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Zhang C, Zhang G, Chen Y, Zheng S, Du J, Zhao Z, Zhao Y, Wang N, Chen C, Gao Z, Li S, Liu K. Sphingobacterium tenebrionis sp. nov., isolated from intestine of mealworm. Int J Syst Evol Microbiol 2024; 74. [PMID: 39023139 DOI: 10.1099/ijsem.0.006455] [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: 07/20/2024] Open
Abstract
A bacterial strain designated PU5-4T was isolated from the mealworm (the larvae of Tenebrio molitor) intestines. It was identified to be Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Strain PU5-4T was observed to grow at 10-40 °C, at pH 7.0-10.0, and in the presence of 0-3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PU5-4T should be assigned to the genus Sphingobacterium. The 16S rRNA gene sequence similarity analysis showed that strain PU5-4T was closely related to the type strains of Sphingobacterium lactis DSM 22361T (98.49 %), Sphingobacterium endophyticum NYYP31T (98.11 %), Sphingobacterium soli NCCP 698T (97.69 %) and Sphingobacterium olei HAL-9T (95.73 %). The predominant isoprenoid quinone is MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 03-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 9 (iso-C17 : 0 ω9c). The polar lipids are phosphatidylethanolamine, one unidentified phospholipid, and six unidentified lipids. The genomic DNA G+C content of strain PU5-4T is 40.24 mol%. The average nucleotide identity of strain PU5-4T exhibited respective values of 73.88, 73.37, 73.36 and 70.84 % comparing to the type strains of S. lactis DSM 22361T, S. soli NCCP 698T, S. endophyticum NYYP31T and S. olei HAL-9T, which are below the cut-off level (95-96 %) for species delineation. Based on the above results, strain PU5-4T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium temoinsis sp. nov. is proposed. The type strain is PU5-4T (=CGMCC 1.61908T=JCM 36663T).
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Affiliation(s)
- Chengsong Zhang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255000, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Yuexing Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jieke Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhiyi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Yushuo Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Cheng Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, PR China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, PR China
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
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Kim S, Heo J, Choi H, Lee D, Kwon SW, Kim Y. Sphingobacterium oryzagri sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38713185 DOI: 10.1099/ijsem.0.006371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Abstract
An aerobic, Gram-stain-negative and short rod-shaped bacterial strain, designated M6-31T, was isolated from rice paddy soil sampled in Miryang, Republic of Korea. Growth was observed at 4-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-4 % (w/v) NaCl (optimum, 0 % w/v). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain M6-31T with Sphingobacterium bambusae IBFC2009T, Sphingobacterium griseoflavum SCU-B140T and Sphingobacterium solani MLS-26-JM13-11T in the same clade, with the 16S rRNA gene sequence similarities ranging from 95.8 to 96.6 %. A genome-based phylogenetic tree reconstructed by using all publicly available Sphingobacterium genomes placed strain M6-31T with S. bambusae KACC 22910T, 'Sphingobacterium deserti' ACCC 05744T, S. griseoflavum CGMCC 1.12966T and Sphingobacterium paludis CGMCC 1.12801T. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain M6-31T and its closely related strains were lower than 74.6 and 22.0 %, respectively. The respiratory quinone was menaquinone-7, and the major polar lipid was phosphatidylethanolamine. The major fatty acids (>10 %) were C15 : 0 iso, C17 : 0 iso 3OH and summed feature 3. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strain M6-31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium oryzagri sp. nov. (type strain M6-31T=KACC 22765T=JCM 35893T) is proposed.
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Affiliation(s)
- Seunghwan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Hyorim Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
- Department of Biotechnology, Jeonbuk National University, Iksan 55496, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
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Ahn JS, Choi YJ, Kim HB, Chung HJ, Hong ST. Identification of the Intestinal Microbes Associated with Locomotion. Int J Mol Sci 2023; 24:11392. [PMID: 37511151 PMCID: PMC10380270 DOI: 10.3390/ijms241411392] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Given the impact of the gut microbiome on human physiology and aging, it is possible that the gut microbiome may affect locomotion in the same way as the host's own genes. There is not yet any direct evidence linking the gut microbiome to locomotion, though there are some potential connections, such as regular physical activity and the immune system. In this study, we demonstrate that the gut microbiome can contribute differently to locomotion. We remodeled the original gut microbiome of mice through fecal microbiota transplantation (FMT) using human feces and compared the changes in locomotion of the same mice before and three months after FMT. We found that FMT affected locomotion in three different ways: positive, none (the same), and negative. Analysis of the phylogenesis, α-diversities, and β-diversities of the gut microbiome in the three groups showed that a more diverse group of intestinal microbes was established after FMT in each of the three groups, indicating that the human gut microbiome is more diverse than that of mice. The FMT-remodeled gut microbiome in each group was also different from each other. Fold change and linear correlation analyses identified Lacrimispora indolis, Pseudoflavonifractor phocaeensis, and Alistipes senegalensis in the gut microbiome as positive contributors to locomotion, while Sphingobacterium cibi, Prevotellamassilia timonensis, Parasutterella excrementihominis, Faecalibaculum rodentium, and Muribaculum intestinale were found to have negative effects. This study not only confirms the presence of gut microbiomes that contribute differently to locomotion, but also explains the mixed results in research on the association between the gut microbiome and locomotion.
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Affiliation(s)
- Ji-Seon Ahn
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
| | - Yu-Jin Choi
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
| | - Han-Byeol Kim
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Jeonju 54907, Republic of Korea
| | - Hea-Jong Chung
- Gwangju Center, Korea Basic Science Institute, Gwangju 61751, Republic of Korea
| | - Seong-Tshool Hong
- Department of Biomedical Sciences and Institute for Medical Science, Chonbuk National University Medical School, Jeonju 54907, Republic of Korea
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Grenier V, Gonzalez E, Brereton NJB, Pitre FE. Dynamics of bacterial and archaeal communities during horse bedding and green waste composting. PeerJ 2023; 11:e15239. [PMID: 37159830 PMCID: PMC10163874 DOI: 10.7717/peerj.15239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.
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Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
| | - Emmanuel Gonzalez
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Nicholas JB Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Frederic E. Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montréal, Québec, Canada
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Besaury L, Floret J, Rémond C. Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction. Int J Syst Evol Microbiol 2021; 71. [PMID: 34406922 PMCID: PMC8513620 DOI: 10.1099/ijsem.0.004963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, arapr2T, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Sphingobacteriaceae and more specifically to the genus Sphingobacterium. The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative Sphingobacterium canadense CR11T and 98.25 % to Sphingobacterium pakistanensis NCCP-246T. Genome relatedness indexes revealed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between arapr2T and its closest relative (S. canadense CR11T) were 92.97 % and 52.00 %, respectively; for S. pakistanensis NCCP-246T, the ANI and dDDH values were 82.46 and 27.6%, respectively. The genomic DNA of strain arapr2T was 6.02 Mbp long, had a DNA G+C content of 40.4 mol% and had 5504 protein-coding genes. The results obtained in this study suggests that strain arapr2T (CIP 111872T=LMG 31848T) represents a new species for which the name Sphingobacterium prati sp. nov. is proposed. Due to the fact that this strain has been isolated using wheat straw as carbon source, this novel bacterial strain represents a promising biotechnological tool for the fractionation of lignocellulosic biomass in the context of biorefinery development.
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Affiliation(s)
- Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
| | - Juliette Floret
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
| | - Caroline Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
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Song J, Joung Y, Li SH, Hwang J, Cho JC. Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:6126-6132. [PMID: 33054902 DOI: 10.1099/ijsem.0.004507] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678T, was isolated from an artificial freshwater reservoir, Chungju Lake, in the Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC25678T belongs to the genus Sphingobacterium with ≤98.7 % sequence similarities to Sphingobacterium species. Whole genome sequencing of strain IMCC25678T revealed a 3.9 Mbp genome size with a DNA G+C content of 42.2 mol%. The IMCC25678T genome shared ≤89.7 % average nucleotide identity and ≤21.4 % digital DNA-DNA hybridization values with closely related species of the genus Sphingobacterium, indicating that the strain represents a novel species. Summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH were found to be the predominant cellular fatty acid constituents in the strain. The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unidentified phosphoglycolipid, one unidentified sphingolipid and three unidentified polar lipids. Based on the phylogenetic and phenotypic characteristics, strain IMCC25678T was considered to represent a novel species within the genus Sphingobacterium, for which the name Sphingobacterium chungjuense sp. nov. is proposed. The type strain is IMCC25678T (=KACC 19485T=NBRC 113130T).
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Affiliation(s)
- Jaeho Song
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Shan-Hui Li
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Juchan Hwang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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Sphingobacterium endophyticum sp. nov., a novel endophyte isolated from halophyte. Arch Microbiol 2020; 202:2771-2778. [PMID: 32737542 DOI: 10.1007/s00203-020-02000-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: 05/07/2020] [Revised: 07/02/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022]
Abstract
A bacterial strain designated NYYP31T was isolated from the leaves of an annual halophytes, Suaeda corniculata Bunge, collected from the southern edge of the Gurbantunggut desert, north-west China. Strain NYYP31T was Gram-staining negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Growth was observed at 4-42 °C, at pH 5.0-10.0, in the presence of up to 8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and coding sequences of 92 protein clusters showed that strain NYYP31T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain NYYP31T was most closely related to the type strain of Sphingobacterium daejeonense (97.9%) and Sphingobacterium lactis (97.7%). The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids were phosphatidylethanolamine, two unidentified phospholipids, three unidentified lipids, three unidentified amino phospholipids, and two unidentified glycolipids. The genomic DNA G + C content was 36.4 mol%. The average nucleotide identity (ANI) values for strain NYYP31T to the type strains of S. daejeonense and S. lactis were 77.9 and 74.1%, respectively, which were below the cut-off level (95-96%) for species delineation. Based on the above results, strain NYYP31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium endophyticum sp. nov. is proposed. The type strain is NYYP31T (= CGMCC 1.16979T = NBRC 114258T).
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He W, Guo J, Guo H, An M, Huang W, Wang Y, Cai H. Sphingobacterium puteale sp. nov., isolated from a deep subsurface aquifer. Int J Syst Evol Microbiol 2019; 69:3356-3361. [PMID: 31502948 DOI: 10.1099/ijsem.0.003521] [Citation(s) in RCA: 5] [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 bacterial strain M05W1-28T was isolated from a well that collected water for irrigation from a deep aquifer at a depth of 400 m. Cells were observed to be rod-shaped, non-motile, aerobic, stained Gram-negative. Optimal growth was obtained at pH 7.0 (range: 6.0-9.0), 28 °C (range: 15-37 °C) and 0 % NaCl (range: 0-1.5 %, w/v) in modified tryptic soy broth (mTSB) without added NaCl and R2A. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c) and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, glycolipid, phosphoglycolipids, phospholipids, and unidentified lipids. The major respiratory quinone was menaquinone-7 (MK-7). The genomic G+C content of strain M05W1-28T was 40.7 %. Based on similarities of 16S rRNA gene sequences, strain M05W1-28T was affiliated with the genus Sphingobacterium, exhibiting the highest sequence similarities with S. multivorum LMG 8342T (97.5 %), S. ginsenosidimutans THG07T (97.1 %) and less than 97.0 % to other members of the genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation values (dDDH) between M05W1-28T and S. multivorum LMG 8342T were 78.1 and 22.5 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilisation differentiated the strain from other Sphingobacterium species. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain M05W1-28T represented a novel species within the genus Sphingobacterium, for which the name Sphingobacterium puteale sp. nov. is proposed. The type strain is M05W1-28T (=CGMCC 1.13711T=KCTC 72027T).
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Affiliation(s)
- Weihong He
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, PR China
| | - Jing Guo
- Zhengzhou Institute of Vegetable Research, Zhengzhou, PR China
| | - Heng Guo
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, PR China
| | - Mingli An
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, PR China
| | - Wen Huang
- Zhengzhou Institute of Vegetable Research, Zhengzhou, PR China
| | - Yanan Wang
- Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, PR China
| | - Haiyuan Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, PR China
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Niu X, Cui W, Cui M, Zhang X, Zhang S, Xu B, Gao M. Sphingobacterium solani sp. nov., isolated from potato stems. Int J Syst Evol Microbiol 2018; 68:1012-1017. [DOI: 10.1099/ijsem.0.002605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xinbin Niu
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Weiguo Cui
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Man Cui
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shuqing Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Bingliang Xu
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Miao Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Zhou XK, Li QQ, Mo MH, Zhang YG, Dong LM, Xiao M, Li WJ, Duan YQ. Sphingobacterium tabacisoli sp. nov., isolated from a tobacco field soil sample. Int J Syst Evol Microbiol 2017; 67:4808-4813. [PMID: 28984223 DOI: 10.1099/ijsem.0.002381] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-motile and rod-shaped bacterium, designated strain h337T, was isolated from an arable soil sample of a tobacco field in Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10-35 °C, at pH 6.0-9.0 and in the presence of up to 3 % (w/v) NaCl, with optimal growth at 30 °C, pH 7.0 and with 1-2 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The cellular polar lipids contained phosphatidylethanolamine, sphingophospholipid, four unidentified phospholipids, five unidentified lipids and three unidentified aminophospholipids. The genomic DNA G+C content was 41.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain h337T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain h337T was most closely related to 'Sphingobacteriumyamdrokense' 3-0-1 (98.8 %) and Sphingobacteriumyanglingense CCNWSP36-1T (98.5 %) and shared less than 97 % similarity with other species of the genus Sphingobacterium. DNA-DNA hybridization data indicated that the isolate represented a novel genomic species belonging to the genus Sphingobacterium. The characteristics determined in this polyphasic taxonomic study indicated that strain h337T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium tabacisoli sp. nov. (type strain h337T=KCTC 52298T=CCTCC AB 2017155T) is proposed.
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Affiliation(s)
- Xing-Kui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Qing-Qing Li
- Life Science College, Southwest Forestry University, Kunming 650224, PR China
- Kunming Xianghao Technology Co. Ltd., Kunming 650204, PR China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Li-Min Dong
- China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd., Kunming 650231, PR China
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Lee Y, Jin HM, Jung HS, Jeon CO. Sphingobacterium humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:4632-4638. [PMID: 28945541 DOI: 10.1099/ijsem.0.002345] [Citation(s) in RCA: 9] [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, facultatively aerobic bacterium, designated strain D1T, was isolated from soil in South Korea. Cells of strain D1T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1T formed a phyletic lineage with Sphingobacterium hotanense XH4T within the genus Sphingobacterium. Strain D1T was most closely related to S. hotanense XH4T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603T (97.2 %), and the DNA-DNA relatedness level between strain D1T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1T (=KACC 18595T=JCM 31225T).
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Affiliation(s)
- Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Xu L, Sun JQ, Wang LJ, Gao ZW, Sun LZ, Wu XL. Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil. Int J Syst Evol Microbiol 2017. [PMID: 28629491 DOI: 10.1099/ijsem.0.001895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-motile, non-spore-forming bacterium designated Y3L14T was isolated from the saline-alkaline soil of a farmland, Inner Mongolia, northern China. Strain Y3L14T could grow at 10-40 °C (optimally at 30 °C), pH 6.0-10.0 (optimally at pH 8.0), and in the presence of 0-6.0 % (w/v) NaCl (optimally with 0-2.0 %). Phylogenetic analysis based on the 16S rRNA gene and DNA gyrase subunit B (gyrB) gene sequences revealed that strain Y3L14T clustered with strains belonging to the genus Sphingobacterium, sharing the highest 16S rRNA gene sequence similarity with Sphingobacterium lactis WCC 4512T (94.99 %). Its major cellular fatty acids contained iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone-7 (MK-7) was the only isoprenoid quinone. Strain Y3L14T contained phosphatidylethanolamine, sphingophospholipid, two unknown phospholipids and three unknown lipids as the major polar lipids. The genomic DNA G+C content of strain Y3L14T was 36.0 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y3L14T represents a novel species within the genus Sphingobacterium, for which Sphingobacterium alkalisoli sp. nov. is proposed; the type strain is Y3L14T (=CGMCC 1.15782T=KCTC 52379T).
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Affiliation(s)
- Lian Xu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Ji-Quan Sun
- College of Engineering, Peking University, Beijing 100871, PR China.,Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Li-Juan Wang
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Zhi-Wei Gao
- Sinopec Shengli Oilfield Xinchun Oil Production Plant, Dongying 257000, PR China
| | - Li-Zhu Sun
- Sinopec Shengli Oilfield Xinchun Oil Production Plant, Dongying 257000, PR China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, PR China
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