Strain identifier

BacDive ID: 17481

Type strain: Yes

Species: Lysobacter gummosus

Strain history: <- ATCC <- P. Christensen, UASM 402 <- F.D. Cook

NCBI tax ID(s): 262324 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2935

BacDive-ID: 17481

DSM-Number: 6980

keywords: 16S sequence, Bacteria, aerobe, mesophilic, polysaccharide production

description: Lysobacter gummosus DSM 6980 is an aerobe, mesophilic bacterium that produces polysaccharides and was isolated from soil.

NCBI tax id

  • NCBI tax id: 262324
  • Matching level: species

strain history

  • @ref: 2935
  • history: <- ATCC <- P. Christensen, UASM 402 <- F.D. Cook

doi: 10.13145/bacdive17481.20230509.8.1

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 gummosus
  • full scientific name: Lysobacter gummosus Christensen and Cook 1978 (Approved Lists 1980)

@ref: 2935

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter gummosus

full scientific name: Lysobacter gummosus Christensen and Cook 1978

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2935CY-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
2935REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
2935R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf

culture temp

@refgrowthtypetemperaturerange
2935positivegrowth28mesophilic
2935positivegrowth30mesophilic
60654positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60654
  • oxygen tolerance: aerobe

compound production

  • @ref: 2935
  • compound: polysaccharides

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
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
6836916024D-mannose+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
4335635581indoleno
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
2935-----+++--+-+----+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2935soilOttawa, OntarioCanadaCANNorth America
60654SoilOntario,OttawaCanadaCANNorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2461.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_1577;98_1919;99_2461&stattab=map
  • Last taxonomy: Lysobacter
  • 16S sequence: AB161361
  • Sequence Identity:
  • Total samples: 16578
  • soil counts: 9924
  • aquatic counts: 1340
  • animal counts: 1424
  • plant counts: 3890

Safety information

risk assessment

  • @ref: 2935
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lysobacter gummosus gene for 16S rRNA, partial sequenceAB1668941482ena262324
2935Lysobacter gummosus gene for 16S rRNA, partial sequenceAB1613611482ena262324

GC content

  • @ref: 2935
  • GC-content: 65.7

External links

@ref: 2935

culture collection no.: DSM 6980, ATCC 29489, NCIB 11896, CCUG 55586, LMG 8763, UASM 402

straininfo link

  • @ref: 86478
  • straininfo: 3552

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
Phylogeny19406775Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field.Ten LN, Jung HM, Im WT, Yoo SA, Oh HM, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.002394-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Korea, Lysobacter/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, *Panax, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2935Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6980)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6980
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
60654Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55586)https://www.ccug.se/strain?id=55586
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
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
86478Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3552.1StrainInfo: A central database for resolving microbial strain identifiers