Strain identifier

BacDive ID: 17476

Type strain: Yes

Species: Lysobacter enzymogenes

Strain Designation: Reichenbach Ly e 1, strain 495

Strain history: <- LMG <- NCIMB <- E Peterson

NCBI tax ID(s): 69 (species)

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General

@ref: 685

BacDive-ID: 17476

DSM-Number: 2043

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Lysobacter enzymogenes Reichenbach Ly e 1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 69
  • Matching level: species

strain history

@refhistory
685<- H. Reichenbach, Ly e1 <- P. Christensen, UASM 495 <- F.D. Cook
67771<- LMG <- NCIMB <- E Peterson

doi: 10.13145/bacdive17476.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter enzymogenes
  • full scientific name: Lysobacter enzymogenes Christensen and Cook 1978 (Approved Lists 1980)

@ref: 685

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter enzymogenes

full scientific name: Lysobacter enzymogenes Christensen and Cook 1978 emend. Lin et al. 2016

strain designation: Reichenbach Ly e 1, strain 495

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
685CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
43356MacConkey Agaryes

culture temp

@refgrowthtypetemperaturerange
685positivegrowth30mesophilic
45040positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45040aerobe
67771aerobe

compound production

@refcompound
685nucleases, extracellular
685protease
20216Nucleases
20216Proteases

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
433562509agar-degradation
4335658187alginate+degradation
4335628938ammonium+nitrogen source
4335622653asparagine+nitrogen source
4335685146carboxymethylcellulose+degradation
4335662968cellulose-degradation
4335617029chitin+degradation
4335616947citrate+assimilation
433565291gelatin+degradation
4335617234glucose-fermentation
433566364laminarin+degradation
4335668837pectate+degradation
4335628017starch-degradation
4335653424tween 20+degradation
4335653426tween 80+degradation
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
4335615688acetoinno
6836935581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
4335617234glucose-
4335615688acetoin-
6836935581indole-

enzymes

@refvalueactivityec
43356catalase+1.11.1.6
43356cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
685-----++++---++---++-+
685-----++++-+-++---++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
685soilOntario, OttawaCanadaCANNorth America
67771From soilCentral Experimental Farm Ottawa Ontario CanadaCanadaCANNorth America
45040SoilOntario,OttawaCanadaCANNorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5079.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_2985;98_3740;99_5079&stattab=map
  • Last taxonomy: Lysobacter
  • 16S sequence: AJ298291
  • Sequence Identity:
  • Total samples: 1027
  • soil counts: 486
  • aquatic counts: 116
  • animal counts: 135
  • plant counts: 290

Safety information

risk assessment

  • @ref: 685
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 685
  • description: Lysobacter enzymogenes 16S rRNA gene, strain DSM 2043T
  • accession: AJ298291
  • length: 1509
  • database: ena
  • NCBI tax ID: 69

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysobacter enzymogenes ATCC 29487GCA_900106525scaffoldncbi69
66792Lysobacter enzymogenes strain ATCC 2948769.16wgspatric69
66792Lysobacter enzymogenes ATCC 294872675903697draftimg69

GC content

  • @ref: 43356
  • GC-content: 69-70.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno58.807no
glucose-fermentno90.417no
flagellatedno90.827no
gram-positiveno98.413no
anaerobicno99.013yes
aerobicyes94.228yes
halophileno96.35no
spore-formingno94.561no
thermophileno99.618no
glucose-utilyes92.338no

External links

@ref: 685

culture collection no.: DSM 2043, ATCC 29487, VKM B-2235, CCUG 7833, LMG 8762, BCRC 11654, KCTC 12131, UASM 495, Ly e1, NCIB 9924, KCTC 22749

straininfo link

  • @ref: 86473
  • straininfo: 13719

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology2833562Comparison of the phosphatases of Lysobacter enzymogenes with those of related bacteria.von Tigerstrom RG, Stelmaschuk SJ Gen Microbiol10.1099/00221287-133-11-31211987Amino Acids/analysis, Cytophagaceae/*enzymology, Gram-Negative Bacteria/*enzymology, Immune Sera, Phosphoric Monoester Hydrolases/*analysis
Phylogeny16403891Lysobacter koreensis sp. nov., isolated from a ginseng field.Lee JW, Im WT, Kim MK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.63955-02006Benzoquinones, Fatty Acids, Korea, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Xanthomonadaceae/chemistry/*classification/isolation & purification/physiologyGenetics
Phylogeny16627636Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils.Weon HY, Kim BY, Baek YK, Yoo SH, Kwon SW, Stackebrandt E, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.64095-02006Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/chemistry/*classification/*isolation & purification/physiologyEnzymology
Phylogeny17329782Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea.Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64473-02007DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/isolation & purificationGenetics
Phylogeny19329586Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.).Aslam Z, Yasir M, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.000588-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny19659731'Lysobacter enzymogenes ssp. cookii ' Christensen 1978 should be recognized as an independent species, Lysobacter cookii sp. nov.Kawamura Y, Tomida J, Morita Y, Naka T, Mizuno S, Fujiwara NFEMS Microbiol Lett10.1111/j.1574-6968.2009.01703.x2009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Lysobacter/chemistry/*classification/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny19684312Lysobacter soli sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.016428-02009Base Composition, Base Sequence, Fatty Acids/analysis, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Soil MicrobiologyGenetics
Phylogeny20952549Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil.Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CXInt J Syst Evol Microbiol10.1099/ijs.0.024448-02010Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phospholipids, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26111851Lysobacter agri sp. nov., a bacterium isolated from soil.Singh H, Won K, Du J, Yang JE, Akter S, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0510-72015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny27180096Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.Chen W, Zhao YL, Cheng J, Zhou XK, Salam N, Fang BZ, Li QQ, Hozzein WN, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0704-72016Base Composition, Caves/*microbiology, China, DNA, Bacterial, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Lysobacter/*classification/genetics/*isolation & purification/metabolism, Nucleic Acid Hybridization, Phenotype, Phospholipids/metabolism, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil MicrobiologyMetabolism
Phylogeny27468934Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov.Miess H, van Trappen S, Cleenwerck I, De Vos P, Gross HInt J Syst Evol Microbiol10.1099/ijsem.0.0013292016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Lysobacter/*classification, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny30422105Lysobacter silvisoli sp. nov., isolated from forest soil.Zhang XJ, Yao Q, Wang YH, Yang SZ, Feng GD, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0031052018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Lysobacter/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny35076363Lysobacter terrestris sp. nov., isolated from soil.Woo CY, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0052042022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lysobacter/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Metabolism35596084Enhancing proteolytic activity of Lysobacter enzymogenes using cold atmospheric plasma.Tabar FF, Valizadeh V, Keramati M, Davoudi M, Molasalehi S, Fakhabi NS, Atyabi SM, Cohan RA, Norouzian DArch Microbiol10.1007/s00203-022-02936-42022Bacteria/metabolism, Bacterial Proteins/genetics/metabolism, *Lysobacter/genetics/metabolism, *Plasma Gases/metabolism/pharmacology
Genetics36033849Comparative genomics provides insights into the potential biocontrol mechanism of two Lysobacter enzymogenes strains with distinct antagonistic activities.Xu S, Zhang Z, Xie X, Shi Y, Chai A, Fan T, Li B, Li LFront Microbiol10.3389/fmicb.2022.9669862022
Phylogeny36260505Lysobacter selenitireducens sp. nov., isolated from river sediment.Mao S, Li S, Guo B, Mu W, Hou X, Liu H, Wei S, Liu A, Kong L, Chen ZInt J Syst Evol Microbiol10.1099/ijsem.0.0055502022*Lysobacter/genetics, RNA, Ribosomal, 16S/genetics, Ubiquinone/chemistry, Phylogeny, Phosphatidylethanolamines/metabolism, Base Composition, Rivers, Sodium Chloride, Cardiolipins, Soil Microbiology, *DNA, Bacterial/genetics, Fatty Acids/chemistry, Bacterial Typing Techniques, Sequence Analysis, DNA, Phospholipids/chemistry, Glycolipids/analysis, Amino Acids/metabolism, NucleotidesMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
685Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2043)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2043
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
43356R.F. Sullivan, M.A. Holtman, G.J. Zylstra, J.F. White Jr, D.Y. Kobayashi10.1046/j.1365-2672.2003.01932Taxonomic positioning of two biological control agents for plant diseases as Lysobacter enzymogenes based on phylogenetic analysis of 16S rDNA, fatty acid composition and phenotypic characteristicsJ. app. Microbiol. 94: 1079-1086 2003
45040Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7833)https://www.ccug.se/strain?id=7833
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86473Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13719.1StrainInfo: A central database for resolving microbial strain identifiers