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Characterization of transcriptional activities at a divergent promoter of the type VI secretion system in enterohemorrhagic Escherichia coli O157:H7
Se Kye Kim , Jun Bong Lee , Jang Won Yoon
J. Microbiol. 2022;60(9):928-934.   Published online August 19, 2022
DOI: https://doi.org/10.1007/s12275-022-2109-9
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AbstractAbstract
The type VI secretion system (T6SS) is a novel secretion system found in many Gram-negative bacteria that plays a role in bacterial competition, virulence, and host immune evasion. The enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain EDL933 has a single functional T6SS gene cluster. In this study, we attempted to characterize the transcriptional pattern of the T6SS effector gene Z0264 in EDL933. Transcriptional analyses showed that Z0264 and other T6SS genes were transcribed in vitro in a growth-phase-dependent manner, but Z0264 was not secreted in the rich medium. Using adapter- and radioactivity-free transcription start site analysis, we identified an overlapping divergent promoter between Z0264 and Z0265. A β-galactosidase assay with truncated promoter regions showed that the divergent promoter is functional. In addition, we demonstrated the role of H-NS as a repressor in the transcription of Z0264. Notably, the cDNA PCR assay showed that the mRNA transcript from the Z0264 promoter did not include the entire main T6SS cluster, suggesting segmented gene expression by multiple promoters in the T6SS cluster. In conclusion, we identified a divergent promoter for Z0264 located in the T6SS cluster of EDL933 and characterized its in vitro transcriptional activity during growth. Our findings provide insights and a preliminary understanding of the regulatory mechanisms underlying T6SS transcription.
Comparative analysis of the colistin resistance-regulating gene cluster in Klebsiella species
Sun Ju Kim , Hongbaek Cho , Kwan Soo Ko
J. Microbiol. 2022;60(5):461-468.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1640-z
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AbstractAbstract
CrrAB two-component regulatory system is associated with colistin resistance in Klebsiella pneumoniae. Recently, some K. pneumoniae isolates lacking crrAB genes have been identified. In this study, we investigated the distribution and structural variation of the crrBAC-kexD cluster. To evaluate the structural variation of the crrBAC-kexD cluster, we explored 59 clinical K. pneumoniae isolates from Korea, and 508 whole genomes of K. pneumoniae and other strains of Klebsiella sp. Significant structural variations in crrBAC-kexD and its surrounding regions were identified among K. pneumoniae genomes. Within the genus Klebsiella, the cluster was identified only in K. pneumoniae, K. variicola, and K. quasipneumoniae, which form the K. pneumoniae complex. Among the 304 available K. pneumoniae genomes, an intact crrBAC-kexD cluster was identified in 178 isolates (58.6%), while the cluster was absent in 90 isolates (29.6%). Partial deletions within the cluster were identified in 22 genomes (7.2%). The most diverse structural patterns of the crrBAC-kexD cluster were observed in ST11 strains. Some clades lacked the crrBAC-kexD cluster. The crrBAC-kexD cluster was identified in the genomes of other bacterial species, including Citrobacter freundii and Enterobacter ludwigii. The crrBAC-kexD cluster is proposed to have been acquired by the ancestor of the K. pneumoniae complex from other bacterial species and the cluster may have been lost and re-acquired repeatedly in K. pneumoniae strains according to the phylogenetic analysis. The dynamic evolution of the crrBAC-kexD cluster suggests that it may have other roles, in addition to colistin resistance, in bacterial physiology.

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  • Roles of crrAB two-component regulatory system in Klebsiella pneumoniae: growth yield, survival in initial colistin treatment stage, and virulence
    Sun Ju Kim, Jong Hyun Shin, Hyunkeun Kim, Kwan Soo Ko
    International Journal of Antimicrobial Agents.2024; 63(1): 107011.     CrossRef
  • High prevalence of polymyxin-heteroresistant carbapenem-resistant Klebsiella pneumoniae and its within-host evolution to resistance among critically ill scenarios
    Xiaoli Wang, Tianjiao Meng, Yunqi Dai, Hong-Yu Ou, Meng Wang, Bin Tang, Jingyong Sun, Decui Cheng, Tingting Pan, Ruoming Tan, Hongping Qu
    Infection.2024;[Epub]     CrossRef
  • Role of efflux pumps, their inhibitors, and regulators in colistin resistance
    Yinhuan Ding, Jingchen Hao, Weijia Xiao, Caihong Ye, Xue Xiao, Chunxia Jian, Min Tang, Guangrong Li, Jinbo Liu, Zhangrui Zeng
    Frontiers in Microbiology.2023;[Epub]     CrossRef
Characterization of components of a reducing system for SoxR in the cytoplasmic membrane of Escherichia coli
Kang-Lok Lee , Kyung-Chang Lee , Joon-Hee Lee , Jung-Hye Roe
J. Microbiol. 2022;60(4):387-394.   Published online March 28, 2022
DOI: https://doi.org/10.1007/s12275-022-1667-1
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AbstractAbstract
A reducing system of SoxR, a regulator of redox-active molecules, was identified as rsxABCDGE gene products and RseC in Escherichia coli through genetic studies. We found that ApbE was an additional component of the reducer system. Bacterial two hybrid analysis revealed that these proteins indeed had multiple interactions among themselves. RseC and RsxB formed the core of the complex, interacting with more than five other components. RsxC, the only cytoplasmic component of the system, interacted with SoxR. It might be linked with the rest of the complex via RsxB. Membrane fractions containing the wild type complex but not the mutant complex reduced purified SoxR using NADH as an electron source. These results suggest that Rsx genes, RseC, and ApbE can form a complex using NAD(P)H to reduce SoxR.

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  • AcrAB-TolC efflux pump overexpression and tet(A) gene mutation increase tigecycline resistance in Klebsiella pneumoniae
    Zhaoxin Xia, Jing zhou, Nana Gao, Ge Li, Runde Liu, Guoping Lu, Jilu Shen
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
  • The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR): Physiological role, structure and function of a redox-driven, molecular machine
    Julia Steuber, Günter Fritz
    Biochimica et Biophysica Acta (BBA) - Bioenergetics.2024; 1865(4): 149485.     CrossRef
  • Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum
    Ruba Abdulrahman Ashy
    Saudi Journal of Biological Sciences.2023; 30(10): 103789.     CrossRef
Lysobacter panacihumi sp. nov., isolated from ginseng cultivated soil
Yue Huo , Jong-Pyo Kang , Joon Hurh , Yaxi Han , Jong-Chan Ahn , Ramya Mathiyalagan , Chunhong Piao , Deok-Chun Yang
J. Microbiol. 2018;56(10):748-752.   Published online September 28, 2018
DOI: https://doi.org/10.1007/s12275-018-8202-4
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AbstractAbstract
A Gram-negative, non-motile, aerobic, catalase-, and oxidasepositive bacterial strain, designated DCY117T, was isolated from ginseng cultivated soil in Gochang-gun, Republic of Korea, and was characterized taxonomically using a multifaceted approach. 16S rRNA gene sequence analysis revealed that strain DCY117T showed highest similarity to Lysobacter ruishenii CTN-1T (95.3%). Phylogenetic analysis revealed that closely related relatives of strain DCY117T were L. aestuarii S2-CT (95.1%), L. daejeonensis GH1-9T (95.0%), and L. caeni BUT-8T (94.9%). Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and phosphatidylethanolamine (PE) were the major polar lipids of strain DCY117T. The major isoprenoid quinone was Q-8. The major cellular fatty acids of strain DCY117T were iso-C15:0, iso-C16:0, and summed feature 9 (comprising iso-C17:1 ω9c and/or 10-methyl-C16:0). Genomic DNA G + C content was 61.8 mol%. On the basis of our findings, strain DCY117T is a novel species in the genus Lysobacter. We propose the name Lysobacter panacihumi sp. nov., and the type strain is DCY117T (= KCTC 62019T = JCM 32168T).

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  • Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
    So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(5): 469.     CrossRef
  • Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
    Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
    Journal of Microbiology.2021; 59(8): 709.     CrossRef
  • Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
Lysobacter pedocola sp. nov., a novel species isolated from Korean soil
Jun Hyeong Jang , Dongwook Lee , Taegun Seo
J. Microbiol. 2018;56(6):387-392.   Published online June 1, 2018
DOI: https://doi.org/10.1007/s12275-018-8046-y
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AbstractAbstract
A Gram-negative, yellow-pigmented bacterial strain, designated IPC6T, was isolated from soil in an arid region of Goyang-si (Gyeonggi-do, South Korea). Cells were strictly aerobic, non-spore-forming, rod-shaped. The strain grew within a temperature range of 10–42°C (optimum, 30°C) and pH of 5.0–11.0 (optimum, pH 8.0) in the presence of 0–2% (w/v) NaCl. Phylogenetically, the novel strain was closely related to members of the Lysobacter genus based on 16S rRNA sequence similarity, and showed the highest sequence similarity to Lysobacter niastensis KACC 11588T (98.5%). The predominant fatty acids were iso-C15:0, iso-C16:0, and summed feature 9 (iso-C17:1 ω9c), with Q-8 identified as the major ubiquinone. The polar lipid content included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophospholipid, and an unidentified phospholipid. DNA-DNA hybridization results indicated that the strain IPC6T was distinct from Lysobacter niastensis KACC 11588T (37.9 ± 0.14%), Lysobacter panacisoli KACC 17502T (56.4 ± 0.13%), Lysobacter soli KCTC 22011T (8.1 ± 0.04%), Lysobacter gummosus KCTC 12132T (9.6 ± 0.03%), and Lysobacter cavernae KCTC 42875T (37.5 ± 0.14%), respectively. The DNA G + C content of the novel strain was 71.1 mol%. Based on the collective phenotypic, genotypic and chemotaxonomic data, the IPC6T strain is considered to represent a novel species in the genus Lysobacter, for which the name Lysobacter pedocola sp. nov. (= KCTC 42811T = JCM 31020T) is proposed.

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  • Lysobacter lactosilyticus sp. nov., a Novel β-Galactosidase Producing Bacterial Strain Isolated from Farmland Soil Applied with Amino Acid Fertilizer
    Xiang Wang, Yu-Huan Wang, Hong-Xing Yang, Shao-Chuang Chuang, Chun-Fu Zhou, Xing Yu, Hao Zhang
    Current Microbiology.2023;[Epub]     CrossRef
  • Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
    So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(5): 469.     CrossRef
  • Corynebacterium kalidii sp. nov, an endophyte from a shoot of the halophyte Kalidium cuspidatum
    Jia-Yi Feng, Lian Xu, Shu-Kun Tang, Ji-Quan Sun
    Archives of Microbiology.2022;[Epub]     CrossRef
  • Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia
    Janez Mulec, Andreea Oarga-Mulec, Ladislav Holko, Lejla Pašić, Andreja Nataša Kopitar, Tina Eleršek, Andrej Mihevc
    Scientific Reports.2021;[Epub]     CrossRef
  • Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
    Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
    Journal of Microbiology.2021; 59(8): 709.     CrossRef
  • Sphingomonas xanthus sp. nov., Isolated from Beach Soil
    Hyungdong Kim, Geeta Chhetri, Taegun Seo
    Current Microbiology.2021; 78(1): 403.     CrossRef
  • Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil
    Lian Xu, Xiao-Xian Huang, De-Liang Fan, Ji-Quan Sun
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(2): 1273.     CrossRef
  • Echinicola soli sp. nov., isolated from alkaline saline soil
    Ya-Ting Xing, Lian Xu, Hai-Tao Wang, Xiao-Xian Huang, Shuai Wang, Ji-Quan Sun
    International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4139.     CrossRef
Lysobacter spongiae sp. nov., isolated from spongin
Heejae Choi , Wan-Taek Im , Jin-Sook Park
J. Microbiol. 2018;56(2):97-103.   Published online February 2, 2018
DOI: https://doi.org/10.1007/s12275-018-7462-3
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AbstractAbstract
A Gram-negative, motile, aerobic and rod-shaped bacterial strain designated 119BY6-57T was isolated from spongin. The taxonomic position of the novel isolate was confirmed using the polyphasic approach. Strain 119BY6-57T grew well at 25– 30°C on marine agar. On the basis of 16S rRNA gene sequence similarity, strain 119BY6-57T belongs to the family Xanthomonadaceae and is related to Lysobacter aestuarii S2-CT (99.8% sequence similarity), L. maris KMU-14T (97.5%), and L. daejeonensis GH1-9T (97.3%). Lower sequence similarities (97.0%) were found with all of the other recognized members of the genus Lysobacter. The G + C content of the genomic DNA was 69.9 mol%. The major respiratory quinone was Q-8 and the major fatty acids were C16:0 iso, C15:0 iso, summed feature 9 (comprising C17􍾙:1 iso ω9c and/or C16:0 10-methyl), summed feature 3 (comprising C16􍾙:1 ω7c and/or C16:1 ω6c), and C11:0 iso 3-OH. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, and an unidentified polar lipid. DNADNA relatedness values between strain 119BY6-57T and its closest phylogenetically neighbors were below 48.0 ± 2.1%. Based on genotypic and phenotypic characteristics, it is concluded that strain 119BY6-57T is a new member within the genus Lysobacter, for which the name Lysobacter spongiae sp. nov. is proposed. The type strain is 119BY6-57T (= KACC 19276T = LMG 30077T).

Citations

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  • Extended-Spectrum Beta-Lactamase Producing Escherichia coli in Raw Cow Milk At Selling Points and Determinants of Contamination in and Around Chencha, Southern Ethiopia
    Tomas Torka
    Veterinary Medicine: Research and Reports.2024; Volume 15: 159.     CrossRef
  • Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
    Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
  • Lysobacter changpingensis sp. nov., a novel species of the genus Lysobacter isolated from a rhizosphere soil of strawberry in China
    Bang-Yan Niu, Dong-Jun Ren, Fang-Bo Zhang, Hong-Tu Zhu, Hai-Lei Wei, Ming-Chao Ma, Miao Gao
    Folia Microbiologica.2023; 68(6): 991.     CrossRef
  • An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota ) Isolated from Aquatic Host Species Described in 2018 to 2021
    Claire R. Burbick, Erik Munson, Sara D. Lawhon, Amanda Zapp, Maia Villaflor, Elizabeth Thelen, Romney M. Humphries
    Journal of Clinical Microbiology.2023;[Epub]     CrossRef
  • Parvicella tangerina gen. nov., sp. nov. (Parvicellaceae fam. nov., Flavobacteriales), first cultured representative of the marine clade UBA10066, and Lysobacter luteus sp. nov., from activated sludge of a seawater-processing wastewater treat
    Teresa Lucena, Olga Sánchez, Isabel Sanz-Saez, Silvia G. Acinas, Laura Garrido, Jordi Mas, M. Carmen Macián, María A. Ruvira, David R. Arahal, María J. Pujalte
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
    So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(5): 469.     CrossRef
  • Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
    Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
    Journal of Microbiology.2021; 59(8): 709.     CrossRef
  • List of new names and new combinations previously effectively, but not validly, published
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247.     CrossRef
  • Lysobacter penaei sp. nov., isolated from intestinal content of a Pacific white shrimp (Penaeus vannamei)
    Shuaishuai Xu, Anzhang Li, Ming-Xia Zhang, Qing Yao, Honghui Zhu
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
  • Lysobacter panacihumi sp. nov., isolated from ginseng cultivated soil
    Yue Huo, Jong-Pyo Kang, Joon Hurh, Yaxi Han, Jong-Chan Ahn, Ramya Mathiyalagan, Chunhong Piao, Deok-Chun Yang
    Journal of Microbiology.2018; 56(10): 748.     CrossRef
Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil
Juan Du , Hina Singh , Hien T.T. Ngo , KyungHwa Won , Ki-Young Kim , Tae-Hoo Yi
J. Microbiol. 2015;53(6):365-370.   Published online May 30, 2015
DOI: https://doi.org/10.1007/s12275-015-4729-9
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AbstractAbstract
A novel Gram-negative, rod-shaped (0.2-0.5 um x 1.5-2.5 um), aerobic, non-motile bacterium was isolated from Gyeryongsan national park soil, Republic of Korea. The novel isolate was designated as THG-DN8.2T. The strain grows optimally at 28oC, at pH 7 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel isolate shared the highest sequence similarity with Lysobacter oryzae KCTC 22249T followed by Lysobacter yangpyeongensis KACC 11407T and Lysobacter niabensis KACC 11587T. The DNA G+C content of strain THG-DN8.2T is 66.0 mol% and ubiquinone Q-8 is the main isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidyl-N-methylethanolamine. The major fatty acids of strain THG-DN8.2T were identified as iso-C15:0, iso-C16:0, and C16:1w7c alcohol. The phylogenetic distinctiveness and phenotypic characteristics differentiated strain THG-DN8.2T from closely related Lysobacter species. The results of polyphasic taxonomic analysis suggest that strain THG-DN8.2T represents a novel species of the genus Lysobacter, for which the name Lysobacter tyrosinelyticus sp. nov. is proposed. The type strain is THG-DN8.2T (=KCTC 42235T =JCM 30320T).

Citations

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  • Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
    So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(5): 469.     CrossRef
  • Application of Bioorganic Fertilizer on Panax notoginseng Improves Plant Growth by Altering the Rhizosphere Microbiome Structure and Metabolism
    Rui Shi, Shu Wang, Bingjie Xiong, Haiyan Gu, Huiling Wang, Chao Ji, Weijia Jia, Abraham Rami Horowitz, Wenjie Zhen, Jiftah Ben Asher, Xiahong He
    Microorganisms.2022; 10(2): 275.     CrossRef
  • Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
    Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
    Journal of Microbiology.2021; 59(8): 709.     CrossRef
  • Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)
    Ying Wang, Jinhua Zhang, Qiubai Zhou, Zirui Wang, Miao Gao, Xin Yang, Yu Liu, Zhengzhou Zhang, Wenhao Jiang, Chonghua Hu, Wenping Zhang
    Frontiers in Microbiology.2020;[Epub]     CrossRef
  • Lysobacter terricola sp. nov., isolated from greenhouse soil
    Soo-Jin Kim, Jae-Hyung Ahn, Hang-Yeon Weon, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon
    International Journal of Systematic and Evolutionary Microbiology.2016; 66(3): 1401.     CrossRef
  • Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation
    Xinqi Huang, Liangliang Liu, Teng Wen, Jinbo Zhang, Fenghe Wang, Zucong Cai
    Applied Microbiology and Biotechnology.2016; 100(12): 5581.     CrossRef
  • Diversity and Activity of Lysobacter Species from Disease Suppressive Soils
    Ruth Gómez Expósito, Joeke Postma, Jos M. Raaijmakers, Irene De Bruijn
    Frontiers in Microbiology.2015;[Epub]     CrossRef
Research Support, Non-U.S. Gov't
Lysobacter daecheongensis sp. nov., Isolated from Sediment of Stream Near the Daechung Dam in South Korea
Leonid N. Ten , Hae-Min Jung , Wan-Taek Im , Soon-Ae Yoo , Sung-Taik Lee
J. Microbiol. 2008;46(5):519-524.   Published online October 31, 2008
DOI: https://doi.org/10.1007/s12275-008-0047-9
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AbstractAbstract
A Gram-negative, aerobic, rod shaped, non-spore-forming bacterial strain, designated Dae08T, was isolated from sediment of the stream near Daechung dam in South Korea, and was characterized in order to determine its taxonomic position, using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Dae08T belongs to the family Xanthomonadaceae of the Gammaproteobacteria, and is related to Lysobacter brunescens ATCC 29482T (97.3%). The phylogenetic distances from any other species with validly published names within the genus Lysobacter were greater than 3.7%. The G+C contents of the genomic DNA of strain Dae08T was 69.3 mol%. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with iso-C15:0, iso-C17:1 ω9c, iso-C17:0, iso-C16:0, and iso-C11:0 3-OH as the major acids supported the affiliation of strain Dae08T to the genus Lysobacter. DNA-DNA relatedness between strain Dae08T and its phylogenetically closest neighbour was 28%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Dae08T (= KCTC 12600T) should be classified in the genus Lysobacter as the novel species, for which the name Lysobacter daecheongensis sp. nov. is proposed.

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