavobacterium odoriferum sp. nov. (type strain HXWNR29T = KCTC 92446T = CGMCC 1.61821T), Flavobacterium fragile sp. nov. (type strain HXWNR69T = KCTC 92468T = CGMCC 1.61442T) and Flavobacterium luminosum sp. nov. (type strain HXWNR70T = KCTC 92447T = CGMCC 1.61443T) are proposed.
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Affiliation(s)
- Qi Ran
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Xinran Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, PR China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
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Osman G, Sayim G, Yang H, Gu M, Sun J, Gao Y, Zhu J, Song S, Yi Y, Wang W, Zhang Z. Pontibacter harenae sp. nov., isolated from the soil of a Populus euphratica forest. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917138 DOI: 10.1099/ijsem.0.006128] [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: 11/03/2023] Open
Abstract
A Gram-negative, rod-shaped, aerobic and light pink-pigmented bacterium, designated XAAS-A31T, was isolated from the soil of a Populus euphratica forest located near Hotan City, Xinjiang, PR China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that XAAS-A31T belongs to the genus Pontibacter, family Hymenobacteraceae, and shows highest sequence similarity to Pontibacter silvestris XAAS-R86T (96.2 %). The digital DNA-DNA hybridization (22.0 %-19.2 %) and orthologous average nucleotide identity (74.1 %-72.7 %) values relative to closest validly published Pontibacter species were lower than the recommended thresholds of 70 and 96 %, respectively. The cells grew at 4-40 °C (optimum, 28-30 °C), at pH 6.5-8.5 (pH 7.0-7.5) and with 0-8% NaCl (0.5-2.0% NaCl). The main respiratory quinone of XAAS-A31T is MK-7, and the principal cellular fatty acids are iso-C15 : 0, iso-C17 : 0 3OH and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The major polar lipids are phosphatidylethanolamine, three unidentified amino-phospholipids, one unidentified glycolipid and eight unidentified lipids. The genome length of strain XAAS-A31T is 5.48 Mbp with a DNA G+C content of 44.2 mol% and 4013 protein-coding genes. Phenotypic and genotypic data suggested that XAAS-A31T represents a novel Pontibacter species, for which we propose the name Pontibacter harenae sp. nov. and type strain XAAS-A31T (=CCTCC AB 2017162T=KCTC 62049T).
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Affiliation(s)
- Ghenijan Osman
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
- College of Grassland Science, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Gulnisa Sayim
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Hongmei Yang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Meiying Gu
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Jian Sun
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Yan Gao
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Jing Zhu
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Suqin Song
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Yuanyang Yi
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Wei Wang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
| | - Zhidong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, PR China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
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Prince RC, Dutton PL, Gunner MR. The aprotic electrochemistry of quinones. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148558. [PMID: 35413248 DOI: 10.1016/j.bbabio.2022.148558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/26/2022] [Accepted: 04/05/2022] [Indexed: 05/09/2023]
Abstract
Quinones play important roles in biological electron transfer reactions in almost all organisms, with specific roles in many physiological processes and chemotherapy. Quinones participate in two-electron, two-proton reactions in aqueous solution at equilibrium near neutral pH, but protons often lag behind the electron transfers. The relevant reactions in proteins are often sequential one electron redox processes without involving protons. Here we report the aprotic electrochemistry of the two half-couples, Q/Q.- and Q.-/Q=, of 11 parent quinones and 118 substituted 1,4-benzoquinones, 91 1,4-naphthoquinones, and 107 9,10-anthraquinones. The measured redox potentials are fit quite well with the Hammett para sigma (σpara) parameter. Occasional exceptions can involve important groups, such as methoxy substituents in ubiquinone and hydroxy substituents in therapeutics. These can generally be explained by reasonable conjectures involving steric clashes and internal hydrogen bonds. We also provide data for 25 other quinones, 2 double quinones and 15 non-quinones, all measured under similar conditions.
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Affiliation(s)
| | - P Leslie Dutton
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 10104, USA
| | - M R Gunner
- Physics Department City College of New York in the City University of New York, NY 10031, USA.
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10
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Zi ZD, Wen W, Ma F, Li W, Wang ZX, Lu J, Lv J. Microvirga puerhi sp. nov., isolated from Puerh tea garden soil. Arch Microbiol 2022; 204:390. [PMID: 35699786 DOI: 10.1007/s00203-022-02988-6] [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] [Received: 12/20/2021] [Revised: 04/18/2022] [Accepted: 05/12/2022] [Indexed: 11/02/2022]
Abstract
Strain WGZ8T was isolated from a soil sample of Puerh tea garden in Pu'er city, Southwest China. The isolate was rod-shaped, Gram-stain negative, facultative anaerobic, non-motile. Growth occurred within 0-3.0% (w/v) NaCl (optimal concentration, 0-1.0%), pH 5.0-11.0 (optimal pH, 7.0) and 10-40 °C (optimal temperature, 28 °C). 16S rRNA gene sequence-based phylogenetic and phylogenomic analysis revealed that WGZ8T belonged to the genus Microvirga. Its major cellular fatty acids were C19:0 cyclo ω8c, C16:0, C18:1ω7c and/or C18:1ω6c. The profile of polar lipids included phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phosphatidylglycerol. The only respiratory quinone was detected as ubiquinone 10 (Q-10). The genome size of strain WGZ8T was 5.17 MB, and the content of DNA G + C was 61 mol%. Based on the results of digital DNA-DNA hybridization and phenotypic results, strain WGZ8T could be concluded as a novel species of the genus Microvirga, for which the name Microvirga puerhi sp. nov. is proposed. The type strain is WGZ8T (= CGMCC 1.19171 T = JCM 35317 T).
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Affiliation(s)
- Zhi-Da Zi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wen Wen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fu Ma
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhao-Xuan Wang
- Shijiazhuang People's Medical College, Shijiazhuang, 050091, Hebei, China
| | - Jun Lu
- Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, 1142, New Zealand
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Li W, Wang ZX, Ma F, Zi ZD, Chen HY, Zhou D, Lv J. Brevibacillus dissolubilis sp. nov., Isolated from Fresh Water. Curr Microbiol 2022; 79:194. [PMID: 35579716 DOI: 10.1007/s00284-022-02891-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
Abstract
A Gram-positive-staining, strictly aerobic, motile, ellipsoidal endospore-forming bacterial strain, designated CHY01T, was isolated from the Chishui river in a section of Maotai Town, Guizhou Province, Southwest China. Strain CHY01T was found to grow optimally at pH 8.0 and 28 °C. The 16S rRNA gene sequence analysis indicated that strain CHY01T belonged to the genus Brevibacillus and clustered with the type strain of Brevibacillus panacihumi, with which it exhibited 16S rRNA gene sequence similarity values of 97.8%. The predominant respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major fatty acids were C14:0, iso-C15:0, anteiso-C15:0, C16:0, C15:1iso-H and/or C13:0 3-OH, and C16:1ω7c and/or C16:1ω6c. Genome sequencing revealed a genome size of 6.1 Mbp and a G + C content of 50.6%. The results of physiological and biochemical tests allowed strain CHY01T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Pairwise determined whole-genome average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values suggested that strain CHY01T represents a new species, for which we propose the name Brevibacillus dissolubilis sp. nov. with the type strain CHY01T (= CGMCC 1.15916 T = KCTC 33863 T).
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Affiliation(s)
- Wei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhao-Xuan Wang
- Shijiazhuang People's Medical College, Shijiazhuang, 050091, Hebei, China
| | - Fu Ma
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhi-Da Zi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Han-Yi Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - De Zhou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Yang R, Zhou D, Wang Q, Peng W, Gong W, Zhao M, Ji A, Wang X, Yan L, Lv J, Sheng J. Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar. Int J Syst Evol Microbiol 2021; 71. [PMID: 34499597 DOI: 10.1099/ijsem.0.004992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3T, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Massilia. The closest phylogenetic relative was Massilia arenae CICC 24458T (99.5 %), followed by M. timonae CCUG45783T (97.9 %), M. oculi CCUG43427AT (97.8 %), and M. aurea DSM 18055T (97.8 %). The major fatty acids were C16 : 0 and C16 : 1 ω7c and/or C16 : 1 ω6c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA-DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3T and Massilia arenae CICC 24458T was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3T represents a new species, for which we propose the name Massilia puerhi sp. nov. with the type strain SJY3T (=CGMCC 1.17158T=KCTC 82193T).
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Affiliation(s)
- Ruijuan Yang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, PR China.,College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, PR China.,College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - De Zhou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qiaomei Wang
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - Wenshu Peng
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - Wanying Gong
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - Miaomiao Zhao
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - Aibing Ji
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - Xuanjun Wang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, PR China.,College of Science, Yunnan Agricultural University, Kunming 650201, PR China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650201, PR China
| | - Liang Yan
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan 665000, PR China.,Pu'er Institute of Pu-erh Tea, Pu'er, Yunnan 665000, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jun Sheng
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, PR China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650201, PR China
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Litoribacter populi sp. nov., isolated from the soil of a Populus euphratica forest. Arch Microbiol 2021; 203:5011-5016. [PMID: 34282466 DOI: 10.1007/s00203-021-02488-z] [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: 04/11/2020] [Revised: 06/23/2021] [Accepted: 07/10/2021] [Indexed: 10/20/2022]
Abstract
A Gram-stain-negative, rod-shaped, and orange-pigmented bacterium, designated XAAS-A1T, was isolated from the soil of a Populus euphratica forest. The main respiratory quinone of XAAS-A1T is MK-7, and the principal cellular fatty acids are iso-C15:0, C17:1 ω6c, Iso-C17:0 3OH, and summed feature 3 (C16:1ω6c and/or C16:1ω7c). The major polar lipids are phosphatidylethanolamine, phosphatidylcholine, and two unidentified lipids. The 16S rRNA gene sequence analysis indicated that XAAS-A1T belongs to the genus Litoribacter within the family Cyclobacteriaceae, having the highest sequence similarities to Litoribacter ruber KCTC 22899T (97.1%) and L. alkaliphilus KCTC 32217T (96.9%). XAAS-A1T has a DNA G + C content of 42.1 mol%. The orthoANI and the digital DNA-DNA hybridization values were markedly lower than the recommended threshold values of 96% and 70%. Phenotypic and genotypic data suggest that XAAS-A1T represents a novel species of the genus Litoribacter, for which we propose the name Litoribacter populi sp. nov. and XAAS-A1T (= CCTCC AB 2017159T = KCTC 62045T) as the type strain.
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Devosia sediminis sp. nov., isolated from subterranean sediment. Arch Microbiol 2021; 203:4517-4523. [PMID: 34146114 DOI: 10.1007/s00203-021-02448-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
A novel Gram-negative, cream-colored, rod-shaped, aerobic, non-motile bacterium, designated MSA67T, was isolated from a subterranean sediment sample of the Mohe Basin in Northeast China. Strain MSA67T was detected to grow at 4-40 °C (optimum 28-30 °C), pH 5.0-10.0 (optimum, pH 7.0) and in 0.0-8.0% (w/v) NaCl (optimum 2.0-3.0%). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MSA67T was a member of the genus Devosia, with the highest similarity with D. riboflavina IFO13584T (98.0%) and D. chinhatensis IPL18T (97.0%). The major cellular fatty acids are C16:0, C18:1ω7c 11-methyl and C18:1ω6c and/or C18:1ω7c. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, glycolipids and three unidentified phospholipids. The major respiratory quinone is ubiquinone 10 (Q-10). The genomic size of strain MSA67T is 4.1 MB and DNA G + C content is 63.6%. Based on genotypic, phenotypic and phylogenetic results, strain MSA67T is concluded to represent a novel species of the genus Devosia, for which the name Devosia sediminis sp. nov. is proposed. The type strain is MSA67T (= CGMCC 1.18467T = KCTC 82192T).
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A rapid and efficient method for the extraction and identification of menaquinones from Actinomycetes in wet biomass. BMC Microbiol 2021; 21:175. [PMID: 34103006 PMCID: PMC8188722 DOI: 10.1186/s12866-021-02240-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Menaquinones are constituents of prokaryote cell membranes where they play important functions during electron transport. Menaquinone profiles are strongly recommended for species classification when proposing a new Actinomycetes taxon. Presently, the most widely used methods to determine menaquinones are based on freeze-dried cells. Taxonomic research in our lab has revealed that menaquinone concentrations are low for some species of the genus Microbacterium, leading to difficulties in identifying menaquinones. Results Menaquinones extracted using the novel lysozyme-chloroform-methanol (LCM) method were comparable in quality to those obtained using the Collins method, the most widely used method. All tested strains extracted via the LCM method showed higher concentrations of menaquinones than those extracted via the Collins method. For some Microbacterium strains, the LCM method exhibited higher sensitivity than the Collins method, and more trace menaquinones were detected with the LCM method than the Collins method. In addition, LCM method is faster than the Collins method because it uses wet cells. Conclusion The LCM method is a simple, rapid and efficient technique for the extraction and identification of menaquinones from Actinomycetes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02240-z.
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Godinho O, Botelho R, Albuquerque L, Wiegand S, Kallscheuer N, da Costa MS, Lobo-da-Cunha A, Jogler C, Lage OM. Bremerella alba sp. nov., a novel planctomycete isolated from the surface of the macroalga Fucus spiralis. Syst Appl Microbiol 2021; 44:126189. [PMID: 33852992 DOI: 10.1016/j.syapm.2021.126189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
A bacterial strain, designated FF15T, was isolated from the thallus surface of the macroalga Fucus spiralis sampled on a rocky beach in Porto, Portugal. Based on the 16S rRNA gene sequence, strain FF15T was affiliated to the phylum Planctomycetes. This strain forms white colonies on modified M13 medium and the cells are pear-shaped, can form rosettes, divide by polar budding and are motile. The novel isolate is mesophilic and neutrophilic with an optimum growth temperature of about 30 °C and an optimum pH for growth between 6.5 and 7.5. It showed growth over a broad range of salinities (0-9% NaCl - optimum at 1.5%). No additional vitamins are required for growth. It is cytochrome c oxidase and catalase positive. The major respiratory quinone was menaquinone 6 (MK-6). Genome sequencing revealed a genome size of 6.37 Mbp and a DNA G + C content of 54.2%. Analysis of phylogenetic markers, including similarities of the 16S rRNA gene sequence, rpoB gene sequence, as well as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI), suggest the affiliation of strain FF15T to "Bremerella", a recently described genus in the family Pirellulaceae. Based on the genotypic, phylogenetic, chemotaxonomic, physiological and biochemical characterization, we described a new species represented by strain FF15T (=CECT 8078T = LMG 31936T), for which we propose the name Bremerella alba snov.
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Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Raquel Botelho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Luciana Albuquerque
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-504 Coimbra, Portugal
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands; Institute for Biological Surfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Milton S da Costa
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-504 Coimbra, Portugal; Departamento de Ciências da Vida, Universidade de Coimbra, 3000-456 Coimbra, Portugal
| | - Alexandre Lobo-da-Cunha
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
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Darji H, Verma N, Lugani Y, Mehrotra P, Sindhu DK, Vemuluri VR. Polyphasic characterization of and genomic insights into a haloalkali-tolerant Saccharibacillus alkalitolerans sp. nov., that produces three cellulase isozymes and several antimicrobial compounds. Antonie van Leeuwenhoek 2021; 114:1043-1057. [PMID: 33913068 DOI: 10.1007/s10482-021-01575-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
A cellulase producing novel bacterial strain VR-M41T was isolated from an open-air vegetable and fruit market. Cells are found to be rod-shaped, endospore forming, positive for Gram's stain and negative for catalase, oxidase and urease. Strain VR-M41T was halotolerant (upto 8.0% NaCl, w/v), motile and facultative anaerobe. It grew at wide range of pH (6.0-10.0) and temperatures (20-40 °C). Strain VR-M41T produced three isozymes of Carboxymethylcellulase. The 16S rRNA gene sequence of strain VR-M41T was 97.3% similar to both Saccharibacillus kuerlensis DSM 22868T and Saccharibacillus sacchari DSM 19268T, and less than 96.4% with the rest of the valid species of the genus Saccharibacillus. Whole-genome ANI, dDDH and genome phylogenetic tree analysis revealed that strain VR-M41T significantly differed from Saccharibacillus kuerlensis DSM 22868T and Saccharibacillus sacchari DSM 19268T (ANI 79.6-79.7% and dDDH 23.1%). The strain comprised of MK-7 and anteiso-C 15:0 (42.2%) as predominant isoprenoid quinone and fatty acid respectively. Major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The draft genome of strain VR-M41T consisted of 5,386,426 base pairs with 5103 annotated genes, out of which 2147 corresponded to hypothetical proteins and 2956 with functional assignments. Pan-genome analysis revealed the presence of 2998 core genes, 828 accessory genes, and 1131 unique genes of Saccharibacillus. Strain VR-M41T produced antimicrobials against Staphylococcus aureus, Streptococcus pneumoniae, Micrococcus luteus and Shigella flexneri. Significant phenotypic and genotypic differentiating characteristics from closely related species, indicated that strain VR-M41T is a novel species of the genus Saccharibacillus, for which the name Saccharibacillus alkalitolerans sp. nov., is proposed. The type strain is VR-M41T (= KCTC 43183T=NBRC 114337T).
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Affiliation(s)
- Himanshu Darji
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Neha Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Yogita Lugani
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Priyam Mehrotra
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Dev Kant Sindhu
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Venkata Ramana Vemuluri
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Yang RJ, Zhou D, Wang QM, Han L, Peng WS, Liu L, Wang XJ, Yan L, Lv J, Sheng J. Puerhibacterium puerhi gen. nov., sp. nov., a novel member of the family Promicromonosporaceae, isolated from Pu-erh tea pile-fermentation. Arch Microbiol 2021; 203:1509-1518. [PMID: 33398399 DOI: 10.1007/s00203-020-02151-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/28/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
A Gram-staining positive aerobic bacterium, designated TLY-12T, was isolated from the Pu-erh tea pile-fermentation process in Pu'er city, Yunnan, China. Strain TLY-12T grew at 15-37 °C (optimum, 30 °C), pH 6.0-11.0 (optimum, pH 9.0) and 0-9.0% (w/v) NaCl (optimum, 3.0%). The major cellular fatty acids were anteiso-C15:0, C16:0 and iso-C16:0. The respiratory quinone were menaquinones MK-9 (H2) and MK-9 (H4). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phosphoglycolipid (PGL), glycolipid (GL) and an unidentified phospholipid (PL). The peptidoglycan contained glutamic acid, aspartic acid, alanine and lysine, with the last named being the diagnostic diamino acid. Whole-cell sugars of the isolate were ribose, galactose and glucose. Phylogenetic analyses of 16S rRNA gene showed that this strain belonged to the family Promicromonosporaceae, and was most closely related to Isoptericola cucumis DSM 101603 T, which gave sequence similarity of 97.9%. Genome sequencing revealed a genome size of 3.91 Mbp and a G + C content of 75.0%. Average nucleotide identity and digital DNA-DNA hybridization values were all below the species threshold of described Promicromonosporaceae species. Genome phylogenetic analysis showed that strain TLY-12T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae. Based on the phylogenetic, phenotypic, chemotaxonomic and genome pairwise data, strain TLY-12T is considered to represent a novel species in a new genus in the family Promicromonosporaceae, for which the name Puerhibacterium puerhi gen. nov, sp. nov. is proposed. The type strain is TLY-12T (= CGMCC 1.17157T = KCTC 49467T).
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Affiliation(s)
- Rui-Juan Yang
- Key Laboratory of Pu-Er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.,College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan, 665000, China.,Pu'er Institute of Pu-Erh Tea, Pu'er, Yunnan, 665000, China
| | - De Zhou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qiao-Mei Wang
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan, 665000, China.,Pu'er Institute of Pu-Erh Tea, Pu'er, Yunnan, 665000, China
| | - Lu Han
- MyGenostics Inc., Beijing, 101318, China
| | - Wen-Shu Peng
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan, 665000, China.,Pu'er Institute of Pu-Erh Tea, Pu'er, Yunnan, 665000, China
| | - Li Liu
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan, 665000, China.,Pu'er Institute of Pu-Erh Tea, Pu'er, Yunnan, 665000, China
| | - Xuan-Jun Wang
- Key Laboratory of Pu-Er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.,College of Science, Yunnan Agricultural University, Kunming, 650201, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650201, China
| | - Liang Yan
- College of Tea (Pu'er), West Yunnan University of Applied Sciences, Pu'er, Yunnan, 665000, China. .,Pu'er Institute of Pu-Erh Tea, Pu'er, Yunnan, 665000, China.
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Jun Sheng
- Key Laboratory of Pu-Er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650201, China.
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19
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Paenibacillus puerhi sp. nov., isolated from the rhizosphere soil of Pu-erh tea plants (Camellia sinensis var. assamica). Arch Microbiol 2021; 203:1375-1382. [PMID: 33386866 DOI: 10.1007/s00203-020-02135-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
An aerobic, Gram-staining-positive, rod-shaped, endospore-forming and motile bacterial strain, designated SJY2T, was isolated from the rhizosphere soil of tea plants (Camellia sinensis var. assamica) collected in the organic tea garden of the Jingmai Pu-erh tea district in Pu'er city, Yunnan, southwest China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Paenibacillus. The closest phylogenetic relative was Paenibacillus filicis DSM 23916T (98.1% similarity). The major fatty acids (> 10% of the total fatty acids) were anteiso-C15:0 and isoC16:0. The major respiratory quinone was MK-7 and the major polar lipid was diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The peptidoglycan contained glutamic acid, serine, alanine and meso-diaminopimelic acid. Genome sequencing revealed a genome size of 6.71 Mbp and a G + C content of 53.1%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA-DNA hybridization (dDDH) values suggested that strain SJY2T represents a new species, for which we propose the name Paenibacillus puerhi sp. nov. with the type strain SJY2T (= CGMCC 1.17156T = KCTC 43242T).
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20
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Shin SK, Yi H. Urechidicola croceus gen. nov., sp. nov., a member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2020; 70:1751-1757. [DOI: 10.1099/ijsem.0.003966] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-flagellated, non-gliding, aerobic bacterial strain, designated LPB0138T, was isolated from a marine spoon worm (Urechis unicinctus). The strain LPB0138T contains a circular chromosome of 3.43 Mb with a DNA G+C content of 30.4 mol%. The genome includes 2987 protein-coding genes and two copies of rRNA operons. The 16S rRNA gene sequence analysis showed that the isolate occurred within a clade containing only members of the family
Flavobacteriaceae
. The highest sequence similarity was observed with the genus
Lutibacter
(93.0–94.3 %), but the phylogenetic leaf of the new isolate did not belong to any of the genera known in the family
Flavobacteriaceae
. The low sequence similarity and the phylogenetic tree topology implied the novel generic status of the new isolate. The phenotypic properties of the strain LPB0138T also differentiated this isolate from its neighbour genera by showing a distinctive fatty acid composition, unique polar lipids profile, and low DNA G+C content. The LPB0138T strain contained menaquinone 6 as the isoprenoid quinone; iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH, and iso-C17 : 0 3-OH as the major fatty acids; and phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, and unidentified lipids as the major polar lipids. Based on the polyphasic taxonomic data obtained, the LPB0138T strain is considered to represent a novel species in a novel genus of the family Flavobacteriaceae, for which the name Urechidicola croceus gen. nov., sp. nov. was proposed. The type strain is LPB0138T (=KACC 18889T;=JCM 31563T).
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Affiliation(s)
- Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
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21
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He XL, Zhou D, Gao H, Huang FQ, Li H, Lv J. Dyadobacter bucti sp. nov., isolated from subsurface sediment. Int J Syst Evol Microbiol 2020; 70:2281-2287. [PMID: 32039747 DOI: 10.1099/ijsem.0.004030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, yellow-pigmented, rod-shaped, aerobic, non-motile, non-spore-forming bacterium, designated strain QTA69T, was isolated from a subsurface sediment sample collected at the Qiangtang basin, Qinghai-Tibetan Plateau, PR China. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain QTA69T was a member of the genus Dyadobacter and was closely related to Dyadobacter sediminis, Dyadobacter ginsengisoli and Dyadobacter psychrophilus with sequence similarities from 97.90 % to 96.85 %. Strain QTA69T grew at 4-35 °C, and the optimum temperature was 25-28 °C. It grew at the pH range of 6.0-9.0 (optimum, pH 7.0-8.0) and its NaCl tolerance was 0-2.0 % (optimum, 0-1.0 %). The major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and C 16:1ω6c/C16 : 1ω7c), iso-C15 : 0 and C16 : 1ω5c. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. Genome sequencing revealed a genome size of 8.41 Mbp and a G+C content of 46.87 mol%. Based on whole genome average nucleotide identity values, phenotypic data, phylogenetic data and genotypic data, strain QTA69T represents a novel species of genus Dyadobacter, for which the name Dyadobacter bucti sp. nov is proposed. The type strain is QTA69T (=CGMCC 1.13688T=KCTC 72024T).
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Affiliation(s)
- Xian-Lin He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - De Zhou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Huiqun Gao
- Huiqun fertilizer co Ltd., Horqin Left Middle Banner, Inner Mongolia Autanomous Region 029315, PR China
| | - Fa-Qi Huang
- Dongguan Science & Technology Consulting Service Center, Dongguan city, Guangdong Province 523007, PR China
| | - Hao Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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22
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Baek MG, Shin SK, Yi H. Sphingorhabdus lutea sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2019; 69:3593-3598. [DOI: 10.1099/ijsem.0.003662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Min-gyung Baek
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
- School of Biosystem, and Biomedical Science, Korea University, Seoul, Republic of Korea
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23
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Zhou D, Tan X, Zhang W, Chen HY, Fan QM, He XL, Lv J. Rhodoferax bucti sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2019; 69:3903-3909. [PMID: 31498061 DOI: 10.1099/ijsem.0.003700] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, peach-brown-pigmented, slightly curved-rod-shaped, aerobic, non-motile bacterium, designated GSA243-2T, was isolated from fresh water samples collected from the Chishui River flowing through Maotai, Guizhou, south-west PR China. Phenotypic, chemotaxonomic and genomic traits were investigated. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Rhodoferax. The closest phylogenetic relative was Rhodoferax saidenbachensis ATCC BAA-1852T (98.35 %). The major fatty acids were C16: 0 and C16 : 1ω6c and/or C16 : 1ω7c. The major respiratory quinone was ubiquinone Q-8 and the major polar lipid was phosphatidylethanolamine. Genome sequencing revealed a genome size of 3.67 Mbp and a G+C content of 61.17 mol%. Pairwise-determined whole genome average nucleotide identity values and digital DNA-DNA hybridization values suggested that strain GSA243-2T represents a new species, for which we propose the name Rhodoferaxbucti sp. nov. with the type strain GSA243-2T (=CGMCC 1.16288T=KCTC 62564T).
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Affiliation(s)
- De Zhou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Xu Tan
- Nutraceutical Research Division, Tasly Holding Group Co., Ltd., Tianjin 300040, PR China
| | - Wei Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Han-Yi Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qiu-Ming Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Xian-Lin He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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24
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Koehn JT, Beuning CN, Peters BJ, Dellinger SK, Van Cleave C, Crick DC, Crans DC. Investigating Substrate Analogues for Mycobacterial MenJ: Truncated and Partially Saturated Menaquinones. Biochemistry 2019; 58:1596-1615. [DOI: 10.1021/acs.biochem.9b00007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Fan QM, Zhang RG, Chen HY, Feng QQ, Lv J. Sphingomonas floccifaciens sp. nov., isolated from subterranean sediment. Int J Syst Evol Microbiol 2018; 69:1531-1536. [PMID: 30204585 DOI: 10.1099/ijsem.0.002983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, non-sporulating, rod-shaped, orange-pigmented bacterium, designated strain FQM01T, was isolated from a subterranean sediment sample in the Mohe permafrost area, China. Strain FQM01T grew optimally at 25 °C, pH 7.0 and NaCl concentration of 0 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FQM01T belonged to the genus Sphingomonas. The closest phylogenetic relative was Sphingomonas spermidinifaciens GDMCC 1.657T (97.6 %), followed by Sphingomonas mucosissima DSM 17494T (97.2 %). The DNA G+C content of the isolate was 66.9 mol%. Strain FQM01T contained Q-10 as the predominant ubiquinone, and C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C16 : 0, C14 : 0 2-OH and C18 : 1ω7c 11 methyl as the major fatty acids. Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified glycolipid. Only sym-homospermidine was detected as the polyamine. On the basis of phylogenetic and phenotypic data, strain FQM01T is considered to represent a novel species of Sphingomonas for which the name Sphingomonasfloccifaciens sp. nov. is proposed. The type strain is FQM01T (=CGMCC 1.15797T=KCTC 52630T).
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Affiliation(s)
- Qiu-Ming Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Ren-Gang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Han-Yi Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qing-Qing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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26
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Osman G, Wang Z, Wang N, Shayimu G, Hou M, Guo W, Yang X. Pontibacter silvestris sp. nov., isolated from the soil of a Populus euphratica forest and emended description of the genus Pontibacter. Int J Syst Evol Microbiol 2018; 68:3243-3247. [PMID: 30141769 DOI: 10.1099/ijsem.0.002972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain XAAS-R86T, a Gram-stain-negative, short rod-shaped, non-motile, aerobic bacterium, was isolated from a Populus euphratica forest near the city of Hotan, Xinjiang, PR China. The cells were found to be positive for catalase and oxidase activities. Growth occurred optimally at 28-30 °C, pH 7.0-7.5 and in the presence of 0.5-2.0 % NaCl (w/v). The results of phylogenetic analysis of the 16S rRNA gene indicated that XAAS-R86T represents a member of the genus Pontibacter within the family Hymenobacteraceae. Pontibacter akesuensis CCTCC AB 206086T is the most closely related species with a validly published name, based on 16S rRNA gene sequence identity (95.7 %). The DNA G+C content of the strain is 43.9 mol%. The main respiratory quinone is MK-7 and the major cellular fatty acids are summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B) and iso-C15 : 0 and its major polar lipids are phosphatidylethanolamine and two unidentified lipids. On the basis of the results of tests performed using a polyphasic approach, XAAS-R86T represents a novel species of the genus Pontibacter, for which the name Pontibactersilvestris sp. nov. is proposed, with the type strain XAAS-R86T (=CCTCC AB 2017165T=KCTC 62047T).
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Affiliation(s)
- Ghenijan Osman
- 1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Zhifang Wang
- 1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Ning Wang
- 1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Gulinisha Shayimu
- 1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Min Hou
- 1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Wenchao Guo
- 1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China.,2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China
| | - Xinping Yang
- 2Xingjian Laboratory of Special Environmental Microbiology, Urumqi, 830091, PR China.,1Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
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27
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Chen H, Han L, Feng Q, Fan Q, Lv J. Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment. Int J Syst Evol Microbiol 2018; 68:2749-2754. [PMID: 30024374 DOI: 10.1099/ijsem.0.002866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming bacterial strain, designated DK6-66T, was isolated from subsurface sandstone sediment located in the Qilian Mountains in Qinghai Province, Northwest China. Strain DK6-66T was found to grow optimally at pH 7.0 and 22 °C. The 16S rRNA gene sequence analysis indicated that strain DK6-66T belonged to the genus Hymenobacter and clustered with the type strain of Hymenobacter arcticus, with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. The DNA G+C content was 60.4 mol%. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, anteiso-C17 : 1 B and/or iso-C17 : 1 I, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω5c. On the basis of phylogenetic and phenotypic data, strain DK6-66T was classified in the genus Hymenobacter as a member of a novel species, for which the name Hymenobacterbucti sp. nov. is proposed. The type strain is DK6-66T (=CGMCC 1.15795T=KCTC 52629T).
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Affiliation(s)
- Hanyi Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qingqing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qiuming Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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28
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Shin SK, Kim E, Yi H. Gramella salexigens sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2018; 68:2381-2385. [PMID: 29851376 DOI: 10.1099/ijsem.0.002850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, aerobic bacterial strain, designated LPB0144T was isolated from the seawater of South Sea, Korea. The 16S rRNA gene sequence was found to share the highest sequence similarity to Gramella sediminilitoris GHTF-27T (97.7 %) and the strain branched within the radiation of the genus Gramella in phylogenetic trees. Thus, the taxonomic position of the novel isolate was investigated using a polyphasic approach and complete genome sequencing. Strain LPB0144T has a circular chromosome of 2.98 Mb with DNA G+C content of 38.2 mol%. The genome includes 2604 protein-coding genes and three copies of rRNA operons. The detected respiratory quinone (MK-6) and the major polar lipid (phosphatidylethanolamine) resemble the chemotaxonomic profile of other Gramella species. The major cellular fatty acid profile (iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 3-OH and anteiso-C15 : 0) is also within the range of Gramella, but detailed composition and amounts were found to be different from those of closely related neighbours. Many biochemical and physiological characteristics also distinguished the isolate from other species within the genus Gramella. On the basis of polyphasic taxonomic data obtained here, we propose strain LPB0144T as a novel Gramella species, for which the name Gramella salexigens sp. nov. is proposed. The type strain is LPB0144T (=KACC 18894T=JCM 31560T).
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Affiliation(s)
- Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Eunji Kim
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea.,School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
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29
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Abstract
A Gram-stain-negative, rod-shaped, aerobic bacterial strain, designated LPB0136T, was isolated from a squid Todarodes pacificus, caught in the East Sea, off Korea. LPB0136T contained a circular chromosome of 3.02 Mb with a DNA G+C content of 30.7 mol%. The genome included 2726 protein-coding genes and three copies of rRNA operons. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this isolate represents a member of the genus Tenacibaculum with an independent genomic species status, showing sequence similarities of 95.9 % to Tenacibaculum aestuarii SMK-4T and Tenacibaculum caenipelagi HJ-26MT. The detected respiratory quinone (MK-6) and major polar lipid (phosphatidylethanolamine) were similar to the chemotaxonomic profile of other species of the genus Tenacibaculum. The major cellular fatty acids profile (iso-C15 : 0, iso-C15 : 0 3-OH and iso-C15 : 0G) was also similar to those of members of genus Tenacibaculum, but the contents and amounts differed from those of closely related neighbours. Many biochemical and physiological characteristics also distinguished the isolate from other species within the genus Tenacibaculum. On the basis of the pholyphasic taxonomic data determined in this study, strain LPB0136T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculum todarodis sp. nov. is proposed. The type strain is LPB0136T (=KACC 18887T=JCM 31564T).
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Affiliation(s)
- Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Eunji Kim
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea.,Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea.,Institute for Biomaterials, Korea University, Seoul, Republic of Korea
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30
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Shin SK, Kim E, Yi H. Paenibacillus crassostreae sp. nov., isolated from the Pacific oyster Crassostrea gigas. Int J Syst Evol Microbiol 2017; 68:58-63. [PMID: 29068277 DOI: 10.1099/ijsem.0.002444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, endospore-forming, rod-shaped, aerobic bacterium, designated LPB0068T, was isolated from a Pacific oyster (Crassostrea gigas) in Korea. This isolate was found to share the highest 16S rRNA gene sequence similarity with Paenibacillus macquariensis subsp. macquariensis DSM 2T (98.1 %) and Paenibacillus macquariensis subsp. defensor JCM 14954T (98.0 %). To establish the genomic relatedness of this isolate to its phylogenetic neighbours, its genome sequence and those of Paenibacillus antarcticus CECT 5836T, P. macquariensis subsp. macquariensis DSM 2T, P. macquariensis subsp. defensor JCM 14954T, and Paenibacillus glacialis DSM 22343T were determined. The low average nucleotide identity and digital DNA-DNA hybridization values exhibited by LPB0068T in relation to the other strains in this analysis revealed that it is distinct from other Paenibacillus species. The genome of strain LPB0068T consists of one chromosome and three circular plasmids, and had a DNA G+C content of 40.0 mol%. The major respiratory quinone was menaquinone-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified glycolipid, and two unidentified polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C14 : 0, and C16 : 0. Based on genomic, phylogenetic, and phenotypic characteristics, this strain was clearly distinguished from other Paenibacillus species with validly published names and should therefore be classified as a novel species of the genus. The name Paenibacillus crassostreae sp. nov. is proposed, the type strain of which is LPB0068T (=KACC 18694T=JCM 31183T).
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Affiliation(s)
- Su-Kyoung Shin
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea
| | - Eunji Kim
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- Department of Public Health Sciences, BK21PLUS Program in Embodiment: Health-Society Interaction, Graduate School, Korea University, Seoul, Republic of Korea.,School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
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31
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Sphingorhabdus buctiana sp. nov., isolated from fresh water, and reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. Antonie van Leeuwenhoek 2017; 111:323-331. [DOI: 10.1007/s10482-017-0954-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/30/2017] [Indexed: 02/07/2023]
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32
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Limnobacter humi sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from humus soil, and emended description of the genus Limnobacter Spring et al. 2001. J Microbiol 2017; 55:508-513. [PMID: 28664518 DOI: 10.1007/s12275-017-6645-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
Three Gram-negative, strictly aerobic, chemolithoheterotrophic bacterial strains, designated UCM-30, UCM-33, and UCM-39T, were isolated in South Korea. Based on their 16S rRNA gene sequences, the three isolated strains were found to be similar to Limnobacter thiooxidans CS-K2T (97.41-97.68%), Limnobacter litoralis KP1-19T (95.55-95.76%), and various genera belonging to the class Betaproteobacteria (90.34-93.34%). DNA-DNA hybridization showed 79.3-83.9% similarity between the genomic DNA of UCM-39T, UCM-30, and UCM-33, while the sequence similarity between UCM-39T and L. thiooxidans KACC 13837T or L. litoralis LMG 24869T was 23.7% and 18.6%, respectively. The DNA G+C content of UCM 39T was 59.7 mol%, the major ubiquinone was Q-8, and the optimal oxidation rate was observed at 10 mM thiosulfate. The major fatty acids (≥ 10%) were summed features 3 (C16:1 ω7c and/or C16:1 ω6c) and 8 (C18:1 ω7c and/or C18:1 ω6c), and C16:0. The major polar lipids (diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol) were found in all members of genus Limnobacter. Based on phenotypic, physiological, and phylogenetic analyses, the UCM-39T strain was found to be significantly distinct to represent a novel species affiliated to the genus Limnobacter. We propose to name it Limnobacter humi sp. nov. with the type strain UCM-39T (=KACC 18574T =NBRC 111650T).
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Praet J, Cnockaert M, Meeus I, Smagghe G, Vandamme P. Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut. Syst Appl Microbiol 2017; 40:199-204. [PMID: 28442157 DOI: 10.1016/j.syapm.2017.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 11/25/2022]
Abstract
Spectra of five isolates (LMG 28358T, LMG 29879T, LMG 29880T, LMG 28359T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359T and R-53705 which also grouped in the same MALDI-TOF MS cluster, while different DNA fingerprints were obtained for the other isolates. Comparative 16S rRNA gene sequence analysis of the four different strains identified Gilliamella apicola NCIMB 14804T as nearest neighbour species. Average nucleotide identity values of draft genome sequences of the four isolates and of G. apicola NCIMB 14804T were below the 96% threshold value for species delineation and all four strains and G. apicola NCIMB 14804T were phenotypically distinct. Together, the draft genome sequences and phylogenetic and phenotypic data indicate that the four strains represent four novel Gilliamella species for which we propose the names Gilliamella intestini sp. nov., with LMG 28358T as the type strain, Gilliamella bombicola sp. nov., with LMG 28359T as the type strain, Gilliamella bombi sp. nov., with LMG 29879T as the type strain and Gilliamella mensalis sp. nov., with LMG 29880T as the type strain.
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Affiliation(s)
- Jessy Praet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
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Ber P, Trappen SV, Vandamme P, Trček J. Aeromicrobium choanae sp. nov., an actinobacterium isolated from the choana of a garden warbler. Int J Syst Evol Microbiol 2017; 67:357-361. [DOI: 10.1099/ijsem.0.001632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Polona Ber
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Stefanie Van Trappen
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Janja Trček
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
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França L, Albuquerque L, Zhang DC, Nouioui I, Klenk HP, da Costa MS, Margesin R. Nakamurella silvestris sp. nov., an actinobacterium isolated from alpine forest soil. Int J Syst Evol Microbiol 2016; 66:5460-5464. [PMID: 27707433 DOI: 10.1099/ijsem.0.001541] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile, catalase-positive and cytochrome c oxidase-negative bacterium, designated strain S20-107T, was isolated from alpine forest soil. Growth occurred at 0-30 °C, at pH 6-9 and in the presence of 0-3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S20-107T was related to the genus Nakamurella and had the highest 16S rRNA gene sequence similarity with Nakamurella flavida DS-52T (96.1 %). Strain S20-107T showed <96.1% 16S rRNA gene sequence similarities to all other recognized members of the genus Nakamurella. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major whole-cell sugars were glucose, galactose, mannose, arabinose, ribose and rhamnose. The strain contained MK-8(H4) as the predominant menaquinone and diphosphatidylglycerol, phosphatidylethanolamine and an unidentified aminophospholipid as the major polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C16 : 0. The genomic DNA G+C content was 70.5 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-107T represents a novel species of the genus Nakamurella, for which the name Nakamurella silvestris sp. nov. is proposed. The type strain is S20-107T (=DSM 102309T=LMG 29427T).
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Affiliation(s)
- Luis França
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - De-Chao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, 266071 Qingdao, PR China
| | - Imen Nouioui
- School of Biology, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Hans-Peter Klenk
- School of Biology, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Milton S da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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Han L, Teng YW, Feng QQ, Zhang RG, Zhao XM, Lv J, Xie B. Description of Sphingomonas mohensis sp. nov., Isolated from Sediment. Curr Microbiol 2016; 73:386-392. [PMID: 27262460 DOI: 10.1007/s00284-016-1074-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/25/2016] [Indexed: 11/24/2022]
Abstract
An aerobic, gram-reaction-negative, rod-shaped bacterium, designated strain Z6(T), was isolated from sediment collected at Mohe Basin, China. And its taxonomic position was investigated by applying a polyphasic approach. Growth occurs at 10-45 °C (optimum, 30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-3.0 % (w/v) NaCl (optimum, 0 %). The polar lipid profile of strain Z6(T) revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and two unidentified phospholipids, and the major quinone was Q-10. The major fatty acids were C18:1 ω7c and/or C18:1 ω6c (summed feature 8) and C16:1 ω6c and/or C16:1 ω7c (summed feature 3). The predominant polyamine was homospermidine. The DNA G + C content of strain Z6(T) is 65.2 mol%. On the basis of the polyphasic evidence presented, strain Z6(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas mohensis sp. nov. is proposed. The type strain is Z6(T) (=CGMCC 1.12891(T) = JCM 19983(T)).
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Affiliation(s)
- Lu Han
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, People's Republic of China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yue-Wen Teng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Qing-Qing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Ren-Gang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xing-Min Zhao
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, People's Republic of China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Bing Xie
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, People's Republic of China.
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Feng XM, Mo YX, Han L, Nogi Y, Zhu YH, Lv J. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2016. [PMID: 26220187 DOI: 10.1099/ijsem.0.000472] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, non-motile, facultatively aerobic bacterium, designated strain M1T, was isolated from a subterrestrial sediment sample of Qiangtang Basin in Qinghai-Tibetan plateau, China. The strain formed rough yellow colonies on R2A plates. Cells were oval or short rod-shaped, catalase-positive and oxidase-negative. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 96.2–96.4 % 16S rRNA gene sequence similarities to its closest relatives. Chemotaxonomic analysis revealed ubiquinone-10 (Q10) as the dominant respiratory quinone of strain M1T and C17 : 1ω6c (44.2 %) and C18 : 1ω7c (13.7 %) as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, three unidentified glycolipids, one unidentified phosphoglycolipid and one unidentified lipid. The DNA G+C content of strain M1T was 73.7 mol%. On the basis of phenotypic, phylogenetic and genotypic data presented in this study, strain M1T represents a novel species of a new genus in the family Erythrobacteraceae, for which the name Qipengyuania sediminis gen. nov., sp. nov. is proposed. The type strain of the type species is M1T ( = CGMCC 1.12928T = JCM 30182T).
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Affiliation(s)
- Xiao-Min Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Yong-Xin Mo
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China.,College of Resources and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - You-Hai Zhu
- Oil and Gas Survey, China Geological Survey, Beijing 10029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
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Abstract
This article summarizes what is currently known of the structures, physiological roles, involvement in pathogenicity, and biogenesis of a variety of noncovalently bound cell envelope lipids and glycoconjugates of Mycobacterium tuberculosis and other Mycobacterium species. Topics addressed in this article include phospholipids; phosphatidylinositol mannosides; triglycerides; isoprenoids and related compounds (polyprenyl phosphate, menaquinones, carotenoids, noncarotenoid cyclic isoprenoids); acyltrehaloses (lipooligosaccharides, trehalose mono- and di-mycolates, sulfolipids, di- and poly-acyltrehaloses); mannosyl-beta-1-phosphomycoketides; glycopeptidolipids; phthiocerol dimycocerosates, para-hydroxybenzoic acids, and phenolic glycolipids; mycobactins; mycolactones; and capsular polysaccharides.
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Praet J, Aerts M, Brandt ED, Meeus I, Smagghe G, Vandamme P. Apibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota. Int J Syst Evol Microbiol 2016; 66:1645-1651. [PMID: 26813786 DOI: 10.1099/ijsem.0.000921] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Isolates LMG 28357T (=R-53146T) and LMG 28623 were obtained from gut samples of Bombus lapidarius bumblebees caught in Ghent, Belgium. They had identical 16S rRNA gene sequences which were 95.7 % identical to that of Apibacter adventoris wkB301T, a member of the family Flavobacteriaceae. Both isolates had highly similar matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and randomly amplified polymorphic DNA (RAPD) profiles. A draft genome sequence was obtained for strain LMG 28357T (Gold ID Gp0108260); its DNA G+C content was 30.4%, which is within the range reported for members of the family Flavobacteriaceae (27 to 56 mol%) and which is similar to that of the type strain of A. adventoris (29.0 mol%). Whole-cell fatty acid methyl ester analysis of strain LMG 28357T revealed many branched-chain fatty acids, a typical characteristic of bacteria of the family Flavobacteriaceae and a profile that was similar to that reported for A. adventoris wkB301T. MK6 was the major respiratory quinone, again conforming to bacteria of the family Flavobacteriaceae. The isolates LMG 28357T and LMG 28623 could be distinguished from A. adventoris strains through their oxidase activity. On the basis of phylogenetic, genotypic and phenotypic data, we propose to classify both isolates as representatives of a novel species of the genus Apibacter, Apibacter mensalis sp. nov., with LMG 28357T (=DSM 100903T=R-53146T) as the type strain.
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Affiliation(s)
- Jessy Praet
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Maarten Aerts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Evie De Brandt
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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França L, Albuquerque L, Sánchez C, Fareleira P, da Costa MS. Ampullimonas aquatilis gen. nov., sp. nov. isolated from bottled mineral water. Int J Syst Evol Microbiol 2016; 66:1459-1465. [PMID: 26782963 DOI: 10.1099/ijsem.0.000903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates, designated B15.09-116T and B15.09-124, were recovered from bottled mineral water in Portugal. Based on 16S rRNA gene sequence analysis, these strains were related most closely to species of the genus Derxia (belonging to the family Alcaligenaceae) with pairwise sequence similarities of 93.0-93.6 %. The isolates were not pigmented and formed Gram-stain-negative, short, motile rod-shaped cells. The organisms were strictly aerobic, oxidase-positive and catalase-negative. These organisms also fixed N2. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 was the major respiratory quinone. The DNA G+C content of strain B15.09-116T was 49.8 mol%. Based on phylogenetic, physiological and biochemical characteristics the two strains are considered to represent a novel species of a new genus, for which the name Ampullimonas aquatilis gen. nov., sp. nov. is proposed. The type strain of Ampullimonas aquatilis is B15.09-116T ( = CECT 8581T = LMG 28208T).
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Affiliation(s)
- Luís França
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Claudia Sánchez
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Milton S da Costa
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
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Piao AL, Feng XM, Nogi Y, Han L, Li Y, Lv J. Sphingomonas qilianensis sp. nov., Isolated from Surface Soil in the Permafrost Region of Qilian Mountains, China. Curr Microbiol 2015; 72:363-9. [PMID: 26676296 DOI: 10.1007/s00284-015-0957-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/03/2015] [Indexed: 11/25/2022]
Abstract
A Gram-stain-negative, strictly aerobic, non-motile and rod-shaped bacterial strain, designated X1(T), was isolated from the permafrost region of Qilian Mountains in northwest of China. Phylogenetic analyses of 16S rRNA gene sequence revealed that strain X1(T) was a member of the genus Sphingomonas and shared the highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica JCM 12082(T) (96.9%), followed by Sphingomonas glacialis CGMCC 1.8957(T) (96.7%) and Sphingomonas alpina DSM 22537(T) (96.4%). Strain X1(T) was able to grow at 15-30 °C, pH 6.0-10.0 and with 0-0.3% NaCl (w/v). The DNA G+C content of the isolate was 64.8 mol%. Strain X1(T)-contained Q-10 as the dominant ubiquinone and C(18:1)ω7c, C(16:1)ω7c, C(16:0) and C(14:0) 2-OH as the dominant fatty acids. The polar lipid profile of strain XI(T)-contained sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and two unidentified phospholipid. Due to the phenotypic and genetic distinctiveness and other characteristic studied in this article, we consider X1(T) as a novel species of the genus Sphingomonas and propose to name it Sphingomonas qilianensis sp. nov. The type strain is X1(T) (=CGMCC 1.15349(T) = KCTC 42862(T)).
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Affiliation(s)
- Ai-Lian Piao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xiao-Min Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yonghong Li
- Qinghai No.105 Coal Geological Exploration Team, Xining, 810007, Qinghai, China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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França L, Albuquerque L, da Costa MS. Cavicella subterranea gen. nov., sp. nov., isolated from a deep mineral-water aquifer, and emended description of the species Perlucidibaca piscinae. Int J Syst Evol Microbiol 2015; 65:3812-3817. [PMID: 28875925 DOI: 10.1099/ijsem.0.000493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023] Open
Abstract
One strain designated W2.09-231T was isolated from an aquifer through a 150-metre-deep borehole feeding a mineral-water bottling plant in Central Portugal. Based on 16S rRNA gene sequence analysis, the novel organism is most closely related to the species of the genera Perlucidibaca and Paraperlucidibaca, belonging to the family Moraxellaceae, with 16S rRNA gene pairwise sequence similarity of 94.5 and 93.1 %, respectively. The strain was not pigmented and formed Gram-stain-negative, non-motile, short rod-shaped cells. The organism was strictly aerobic, and oxidase- and catalase-positive. Strain W2.09-231T was organotrophic, but grew only on a very limited number of single carbon sources. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one major unknown phospholipid. Ubiquinone 12 (U-12) was the major respiratory quinone. The DNA G+C content of strain W2.09-231T was 62.0 mol%. Based on phylogenetic, physiological and biochemical characteristics, we describe a novel species of a novel genus represented by strain W2.09-231T ( = CECT 8582T = LMG 28332T) for which we propose the name Cavicella subterranea gen. nov., sp. nov. We also propose to emend the description of the species Perlucidibaca piscinae to reflect new results obtained in this study.
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Affiliation(s)
- Luís França
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Milton S da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal
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Flavobacterium buctense sp. nov., isolated from freshwater. Arch Microbiol 2015; 197:1109-15. [DOI: 10.1007/s00203-015-1149-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 08/30/2015] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
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44
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Jia L, Zheng Z, Feng X, Nogi Y, Yang A, Zhang Y, Han L, Lu Z, Lv J. Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China. Antonie van Leeuwenhoek 2015; 108:1341-1347. [PMID: 26363912 DOI: 10.1007/s10482-015-0586-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/08/2015] [Indexed: 10/23/2022]
Abstract
A Gram-negative, rod-shaped, non-motile, non-spore forming, aerobic, orange-pigmented bacterium, designated strain 6P(T), was isolated from a soil sample collected from the Hoh Xil basin, China. Strain 6P(T) grew optimally at 25 °C, pH 7.0-7.5 and NaCl concentration of 0-1 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6P(T) belongs to the genus Sphingomonas, with high sequence similarity (97.1 %) to Sphingomonas fennica. The DNA-DNA hybridization homology with S. fennica DSM 13665(T) was 45.3 %. The DNA G+C content of the novel strain is 65.3 mol%. The isolate contained Q-10 as the only respiratory quinone. The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and sphingoglycolipid (SGL). C18:1 ω7c and C16:1 ω7c are the major fatty acids. On the basis of the polyphasic evidence presented, strain 6P(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas arantia sp. nov. is proposed. The type strain is 6P(T) (=CGMCC 1.12702(T) = JCM 19855(T)).
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Affiliation(s)
- Li Jia
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Zhong Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xiaomin Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-EarthScience and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Aichen Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yali Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Resources and Environmental Science, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, People's Republic of China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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45
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Jia L, Feng X, Zheng Z, Han L, Hou X, Lu Z, Lv J. Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter. Int J Syst Evol Microbiol 2015; 65:3920-3925. [PMID: 26246176 DOI: 10.1099/ijsem.0.000514] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain D40PT, representing a novel Gram-stain-negative, obligately aerobic, bacteriochlorophyll a-containing bacterium of the α-4 subgroup of the phylum Proteobacteria, was isolated from permafrost soil of Kunlun mountains gap, Qinghai-Tibet plateau. Cells were non-motile rod-cocci and formed brown-pigmented colonies. According to the absorption spectrum, carotenoids and two different photosynthetic light-harvesting complexes, an LHI complex and a B800-835-type peripheral LHII complex, were present in the cells. The strain was oxidase-negative and catalase-positive. The predominant fatty acids of strain D40PT were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, two glycolipids and sphingoglycolipid. The major respiratory quinone was ubiquinone-10, whereas ubiquinone-9 was present in smaller amounts. The 16S rRNA gene sequence similarity to the closest phylogenetic relative, Polymorphobacter multimanifer JCM 18140T, was 97.5 %. DNA-DNA relatedness (ΔTm) between strain D40PT and P. multimanifer was 12.4 °C. The G+C content of the genomic DNA of strain D40PT was 67.4 mol%. Accordingly, the strain represents a novel species, for which the name Polymorphobacter fuscus sp. nov. is proposed. The type strain is D40PT ( = CGMCC 1.12714T = JCM 19740T). An emended description of the genus Polymorphobacter is also proposed.
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Affiliation(s)
- Li Jia
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Xiaomin Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhong Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.,College of Resources and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Xiaocui Hou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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46
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Tian M, Zhang RG, Han L, Zhao XM, Lv J. Dyadobacter sediminis sp. nov., isolated from a subterranean sediment sample. Int J Syst Evol Microbiol 2015; 65:827-832. [DOI: 10.1099/ijs.0.000025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, flexirubin-type-pigmented, rod-shaped, aerobic, non-motile bacterium, designated strain Z12T, was isolated from a subsurface sediment sample. In a phylogenetic tree based on 16S rRNA gene sequences, strain Z12T formed a distinct clade with the members of the genus
Dyadobacter
(<96.7 % sequence similarity). The G+C content of genomic DNA was 45.4 %. The major fatty acids of strain Z12T were iso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c (summed feature 3) and anteiso-C17 : 1 B and/or iso-C17 : 1 I (summed feature 4). The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. On the basis of phenotypic, phylogenetic and genotypic features, strain Z12T is considered to represent a novel species, for which the name Dyadobacter sediminis sp. nov., is proposed. The type strain is Z12T ( = JCM 30073T = CGMCC 1.12895T).
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Affiliation(s)
- Mu Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Ren-Gang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Lu Han
- College of Resources and Environmental Science, East China Normal University, Shanghai 200241, PR China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Xing-Min Zhao
- Oil and Gas Survey, China Geological Survey, Beijing 10029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
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47
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Feng Q, Gao Y, Nogi Y, Tan X, Han L, Zhang Y, Lv J. Flavobacterium maotaiense sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2015; 65:171-176. [DOI: 10.1099/ijs.0.064139-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel strains, T9T and T10, were isolated from water samples collected from Chishui River flowing through Maotai town, Guizhou, south-west China. The isolates were yellow-pigmented, Gram-reaction-negative, rod-shaped, non-motile and aerobic. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to the genus
Flavobacterium
, and showed highest similarities to
Flavobacterium hibernum
DSM 12611T (97.0 %), followed by
Flavobacterium granuli
Kw05T (96.7 %) and
Flavobacterium pectinovorum
DSM 6368T (96.7 %). The novel strains were able to grow at 20–37 °C (optimum 25 °C), pH 7.0–10.0 (optimum pH 7.0–8.0) and with 0–0.5 % (w/v) NaCl (optimum 0.5 %). The predominant fatty acids were iso-C15 : 0, C16 : 1ω7c, anteiso-C15 : 0, C15 : 0, iso-C15 : 0 3-OH and iso-C15 : 1ω10c, and menaquinone-6 (MK-6) was the main respiratory quinone. The major polar lipids were phosphatidylethanolamine, one unknown glycolipid, two unknown aminolipids and two unidentified lipids. The DNA G+C contents of strains T9T and T10 were 37.7 and 36.4 mol%, respectively. According to the phenotypic and genetic data, strains T9T and T10 represent a novel species in the genus
Flavobacterium
, for which the name Flavobacterium maotaiense sp. nov. is proposed. The type strain is T9T ( = CGMCC 1.12712T = JCM 19927T).
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Affiliation(s)
- Qingqing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Yuan Gao
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Xu Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Lu Han
- College of Resources and Environmental Science, East China Normal University, Shanghai, 200241, PR China
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Yali Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing 100029, PR China
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Palleronia abyssalis sp. nov., isolated from the deep Mediterranean Sea and the emended description of the genus Palleronia and of the species Palleronia marisminoris. Antonie van Leeuwenhoek 2014; 107:633-42. [DOI: 10.1007/s10482-014-0358-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/12/2014] [Indexed: 11/27/2022]
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Paiva G, Abreu P, Proença DN, Santos S, Nobre MF, Morais PV. Mucilaginibacter pineti sp. nov., isolated from Pinus pinaster wood from a mixed grove of pines trees. Int J Syst Evol Microbiol 2014; 64:2223-2228. [DOI: 10.1099/ijs.0.057737-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strain M47C3BT was isolated from the endophytic microbial community of a Pinus pinaster tree branch from a mixed grove of pines. Phylogenetic analysis of 16S rRNA gene sequences showed that this organism represented one distinct branch within the family
Sphingobacteriaceae
, most closely related to the genus
Mucilaginibacter
. Strain M47C3BT formed a distinct lineage, closely related to
Mucilaginibacter dorajii
KACC 14556T, with which it shared 97.2 % 16S rRNA gene sequence similarity. The other members of the genus
Mucilaginibacter
included in the same clade were
Mucilaginibacter lappiensis
ATCC BAA-1855T sharing 97.0 % similarity and
Mucilaginibacter composti
TR6-03T that had a lower similarity (95.7 %). The novel strain was Gram-staining-negative, formed rod-shaped cells, grew optimally at 26 °C and at pH 7, and was able to grow with up to 0.3 % (w/v) NaCl. The respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids of the strain were summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH, representing 73.5 % of the total fatty acids. The major components of the polar lipid profile of strain M47C3BT consisted of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The G+C content of the DNA was 40.6 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics we propose the name Mucilaginibacter pineti sp. nov. for the novel species represented by strain M47C3BT ( = CIP 110632T = LMG 28160T).
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Affiliation(s)
- Gabriel Paiva
- IMAR-CMA, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Pedro Abreu
- IMAR-CMA, University of Coimbra, 3004-517 Coimbra, Portugal
| | | | - Susana Santos
- IMAR-CMA, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Maria Fernanda Nobre
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Paula V. Morais
- Department of Life Sciences, FCTUC, University of Coimbra, 3004-517 Coimbra, Portugal
- IMAR-CMA, University of Coimbra, 3004-517 Coimbra, Portugal
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50
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Bondoso J, Albuquerque L, Lobo-da-Cunha A, da Costa MS, Harder J, Lage OM. Rhodopirellula lusitana sp. nov. and Rhodopirellula rubra sp. nov., isolated from the surface of macroalgae. Syst Appl Microbiol 2014; 37:157-64. [DOI: 10.1016/j.syapm.2013.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 11/13/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
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