1
|
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).
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1T. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1T was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria–Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) and iso-C17 : 0 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1T was affiliated with the genus
Sphingobacterium
and had the highest sequence similarity to
Sphingobacterium tabacisoli
h337T (97.0 %) and Sphingobacterium paucimobilis HER1398T (95.6 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain C459-1T and
S. tabacisoli
h337T were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1T from other
Sphingobacterium
species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1T represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium faecale sp. nov. is proposed, with strain is C459-1T (CGMCC 1.18716T=KCTC 82381T) as the type strain.
Collapse
|
4
|
Zhang M, Li A, Xu S, Chen M, Yao Q, Xiao B, Zhu H. Sphingobacterium micropteri sp. nov. and Sphingobacterium litopenaei sp. nov., isolated from aquaculture water. Int J Syst Evol Microbiol 2021; 71. [PMID: 34779757 DOI: 10.1099/ijsem.0.005091] [Citation(s) in RCA: 3] [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
Two novel bacterial strains, designated as DN00404T and DN04309T, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404T and DN04309T were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404T were short rod-shaped and those of DN04309T were long rod-shaped. Strain DN00404T was found to grow at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.5) and in 0-2.0 % (w/v) NaCl (optimum, 1.0 %). Strain DN04309T was found to grow at 15-45 °C (optimum, 20-37 °C), at pH 5.5-11.0 (optimum, 7.5) and in 0-4.0 % (w/v) NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus Sphingobacterium and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0-96.0 % ANI and 70.0 % dDDH for species delineation. The genomic DNA G+C contents of strains DN00404T and DN04309T were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), which were similar to those of other species of this genus. The two major fatty acids C16 : 0 and iso-C17 : 0 3-OH were also found in strain DN00404T. Based on genotypic and phenotypic characteristics, two novel species of the genus Sphingobacterium are proposed: Sphingobacterium micropteri sp. nov. with DN00404T (=GDMCC 1.1865T=KACC 21924T) as the type strain and Sphingobacterium litopenaei sp. nov. with DN04309T (=GDMCC 1.1984T=KCTC 82348T) as the type strain.
Collapse
Affiliation(s)
- Mingxia Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Anzhang Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Shuaishuai Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Meng Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, PR China
| | - Botao Xiao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| |
Collapse
|
5
|
Zhen-Dong Z, Yu-Rong W, Fan-Shu X, Qiang-Chuan H, Zhuang G. Distinct bacterial community of a solid-state fermented Chinese traditional food huase sufu revealed by high-throughput sequencing. Food Sci Biotechnol 2021; 30:1233-1241. [PMID: 34603822 DOI: 10.1007/s10068-021-00963-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 06/25/2021] [Accepted: 07/29/2021] [Indexed: 11/24/2022] Open
Abstract
Sufu is a common solid-state traditional fermented food made from soybean. Huase sufu is a typical type found in several provinces of China, especially in Hubei. However, little is known about the bacterial community. High-throughput sequencing technology revealed that the dominant taxa at phylum level were: Firmicutes, Proteobacteria and Bacteroides, and at the genus level were: Pseudomonas, Lactococcus, Acinetobacter, etc. Additionally, LEfSe revealed that compared with the bacterial community of red sufu and white sufu, the biomarker genera for both huase sufu were Enterococcus, and Myroides. Moreover, there were twenty-eight hubs for the huase sufu samples, and four of them were dominant genera: Citrobacter, Myroides, Vagococcus, and Enterococcus. These results provide a new insight into our understanding of the bacterial diversity of huase sufu, and will facilitate the isolation, screening, and development potential bacterial strains for production of huase sufu. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00963-3.
Collapse
Affiliation(s)
- Zhang Zhen-Dong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Wang Yu-Rong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Xiang Fan-Shu
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Hou Qiang-Chuan
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| | - Guo Zhuang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, Hubei People's Republic of China
| |
Collapse
|
6
|
Kakumanu ML, Marayati BF, Wada-Katsumata A, Wasserberg G, Schal C, Apperson CS, Ponnusamy L. Sphingobacterium phlebotomi sp. nov., a new member of family Sphingobacteriaceae isolated from sand fly rearing substrate. Int J Syst Evol Microbiol 2021; 71:004809. [PMID: 33956595 PMCID: PMC8289205 DOI: 10.1099/ijsem.0.004809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium, designated type strain SSI9T, was isolated from sand fly (Phlebotomus papatasi Scopoli; Diptera: Psychodidae) rearing substrate and subjected to polyphasic taxonomic analysis. Strain SSI9T contained phosphatidylethanolamine as a major polar lipid, MK-7 as the predominant quinone, and C16 : 1ω6c/C16 : 1ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 as the major cellular fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that SSI9T represents a member of the genus Sphingobacterium, of the family Sphingobacteriaceae sharing 96.5-88.0 % sequence similarity with other species of the genus Sphingobacterium. The results of multilocus sequence analysis using the concatenated sequences of the housekeeping genes recA, rplC and groL indicated that SSI9T formed a separate branch in the genus Sphingobacterium. The genome of SSI9T is 5 197 142 bp with a DNA G+C content of 41.8 mol% and encodes 4395 predicted coding sequences, 49 tRNAs, and three complete rRNAs and two partial rRNAs. SSI9T could be distinguished from other species of the genus Sphingobacterium with validly published names by several phenotypic, chemotaxonomic and genomic characteristics. On the basis of the results of this polyphasic taxonomic analysis, the bacterial isolate represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium phlebotomi sp. nov. is proposed. The type strain is SSI9T (=ATCC TSD-210T=LMG 31664T=NRRL B-65603T).
Collapse
Affiliation(s)
- Madhavi L. Kakumanu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Bahjat Fadi Marayati
- Department of Biology, University of North Carolina Greensboro, 235 Eberhart Bldg., Greensboro, North Carolina, USA
| | - Ayako Wada-Katsumata
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Gideon Wasserberg
- Department of Biology, University of North Carolina Greensboro, 235 Eberhart Bldg., Greensboro, North Carolina, USA
| | - Coby Schal
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Charles S. Apperson
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Loganathan Ponnusamy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
7
|
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).
Collapse
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
| | | |
Collapse
|
8
|
Li Y, Wang S, Chang JP, Bian DR, Guo LM, Yang XQ. Sphingomonas corticis sp. nov., and Sphingobacterium corticibacterium sp. nov., from bark canker. Int J Syst Evol Microbiol 2020; 70:5627-5633. [PMID: 32924914 DOI: 10.1099/ijsem.0.004451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas. The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18 : 1 ω7c and/or C18 : 1 ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15 : 0, C16 : 1 ω7c and/or C16 : 1 ω6c and iso-C17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium. The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.
Collapse
Affiliation(s)
- Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Shengkun Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Ju-Pu Chang
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Dan-Ran Bian
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-Min Guo
- Puyang Academy of Forestry, Puyang 457000, PR China
| | - Xu-Qi Yang
- Puyang Academy of Forestry, Puyang 457000, PR China
| |
Collapse
|
9
|
Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
Collapse
|
10
|
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).
Collapse
|
11
|
Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave. Int J Syst Evol Microbiol 2020; 70:2348-2354. [DOI: 10.1099/ijsem.0.004044] [Citation(s) in RCA: 7] [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-stain-negative, non-motile and rod-shaped bacterium, designated strain 5.0403-2T, was isolated from a cave soil sample collected from Tiandong Cave, Guizhou Province, south-west PR China. Cells showed positive oxidase and catalase reactions. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3OH and summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl). The cellular polar lipids contained phosphatidylethanolamine, one unidentified phospholipid, three unidentified phosphoglycolipids and four unidentified lipids. The genomic DNA G+C content was 36.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5.0403-2T should be assigned to the genus
Sphingobacterium
. Results of 16S rRNA gene sequence similarity analysis showed that strain 5.0403-2T was most similar to
Sphingobacterium bovisgrunnientis
KCTC 52685T (98.7 %),
Sphingobacterium composti
KCTC 12578T (98.0 %) and
Sphingobacterium alimentarium
DSM 22362T (97.3 %) and less than 95.0 % similar to other species of the genus
Sphingobacterium
. The average nucleotide identity values between strain 5.0403-2T and
S. bovisgrunnientis
KCTC 52685T,
S. composti
KCTC 12578T and
S. alimentarium
DSM 22362T were 94.2, 82.3 and 77.2 % respectively. The digitalDNA–DNA hybridization values between strain 5.0403-2T and
S. bovisgrunnientis
KCTC 52685T,
S. composti
KCTC 12578T and
S. alimentarium
DSM 22362T were 68.4, 25.6 and 20.7 %. These results indicated that the isolate represented a novel genomic species. The polyphasic taxonomic characteristics indicated that strain 5.0304-2T represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium cavernae sp. nov. (type strain 5.0403–2T=KCTC 62981T=CCTCC AB 2019257T) is proposed.
Collapse
|
12
|
Microbial Populations of Fresh and Cold Stored Donkey Milk by High-Throughput Sequencing Provide Indication for A Correct Management of This High-Value Product. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Donkey milk is receiving increasing interest due to its attractive nutrient and functional properties (but also cosmetic), which make it a suitable food for sensitive consumers, such as infants with allergies, the immunocompromised, and elderly people. Our study aims to provide further information on the microbial variability of donkey milk under cold storage conditions. Therefore, we analysed by high-throughput sequencing the bacterial communities in unpasteurized donkey milk just milked, and after three days of conservation at 4 °C, respectively. Results showed that fresh donkey milk was characterized by a high incidence of spoilage Gram-negative bacteria mainly belonging to Pseudomonas spp. A composition lower than 5% of lactic acid bacteria was found in fresh milk samples, with Lactococcus spp. being the most abundant. The occurrence of microbial species belonging to risk group 2 was found in fresh milk. After three days of cold storage, the bacterial biodiversity of donkey milk was strongly reduced, since about 93% of the bacterial communities were identified as different species of psychrotrophic Pseudomonas. In conclusion, we report a preliminary description of the microbial diversity of donkey milk by using a metagenomic approach and encouraging a correct exploitation of this high-value niche product.
Collapse
|
13
|
He ZW, Tang CC, Liu WZ, Ren YX, Guo ZC, Zhou AJ, Wang L, Yang CX, Wang AJ. Enhanced short-chain fatty acids production from waste activated sludge with alkaline followed by potassium ferrate treatment. BIORESOURCE TECHNOLOGY 2019; 289:121642. [PMID: 31226670 DOI: 10.1016/j.biortech.2019.121642] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/09/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
This study reported an efficient approach, i.e., alkaline followed by potassium ferrate (PF) pretreatment, to enhance short chain fatty acids (SCFAs) production from waste activated sludge anaerobic fermentation process. The optimum condition was initial pH of 10.0 and PF dosage of 28 mg Fe(VI)/g total suspended solid, with the highest SCFAs production of 382 mg chemical oxygen demand/g volatile suspended solid, which was 2.03 and 2.06 times higher than that of corresponding sole treatments. It was found that the alkaline + PF treatment could provide more soluble substrates for subsequent acidification process by accelerating disruption of both microbial cells and extracellular polymeric substances. And the alkaline + PF treatment also benefited to the activity promotion of specific hydrolases and inhibition of methanogens. Besides, the abundances of microorganisms related to SCFAs production, such as Proteiniclasticum and Macellibacteroides, were increased greatly, whereas the main SCFAs consumer, Proteobacteria, was decreased from 29.1% to 14.4%.
Collapse
Affiliation(s)
- Zhang-Wei He
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cong-Cong Tang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Wen-Zong Liu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.
| | - Yong-Xiang Ren
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ze-Chong Guo
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212005, China
| | - Ai-Juan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Ling Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chun-Xue Yang
- School of Geography and Tourism, Harbin University, Harbin 150086, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
| |
Collapse
|
14
|
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).
Collapse
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
| |
Collapse
|
15
|
Pan H, Yang X, Zhong Y, Xu M, Sun G. Response of environmental variables and microbial community to sodium percarbonate addition to contaminated sediment. CHEMOSPHERE 2018; 211:500-509. [PMID: 30086526 DOI: 10.1016/j.chemosphere.2018.07.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
Sodium percarbonate (SPC) is a common reagent used for in situ remediation of contaminated soil. Current studies focus on the effects of SPC on pollutant removal; however, a knowledge gap exists for the biochemical process following SPC addition. In this study, a microcosm batch experiment was conducted to investigate the residual effect caused by different doses of SPC addition on native microbial communities, as well as on the environmental variables of contaminated sediments. The obtained results showed that the more SPC was added, the more dissolved matters were generated and the oxidation-reduction potential was lowered. Furthermore, the metabolic activities of the microbial community were enhanced and the microbial community structure responded differently to different SPC doses: the microbes that increased at high SPC dose mainly belonged to the phylum Firmicutes, the class Clostridia, and the genera Petrimonas and Proteiniclasticum. The microbes that increased at medium SPC dose mainly belonged to the class Alphaproteobacteria and the genus Brevundimonas. In contrast, vulnerable microbes mainly belonged to the phylum Acidobacteria, the class Caldisericia, Holophagae, and the genus Sulfuricurvum. Microbes capable of fermentation, ureolysis, and chemohetrotrophy increased. These results indicate that SPC addition could indirectly provide both electron acceptors and donors, thus improving the metabolic activities of the microorganisms in the contaminated sediment. Furthermore, the utilized SPC dose should be considered to achieve the optimal benefit for in situ remediation. This study forms a valuable reference for the application of SPC in ecological engineering.
Collapse
Affiliation(s)
- Hanping Pan
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Yuming Zhong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Guoping Sun
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| |
Collapse
|
16
|
Liu L, Hui N, Liang LX, Zhang XX, Li LB, Sun QW. Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert. Int J Syst Evol Microbiol 2018; 68:3279-3284. [PMID: 30156529 DOI: 10.1099/ijsem.0.002982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11T grew at salinities of 0-6 % (w/v; optimum 0-2 %), a pH of 7.0-9.0 (pH 7.0-8.0) and temperatures of 20-42 °C (28-30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11T shared the highest similarity to Sphingobacterium gobiense H7T, followed by Sphingobacterium chuzhouense DH-5T and Sphingobacterium arenae H-12T. The unfinished draft genome of strain 5JN-11T was 4.69 Mb. The G+C content of strain 5JN-11T was 42.8 mol%. The average nucleotide identity to S. gobiense H7T was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacteriumhaloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).
Collapse
Affiliation(s)
- Lei Liu
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Nan Hui
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-Xiong Liang
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xiao-Xia Zhang
- 2Key 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
| | - Lu-Bin Li
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Qi-Wu Sun
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| |
Collapse
|
17
|
Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS, Pinnaka AK. Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk. Int J Syst Evol Microbiol 2018; 68:636-642. [PMID: 29388539 DOI: 10.1099/ijsem.0.002562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, rod shaped, non-motile bacterium, designated strain YK2T, was isolated from yak milk from Leh, India. The strain was positive for oxidase- and catalase-activities and negative for starch hydrolysis, nitrate reduction, citrate utilization, urease, lysine decarboxylase and ornithine decarboxylase activities. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH (summed feature 3). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid and six unidentified lipids. The DNA G+C content of the strain was 38.9 mol%. The 16S rRNA gene sequence analysis indicated that strain YK2T was a member of the genus Sphingobacterium and closely related to Sphingobacterium alimentarium and Sphingobacterium composti with pair-wise sequence similarity of 98.3 and 97.9 %, respectively. The sequence similarity to other members of the genus Sphingobacterium was between 92.6 to 96.3 %. Phylogenetic analysis showed that strain YK2T clustered with Sphingobacterium alimentarium and together clustered with Sphingobacterium composti. DNA-DNA hybridization of strain YK2T with Sphingobacterium alimentarium WCC 4521T and Sphingobacterium composti T5-12T showed a relatedness of only 38 and 54 %, respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain YK2T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium bovisgrunnientis sp. nov. is proposed. The type strain of Sphingobacterium bovisgrunnientis sp. nov. is YK2T (=MTCC 12631T=KCTC 52685T=JCM 31951T).
Collapse
Affiliation(s)
- Manpreet Kaur
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India.,Council of Scientific and Industrial Research (CSIR), MTCC-Microbial Type Culture Collection & Gene Bank, Institute of Microbial Technology, Chandigarh 160036, India.,Council of Scientific and Industrial Research (CSIR) - Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Harjodh Singh
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India.,Council of Scientific and Industrial Research (CSIR), MTCC-Microbial Type Culture Collection & Gene Bank, Institute of Microbial Technology, Chandigarh 160036, India.,Council of Scientific and Industrial Research (CSIR) - Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Shivani Sharma
- Council of Scientific and Industrial Research (CSIR), MTCC-Microbial Type Culture Collection & Gene Bank, Institute of Microbial Technology, Chandigarh 160036, India
| | - Sunita Mishra
- Council of Scientific and Industrial Research (CSIR) - Central Scientific Instruments Organisation, Chandigarh 160030, India
| | - Naga Radha Srinivas Tanuku
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India.,CSIR-National Institute of Oceanography, Regional Centre, Lawsons Bay Colony, Visakhapatnam 530017, India
| | - Anil Kumar Pinnaka
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India.,Council of Scientific and Industrial Research (CSIR), MTCC-Microbial Type Culture Collection & Gene Bank, Institute of Microbial Technology, Chandigarh 160036, India
| |
Collapse
|
18
|
Quijada NM, Mann E, Wagner M, Rodríguez-Lázaro D, Hernández M, Schmitz-Esser S. Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment. Int J Food Microbiol 2017; 267:54-61. [PMID: 29291459 DOI: 10.1016/j.ijfoodmicro.2017.12.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/27/2017] [Accepted: 12/24/2017] [Indexed: 10/18/2022]
Abstract
Cheese ripening involves the succession of complex microbial communities that are responsible for the organoleptic properties of the final products. The food processing environment can act as a source of natural microbial inoculation, especially in traditionally manufactured products. Austrian Vorarlberger Bergkäse (VB) is an artisanal washed-rind hard cheese produced in the western part of Austria without the addition of external ripening cultures. Here, the composition of the bacterial communities present on VB rinds and on different processing surfaces from two ripening cellars was assessed by near full length 16S rRNA gene amplification, cloning and sequencing. Non-inoculated aerobic bacteria dominated all surfaces in this study. VB production conditions (long ripening time, high salt concentration and low temperatures) favor the growth of psychro- and halotolerant bacteria. Several bacterial groups, such as coryneforms, Staphylococcus equorum and Halomonas dominated VB and were also found on most environmental surfaces. Analysis of OTUs shared between different surfaces suggests that VB rind bacteria are inoculated naturally during the ripening from the processing environment and that cheese surfaces exert selective pressure on these communities, as only those bacteria better adapted flourished on VB rinds. This study analyzed VB processing environment microbiota and its relationship with VB rinds for the first time, elucidating that the processing environment and the cheese microbiota should be considered as microbiologically linked ecosystems with the goal of better defining the events that take place during cheese maturation.
Collapse
Affiliation(s)
- Narciso M Quijada
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria; Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | - Evelyne Mann
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria
| | - David Rodríguez-Lázaro
- Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos, Burgos, Spain
| | - Marta Hernández
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | - Stephan Schmitz-Esser
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria.
| |
Collapse
|
19
|
Two Draft Genome Sequences of Sphingobacterium sp. Strains Isolated from Honey. GENOME ANNOUNCEMENTS 2017; 5:5/48/e01364-17. [PMID: 29192084 PMCID: PMC5722070 DOI: 10.1128/genomea.01364-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report two annotated draft genome sequences of Sphingobacterium sp. strains isolated from honey. The genomes of strains 1.A.4 and 1.A.5 show a limited similarity to each other and to genomes of other Sphingobacterium species, indicating that these isolates may represent new species.
Collapse
|
20
|
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).
Collapse
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
| |
Collapse
|
21
|
Fu YS, Hussain F, Habib N, Khan IU, Chu X, Duan YQ, Zhi XY, Chen X, Li WJ. Sphingobacteriumsoli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:2284-2288. [PMID: 28699577 DOI: 10.1099/ijsem.0.001946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling County, Yunnan Province, south-west China. The new isolate was characterized taxonomically by using a polyphasic approach. The strain grew optimally at 30 °C, at pH 7.0 and with 0-3 % (w/v) NaCl. It was positive for catalase and oxidase but negative for H2S production. Comparative 16S rRNA gene sequence analysis showed that strain YIM X0211T fell within the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii DSM 11724T (97.93 % similarity). The G+C content of the genomic DNA was 41.2 mol%. The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0 2-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, sphingolipid, and several unknown phospholipids or lipids. The DNA-DNA hybridization value between strain YIM X0211T and S. mizutaii DSM 11724T was 42.3±0.4 %, which is below the 70 % limit for species delineation. These chemotaxonomic data supported the affiliation of strain YIM X0211T to the genus Sphingobacterium. Based on the recorded phenotypic and genotypic characteristics, it is determined that the isolate represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium soli sp. nov. is proposed. The type strain is YIM X0211T (=KCTC 42696T=CGMCC 1.15966T).
Collapse
Affiliation(s)
- Yu-Song Fu
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Firasat Hussain
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Neeli Habib
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Inam Ullah Khan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Xiao Chu
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Xing Chen
- China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, 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.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| |
Collapse
|
22
|
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).
Collapse
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
| |
Collapse
|
23
|
Huys G, Purohit P, Tan CH, Snauwaert C, Vos PD, Saffar HA, Obaid IA, Busse HJ, Seemann T, John Albert M. Sphingobacterium cellulitidis sp. nov., isolated from clinical and environmental sources. Int J Syst Evol Microbiol 2017; 67:1415-1421. [DOI: 10.1099/ijsem.0.001832] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Geert Huys
- Laboratory of Microbiology & BCCM Bacteria Collection, Faculty of Sciences, Ghent University, Gent, Belgium
| | | | - Chuan Hao Tan
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Cindy Snauwaert
- Laboratory of Microbiology & BCCM Bacteria Collection, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Paul De Vos
- Laboratory of Microbiology & BCCM Bacteria Collection, Faculty of Sciences, Ghent University, Gent, Belgium
| | - Huda Al Saffar
- Assad Al Hamad Dermatology Center, Al-Sabah Hospital, Kuwait
| | - Ina'am Al Obaid
- Department of Medical Microbiology, Al-Sabah Hospital, Kuwait
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Wien, Austria
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative, The University of Melbourne, Victoria, Australia
| | - M John Albert
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| |
Collapse
|
24
|
Lai WA, Hameed A, Liu YC, Hsu YH, Lin SY, Young CC. Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium
thermophilum Yabe et al. 2013. Int J Syst Evol Microbiol 2016; 66:5336-5344. [DOI: 10.1099/ijsem.0.001517] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| |
Collapse
|
25
|
Li Y, Song LM, Guo MW, Wang LF, Liang WX. Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2016; 66:3456-3462. [DOI: 10.1099/ijsem.0.001217] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong Li
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-min Song
- The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Min-wei Guo
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lai-fa Wang
- The Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Wen-xing Liang
- The Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, P. R. China
| |
Collapse
|
26
|
Wang X, Zhang CF, Yu X, Hu G, Yang HX, Zhang YK, Zhu SJ, Jin W, Zhang H, Hong Q. Sphingobacterium chuzhouense sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2016; 66:4968-4974. [PMID: 27562767 DOI: 10.1099/ijsem.0.001454] [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
A novel Gram-staining-negative bacterium, designated DH-5T, was isolated from a farmland soil in Chuzhou, Anhui province, China. Cells of strain DH-5T were aerobic, non-motile, non-spore-forming and rod-shaped. The organism grew at 20-37 °C, pH 6.0-9.0 and with 0-5 % NaCl (w/v). The DNA G+C content was 42.8 mol%. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and C16 : 0. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DH-5T was a member of the genus Sphingobacterium and shared the highest similarity with Sphingobacterium gobiense H7T (96.0 %), followed by Sphingobacterium arenae H-12T (94.5 %). Strain DH-5T exhibited low DNA-DNA relatedness with S. gobiense H7T (35.1±1.4 %) and S. arenae H-12T (21.4±1.0 %). On the basis of phenotypic, genotypic and phylogenetic evidence, DH-5T is considered to represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium chuzhouense sp. nov. is proposed. The type strain is DH-5T (=ACCC 19856T=KCTC 42746T).
Collapse
Affiliation(s)
- Xiang Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chen-Fei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xing Yu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Gang Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.,Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Hong-Xing Yang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ying-Kun Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shi-Jun Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wen Jin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hao Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| |
Collapse
|
27
|
Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, Aslam Z. Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost. Int J Syst Evol Microbiol 2016; 66:4433-4439. [PMID: 27498829 DOI: 10.1099/ijsem.0.001370] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7T) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7T belongs to the genus Sphingobacterium of the family Sphingobacteriaceae and was most closely related to Sphingobacterium yanglingense JCM 30166T (92.6 %), Sphingobacterium psychroaquaticum KACC 18188T (92.6 %), and Sphingobacterium thermophilum KCTC 23708T (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7T were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7T to the genus Sphingobacterium. However, strain GJ30-7T could be distinguished genotypically and phenotypically from species of the genus Sphingobacterium with validly published names. The novel isolate therefore represents a novel species, for which the name Sphingobacterium jejuense sp. nov. is proposed, with the type strain GJ30-7T (=KACC 18625T=JCM 30948T).
Collapse
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | | | - Kang Duk Choi
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Zubair Aslam
- Department of Agronomy, Faculty of Agriculture, University of Agriculture, Faisalabad-38040, Pakistan
| |
Collapse
|
28
|
Zhang Y, Chen L, Sun R, Dai T, Tian J, Zheng W, Wen D. Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay. J Environ Sci (China) 2016; 44:57-68. [PMID: 27266302 DOI: 10.1016/j.jes.2015.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 10/30/2015] [Accepted: 11/25/2015] [Indexed: 06/06/2023]
Abstract
Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea, Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community.
Collapse
Affiliation(s)
- Yan Zhang
- School of Environment, Tsinghua University, Beijing 100084, China; Zhejiang Shuangyi Environmental Technology Development Co., Ltd., Jiaxing 314000, China
| | - Lujun Chen
- School of Environment, Tsinghua University, Beijing 100084, China; Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, Jiaxing 314050, China
| | - Renhua Sun
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jinping Tian
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei Zheng
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, Jiaxing 314050, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|
29
|
Sphingobacterium griseoflavum sp. nov., isolated from the insect Teleogryllus occipitalis living in deserted cropland. Int J Syst Evol Microbiol 2016; 66:1956-1961. [DOI: 10.1099/ijsem.0.000970] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
30
|
Sun JQ, Liu M, Wang XY, Xu L, Wu XL. Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata. Int J Syst Evol Microbiol 2015; 65:4508-4513. [DOI: 10.1099/ijsem.0.000600] [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-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).
Collapse
Affiliation(s)
- Ji-Quan Sun
- Institute of Innovation (Baotou), Peking University, Baotou 014030, Inner Mongolia, PR China
- College of Engineering, Peking University, Beijing 100871, PR China
| | - Min Liu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, Inner Mongolia, PR China
| | - Xin-Ying Wang
- Institute of Innovation (Baotou), Peking University, Baotou 014030, Inner Mongolia, PR China
| | - Lian Xu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, Inner Mongolia, PR China
| | - Xiao-Lei Wu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, Inner Mongolia, PR China
- College of Engineering, Peking University, Beijing 100871, PR China
| |
Collapse
|
31
|
Du J, Singh H, Won K, Yang JE, Jin FX, Yi TH. Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose. Int J Syst Evol Microbiol 2015; 65:2949-2954. [DOI: 10.1099/ijs.0.000361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, designated strain THG-SQA8T, was isolated from rhizosphere soil of rose in PR China. Strain THG-SQA8T was closely related to members of the genus Sphingobacterium, showed the highest sequence similarities with Sphingobacterium multivorum KACC 14105T (98.0 %) and Sphingobacterium ginsenosidimutans KACC 14526T (97.4 %). DNA–DNA hybridization showed values of 35.2 ± 0.9 % and 8.8 ± 0.3 % DNA reassociation with S. multivorum KACC 14105T and S. ginsenosidimutans KACC 14526T, respectively. Chemotaxonomic data revealed that strain THG-SQA8T possesses menaquinone-7 as the only respiratory quinone, and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and C16 : 0 as the major fatty acids. The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 40.7 mol%. These data corroborated the affiliation of strain THG-SQA8T to the genus Sphingobacterium. Thus, the isolate represents a novel species, for which the name Sphingobacterium mucilaginosum sp. nov. is proposed, with THG-SQA8T as the type strain ( = CCTCC AB 2014317T = KCTC 42503T).
Collapse
Affiliation(s)
- Juan Du
- Department of Oriental Medicinal Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446–701, Republic of Korea
| | - Hina Singh
- Department of Oriental Medicinal Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446–701, Republic of Korea
| | - KyungHwa Won
- Department of Oriental Medicinal Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446–701, Republic of Korea
| | - Jung-Eun Yang
- Department of Oriental Medicinal Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446–701, Republic of Korea
| | - Feng-Xie Jin
- College of Bio and Food Technology, Dalian Polytechnic University, Qinggong-yuan No. 1, Ganjingzi-qu, Dalia 116034, PR China
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446–701, Republic of Korea
| |
Collapse
|
32
|
Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis. Antonie van Leeuwenhoek 2015; 108:1099-105. [PMID: 26303282 DOI: 10.1007/s10482-015-0563-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/19/2015] [Indexed: 10/23/2022]
Abstract
A novel Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterium, designated YIM 101302(T), was isolated from the faeces of Rhinoceros unicornis dwelling in the Yunnan Wild Animal Park, Yunnan province, South-West China. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain YIM 101302(T) to the genus Sphingobacterium. The newly isolated bacterium was found to be closely related to Sphingobacterium composti T5-12(T) (97.1% 16S rRNA sequence identity) and Sphingobacterium alimentarium WCC 4521(T) (95.6% 16S rRNA sequence identity) forming a distinct clade with these two species. Polar lipids of strain YIM 101302(T) were identified as phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, and three unidentified polar lipids; the predominant menaquinone as MK-7 and the major fatty as iso-C15:0. The genomic DNA G+C content was determined to be 38.9 mol%. The DNA-DNA hybridization values between strain YIM 101302(T) and S. composti T5-12(T), was 53.6 ± 5.8%. These results indicates that strain YIM 101302(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium rhinocerotis sp. nov. is proposed. The type strain is YIM 101302(T) (=CCTCC AB 2013218(T) = KCTC 42533(T)).
Collapse
|
33
|
Peng S, Hong DD, Xin YB, Jun LM, Hong WG. Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol 2014; 64:3862-3866. [PMID: 25168614 DOI: 10.1099/ijs.0.068254-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1(T), was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium. On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1(T) showed 96.8% similarity to Sphingobacterium nematocida CCTCC AB 2010390(T) and less than 95.2% similarity to other members of the genus Sphingobacterium. Growth of strain CCNWSP36-1(T) occurred at 10-40 °C and at pH 5.0-9.0. The NaCl range (w/v) for growth was 0-4%. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C(15:0) and summed feature 3 (comprising C(16:1)ω6c and/or C(16:1)ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1(T) and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1(T) ( =ACCC 19328(T) =JCM 30166(T)).
Collapse
Affiliation(s)
- Shi Peng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dong Dan Hong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yang Bing Xin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Ming Jun
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Wei Ge Hong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| |
Collapse
|
34
|
Feng H, Zeng Y, Huang Y. Sphingobacterium paludis sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2014; 64:3453-3458. [DOI: 10.1099/ijs.0.064915-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative bacteria, designated S37T, was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37T were aerobic, non-motile rods. Growth occurred at 10–37 °C (optimum, 25 °C), pH 5.0–9.7 (optimum, pH 7.5) and with 0–6 % (w/v) NaCl (optimum, 0.5 %). Based on 16S rRNA gene sequence analysis, strain S37T was found to be a member of the genus
Sphingobacterium
and shared highest similarity with
Sphingobacterium composti
4M24T (95.78 %). The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37T represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium
paludis sp. nov. (type strain S37T = CGMCC 1.12801T = NBRC 110386T) is proposed.
Collapse
Affiliation(s)
- Hao Feng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yanhua Zeng
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yili Huang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, PR China
| |
Collapse
|
35
|
Zhao P, Zhou Z, Chen M, Lin W, Zhang W, Wei G. Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert. Int J Syst Evol Microbiol 2014; 64:3931-3935. [PMID: 25201914 DOI: 10.1099/ijs.0.064246-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, short rod-shaped, non-motile, non-spore-forming bacterial strain, designated H7(T), was isolated from the Gobi desert, Xinjiang Province of China. The temperature, NaCl and pH ranges for growth were 8-40 °C (optimum 30 °C), 0-5 % (w/v) NaCl and pH 6-10 (optimum pH 7), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H7(T) belonged to the genus Sphingobacterium and showed highest sequence similarity (91 %) to Sphingobacterium composti DSM 18850. The genomic DNA G+C content was 44.3 mol%. MK-7 was identified as the predominant respiratory quinone. Strain H7(T) contained C16 : 1ω7c and/or C16 : 1ω6c, iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids. These data support the affiliation of strain H7(T) to the genus Sphingobacterium while phenotypic data indicated it is a representative strain of a novel species for which the name Sphingobacterium gobiense sp. nov. is proposed. The type strain is H7(T) ( = ACCC 05757(T) = KCTC 32293(T)).
Collapse
Affiliation(s)
- Peng Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, PR China.,State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, PR China
| | - Wenna Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing 100081, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, 712100 Yangling, Shaanxi, China
| |
Collapse
|
36
|
Cultivation-independent analysis of microbial communities on Austrian raw milk hard cheese rinds. Int J Food Microbiol 2014; 180:88-97. [DOI: 10.1016/j.ijfoodmicro.2014.04.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/24/2014] [Accepted: 04/06/2014] [Indexed: 01/18/2023]
|
37
|
Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie van Leeuwenhoek 2013; 105:325-33. [PMID: 24281734 DOI: 10.1007/s10482-013-0077-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
|
38
|
Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, Lin M, Zhang W, Luo X. Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2013; 64:248-253. [PMID: 24052628 DOI: 10.1099/ijs.0.051706-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-stain-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacterium designated H-12(T) was isolated from a mixed sandy soil sample collected from Xinjiang, China. Strain H-12(T) grew at 20-37 °C (optimum, 30 °C), pH 7.0-11.0 (optimum, pH 8.5) on TGY medium with 0-5 % NaCl (w/v). 16S rRNA gene sequence analysis indicated that strain H-12(T) shared sequence similarities with Sphingobacterium composti DSM 18850(T) (90.0 %). Strain H-12(T) showed a low level of DNA-DNA relatedness to Sphingobacterium composti DSM 18850(T) (45.5 %). The predominant isoprenoid quinone of strain H-12(T) was MK-7 and the major polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were C16:1ω7c and/or C16 : 1ω6c, iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, C16 : 0 3-OH and iso-C15 : 0 3-OH. DNA G+C content of strain H-12(T) was 44.15 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain H-12(T) is proposed to be a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium arenae sp. nov. is suggested and the type strain is H-12(T) ( = ACCC 05758(T) = KCTC 32294(T)).
Collapse
Affiliation(s)
- Shijie Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Life Science and Engineering College, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shiyou Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mingkun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Aihua Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Chen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xuegang Luo
- Life Science and Engineering College, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| |
Collapse
|
39
|
Holmes B, Steigerwalt AG, Nicholson AC. DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov. Int J Syst Evol Microbiol 2013; 63:4639-4662. [PMID: 23934253 DOI: 10.1099/ijs.0.054353-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T) = CCUG 60564(T) = CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T) = CCUG 60559(T) = CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T) = CCUG 60566(T) = CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T) = CCUG 60563(T) = CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T) = X-65(T) = CCTCC AB 208154(T) = NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.
Collapse
Affiliation(s)
- B Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - A G Steigerwalt
- Special Bacteriology Reference Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - A C Nicholson
- Special Bacteriology Reference Laboratory, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| |
Collapse
|
40
|
Sun LN, Zhang J, Chen Q, He J, Li SP. Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2013; 63:2260-2264. [DOI: 10.1099/ijs.0.046987-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of a bacterium, strain DC-8T, isolated from activated sludge, was determined using a polyphasic taxonomic approach. The cells of strain DC-8T were Gram-negative, non-motile, non-spore-forming and rod-shaped. The isolate grew at temperature range of 10–40 °C (optimum 30–35 °C), pH range of 5.0–10.0 (optimum 6.5–8.0) and NaCl concentrations of 0–5 % (optimum 0–1 %). The predominant menaquinone of strain DC-8T was MK-7 and major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 39.7 %), iso-C15 : 0 (33.7 %) and C16 : 0 (5.2 %). The DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DC-8T was a member of the genus
Sphingobacterium
. Strain DC-8T shared the highest similarity with
Sphingobacterium siyangense
SY1T (98.4 %),
Sphingobacterium multivorum
IAM 14316T (98.3 %),
Sphingobacterium canadense
CR11T (98.0 %) and
Sphingobacterium detergens
6.2ST (97.9 %) and shared less than 97 % similarity with other members of the genus
Sphingobacterium
. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain DC-8T and its closest phylogenetic neighbours were below 70 %. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain DC-8T was clearly distinguished from all recognized species of the genus
Sphingobacterium
and should be classified as a representative of a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium caeni sp. nov. is proposed. The type strain is DC-8T ( = CCTCC AB 2012020T = KACC 16850T).
Collapse
Affiliation(s)
- Li-Na Sun
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jun Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, PR China
| | - Qing Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Shun-Peng Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| |
Collapse
|
41
|
Albert RA, Waas NE, Pavlons SC, Pearson JL, Ketelboeter L, Rosselló-Móra R, Busse HJ. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2013; 63:952-958. [DOI: 10.1099/ijs.0.043844-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
A psychrophilic, Gram-negative bacterium, designated MOL-1T, was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1T has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of
Sphingobacterium shayense
HS39T,
S. lactis
WCC 4512T,
S. composti
T5-12T,
S. daejeonense
TR6-04T,
S. bambusae
IBFC2009T and
S. alimentarium
WCC 4521T. The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1T represents a novel
Sphingobacterium
species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1T ( = NRRL B-59232T = DSM 22418T).
Collapse
Affiliation(s)
- Richard A. Albert
- Water Quality Center, Marquette University, Civil & Environmental Engineering, PO Box 1881 Milwaukee, WI 53233, USA
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Nancy E. Waas
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Shawn C. Pavlons
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Jamie L. Pearson
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Laura Ketelboeter
- Department of Biological Sciences, UW-Milwaukee, Milwaukee, WI 53201, USA
- Kleen Test Products, 1611 Sunset Road, Port Washington, WI 53074, USA
| | - Ramon Rosselló-Móra
- Grup de Microbiologia Marina, Institut Mediterrani d’Estudis Avançats, Mallorca, E-07190 Esporles, Spain
| | - Hans-Jürgen Busse
- Institute of Bacteriology, Mycology and Hygiene, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| |
Collapse
|
42
|
Rieser G, Scherer S, Wenning M. Naumannella halotolerans gen. nov., sp. nov., a Gram-positive coccus of the family
Propionibacteriaceae
isolated from a pharmaceutical clean room and from food. Int J Syst Evol Microbiol 2012; 62:3042-3048. [DOI: 10.1099/ijs.0.037218-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-stain-positive, aerobic bacterial strains isolated from a pharmaceutical clean room (strain WS4616T), a dessert milk product (strain WS4617) and from raw milk (strains WS4623 and WS4624) were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences showed that they formed a distinct lineage within the family
Propionibacteriaceae
. Similarity values between 16S rRNA gene sequences of the four novel strains and the type species of all genera belonging to the family
Propionibacteriaceae
were 89.2–94.1 %. The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were MK-8(H4) and MK-9(H4). The cell-wall peptidoglycan of type A3γ contained ll-diaminopimelic acid, alanine, glycine and glutamic acid. The G+C content of the genomic DNA of strain WS4616T was 67.7 mol%. The whole-cell sugar pattern contained ribose, mannose, arabinose, glucose and galactose. On the basis of phenotypic and genetic data, strains WS4616T, WS4617, WS4623 and WS4624 are classified as members of a novel species in a new genus of the family
Propionibacteriaceae
, for which the name Naumannella halotolerans gen. nov., sp. nov. is proposed. The type strain is WS4616T ( = DSM 24323T = LMG 26184T) and three additional strains are WS4617, WS4623 and WS4624.
Collapse
Affiliation(s)
- Gernot Rieser
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, D-85350 Freising, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, D-85350 Freising, Germany
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, D-85350 Freising, Germany
| | - Mareike Wenning
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung ZIEL, Technische Universität München, D-85350 Freising, Germany
| |
Collapse
|
43
|
Marqués AM, Burgos-Díaz C, Aranda FJ, Teruel JA, Manresa À, Ortiz A, Farfán M. Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:3036-3041. [DOI: 10.1099/ijs.0.036707-0] [Citation(s) in RCA: 22] [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 novel Gram-negative-staining strain, designated 6.2ST, was isolated from a soil sample and identified as a biosurfactant producer. Its taxonomic position was investigated using a polyphasic approach. The cells were non-motile, non-spore-forming rods. The organism grew optimally at 30-37 °C, with 0–3 % (w/v) NaCl, and at pH 7.0. Based on 16S rRNA gene sequence analysis, strain 6.2ST was found to be a member of the genus
Sphingobacterium
and was most closely related to four type species of the genus, showing sequence similarities of 96.8–98.9 %. Partial chaperonin 60 (cpn60) gene sequence analysis was useful in resolving the phylogenetic relationships between strain 6.2ST and closely related taxa, with similarities ranging from 85.5 % (with
Sphingobacterium thalpophilum
DSM 11723T) to 90.3 % (with
Sphingobacterium canadense
CR11T and
Sphingobacterium multivorum
JCM 21156T). The results of DNA–DNA hybridization experiments between the novel strain and its closest relatives gave a DNA–DNA relatedness value of less than 70 %, and consequently confirmed that this new strain did not belong to a previously described species of the genus
Sphingobacterium
. The major fatty acids were summed feature 3 (iso-C15 : 0 2 OH and/or C16 : 1ω7c); iso-C15 : 0; iso-C17 : 0 3-OH and C16 : 0. The G+C content of the genomic DNA was 40.0 mol%. According to its phenotypic and genotypic characteristics and the phylogenetic data, strain 6.2ST represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium detergens sp. nov. is proposed. The type strain is 6.2ST ( = CECT 7938T = LMG 26465T).
Collapse
Affiliation(s)
- Ana M. Marqués
- Laboratory of Microbiology, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - César Burgos-Díaz
- Laboratory of Microbiology, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Francisco José Aranda
- Department of Biochemistry and Molecular Biology-A, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - José Antonio Teruel
- Department of Biochemistry and Molecular Biology-A, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - Àngels Manresa
- Laboratory of Microbiology, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Antonio Ortiz
- Department of Biochemistry and Molecular Biology-A, Faculty of Veterinary, University of Murcia, 30100 Murcia, Spain
| | - Maribel Farfán
- Laboratory of Microbiology, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| |
Collapse
|
44
|
Xiao T, He X, Cheng G, Kuang H, Ma X, Yusup K, Hamdun M, Gulsimay A, Fang C, Rahman E. Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense. Int J Syst Evol Microbiol 2012; 63:815-820. [PMID: 22611196 DOI: 10.1099/ijs.0.030155-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative bacterial strain, designated XH4(T), was isolated from soil of a Populus euphratica forest in the Hotan River valley, Xinjiang Uyghur autonomous region, PR China. The cells were strictly aerobic, non-motile, short rods. The isolate grew optimally at 37 °C and at pH 7.0-8.0. Based on 16S rRNA gene sequence analysis, strain XH4(T) belonged to the genus Sphingobacterium and was closely related to Sphingobacterium mizutaii ATCC 33299(T) (96.1 % sequence similarity). The DNA G+C content was 41.2 mol%. The major polar lipid of strain XH4(T) was phosphatidylethanolamine, and several unidentified polar lipids were also present. Strain XH4(T) showed the typical chemotaxonomic features of the genus Sphingobacterium, with the presence of ceramide phosphorylethanolamine 2 (CerPE-2) as the major ceramide. The major cellular fatty acids of strain XH4(T) were iso-C15 : 0 (34.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.7 %) and iso-C17 : 0 3-OH (14.7 %). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic data and phylogenetic inference, strain XH4(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium hotanense sp. nov. is proposed. The type strain is XH4(T) ( = NRRL B-59204(T) = CCTCC AB 209007(T)). Emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense are also given.
Collapse
Affiliation(s)
- Ting Xiao
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Xiang He
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Gang Cheng
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Haiju Kuang
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Xiangru Ma
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Khayir Yusup
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Maryam Hamdun
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Abaidulla Gulsimay
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Chengxiang Fang
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Erkin Rahman
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| |
Collapse
|
45
|
Seiler H, Schmidt V, Wenning M, Scherer S. Bacillus kochii sp. nov., isolated from foods and a pharmaceuticals manufacturing site. Int J Syst Evol Microbiol 2012; 62:1092-1097. [DOI: 10.1099/ijs.0.027771-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-staining-positive, strictly aerobic, motile, catalase-positive, endospore-forming rods, designated WCC 4582T, WCC 4581 and WCC 4583, were isolated from two different food sources and a pharmaceuticals production site. The three isolates were highly similar in their 16S rRNA gene sequences (100 % similarity) and groEL sequences (99.2–100 % similarity), Fourier-transform infrared spectroscopic fingerprints and other features tested. The isolates were most closely related to
Bacillus horneckiae
; the isolates and the type strain of
B. horneckiae
shared 97.6 % and 89.6 % 16S rRNA gene and groEL sequence similarities, respectively. The organisms grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. The cell-wall peptidoglycan of WCC 4582T contained meso-diaminopimelic acid (A1γ) and the genomic DNA G+C content was 36.4 mol%. DNA–DNA relatedness between strain WCC 4582T and
B. horneckiae
NRRL B-59162T was 17 %. The three isolates are considered to represent a novel species of the genus
Bacillus
, for which the name Bacillus kochii sp. nov. is proposed. The type strain is WCC 4582T ( = DSM 23667T = CCUG 59877T = LMG 25855T).
Collapse
Affiliation(s)
- Herbert Seiler
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Verena Schmidt
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Mareike Wenning
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| |
Collapse
|
46
|
Rieser G, Scherer S, Wenning M. Micrococcus cohnii sp. nov., isolated from the air in a medical practice. Int J Syst Evol Microbiol 2012; 63:80-85. [PMID: 22328614 DOI: 10.1099/ijs.0.036434-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-reaction-positive bacteria, isolated from the air in a medical practice (strains WS4601(T), WS4602) or a pharmaceutical clean room (strain WS4599), were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences of the three novel strains showed that they formed a distinct lineage within the genus Micrococcus, sharing 16S rRNA gene sequence similarities of 96.1-98.0 % with other species of this genus. Chemotaxonomic features also supported the classification of the three novel strains within the genus Micrococcus. The major cellular fatty acids of strain WS4601(T) were anteiso-C(15 : 0) and iso-C(15 : 0), the cell-wall peptidoglycan was of type A3α (L-Lys-L-Ala), and the predominant respiratory quinones were MK-7(H(2)) and MK-8(H(2)). The polar lipid profile contained diphosphatidylglycerol and phosphatidylglycerol, but no phosphatidylinositol. The G+C content of the genomic DNA was 70.4 mol%. Numerous physiological properties were found that clearly distinguished strains WS4599, WS4601(T) and WS4602 from established members of the genus Micrococcus. Based on the phenotypic and phylogenetic data, strains WS4599, WS4601(T) and WS4602 are considered to represent three different strains of a novel species of the genus Micrococcus, for which the name Micrococcus cohnii sp. nov. is proposed. The type strain is WS4601(T) (=DSM 23974(T)=LMG 26183(T)).
Collapse
Affiliation(s)
- Gernot Rieser
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Technische Universität München, D-85350 Freising, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, D-85350 Freising, Germany.,Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Technische Universität München, D-85350 Freising, Germany
| | - Mareike Wenning
- Abteilung für Mikrobiologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Technische Universität München, D-85350 Freising, Germany
| |
Collapse
|