Strain identifier

BacDive ID: 7348

Type strain: Yes

Species: Leucobacter komagatae

Strain history: CIP <- 1987, IFO <- 1993, IAM

NCBI tax ID(s): 55969 (species)

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General

@ref: 3409

BacDive-ID: 7348

DSM-Number: 8803

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

description: Leucobacter komagatae DSM 8803 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from culture contaminant.

NCBI tax id

  • NCBI tax id: 55969
  • Matching level: species

strain history

@refhistory
3409<- IFO
67770IFO 15245 <-- IAM 1093 <-- IFO.
67772IFO
120459CIP <- 1987, IFO <- 1993, IAM

doi: 10.13145/bacdive7348.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leucobacter
  • species: Leucobacter komagatae
  • full scientific name: Leucobacter komagatae Takeuchi et al. 1996

@ref: 3409

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leucobacter

species: Leucobacter komagatae

full scientific name: Leucobacter komagatae Takeuchi et al. 1996

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120459positiverod-shapedno

colony morphology

  • @ref: 120459

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3409TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
41479MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120459CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120459CIP Medium 251yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=251
120459CIP Medium 99yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=99

culture temp

@refgrowthtypetemperaturerange
3409positivegrowth30mesophilic
41479positivegrowth30mesophilic
67770positivegrowth30mesophilic
67772positiveoptimum30mesophilic
120459positivegrowth15-30
120459nogrowth10psychrophilic
120459nogrowth37mesophilic
120459nogrowth41thermophilic
120459nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120459
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
120459NaClpositivegrowth0-6 %
120459NaClnogrowth8 %
120459NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-11, MK-10, MK-12

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
120459citrate-carbon source16947
120459esculin-hydrolysis4853
120459hippurate+hydrolysis606565
120459nitrate-reduction17632
120459nitrite-reduction16301
120459nitrate-respiration17632

antibiotic resistance

  • @ref: 120459
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120459
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12045915688acetoin-
12045917234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
120459oxidase-
120459beta-galactosidase-3.2.1.23
120459alcohol dehydrogenase-1.1.1.1
120459gelatinase-
120459amylase-
120459DNase-
120459caseinase-3.4.21.50
120459catalase+1.11.1.6
120459tween esterase+
120459gamma-glutamyltransferase-2.3.2.2
120459lecithinase-
120459lipase-
120459lysine decarboxylase-4.1.1.18
120459ornithine decarboxylase-4.1.1.17
120459phenylalanine ammonia-lyase-4.3.1.24
120459protease-
120459urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120459--++-+++--+---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120459+/----+/-----+/------------------+/----------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120459--+---------------------++--+--+--------+-------+--------+--+--+--+-----+----------+--+-+++++++--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciessampling dategeographic locationcountryorigin.countrycontinentisolation date
3409culture contaminant
67770Contaminant in an ampoule labeled "Pseudomonas riboflavina" IFO 13584Pseudomonas riboflavina
67772Culture contaminant1993OsakaJapanJPNAsia
120459Contaminant on an agar plateJapanJPNAsia1991

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory
  • Cat3: #Contaminant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34091Risk group (German classification)
677721
1204591Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leucobacter komagatae gene for 16S rRNA, partial sequenceAB0074191513ena55969
20218Leucobacter komagatae partial 16S rRNA gene, isolate IFO15245TAJ7463371503ena55969
20218Leucobacter komagatae 16S rRNA gene, strain DSM 8803AM0426911476ena55969
3409Leucobacter komagatae DNA for 16S ribosomal RNA, partial sequenceD177511340ena55969
67770Leucobacter komagatae gene for 16S rRNA, strain: JCM 9414D450631487ena55969

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leucobacter komagatae strain DSM 880355969.10wgspatric55969
66792Leucobacter komagatae DSM 88032814123040draftimg55969
67770Leucobacter komagatae DSM 8803GCA_006716085contigncbi55969

GC content

@refGC-contentmethod
340966high performance liquid chromatography (HPLC)
6777066.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes90.912no
anaerobicno99.302no
halophileno81.805no
spore-formingno92.775no
glucose-utilyes74.795no
thermophileno99.771no
aerobicyes93.11no
motileno86.767no
flagellatedno96.369no
glucose-fermentno90.446no

External links

@ref: 3409

culture collection no.: DSM 8803, IAM 1093, IFO 15245, NBRC 15245, JCM 9414, CCUG 49676, CIP 105084, KCTC 19682, LMG 22181, NCIMB 13513, VKM Ac-2073, UCCCB2

straininfo link

  • @ref: 76798
  • straininfo: 128560

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8863425Leucobacter komagatae gen. nov., sp. nov., a new aerobic gram-positive, nonsporulating rod with 2,4-diaminobutyric acid in the cell wall.Takeuchi M, Weiss N, Schumann P, Yokota AInt J Syst Bacteriol10.1099/00207713-46-4-9671996Aminobutyrates/*analysis, Base Sequence, Cell Wall/chemistry, Gram-Positive Asporogenous Rods/chemistry/*classification, Molecular Sequence Data, Phenotype, PhylogenyGenetics
Phylogeny17392186Leucobacter iarius sp. nov., in the family Microbacteriaceae.Somvanshi VS, Lang E, Schumann P, Pukall R, Kroppenstedt RM, Ganguly S, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64683-02007Actinomycetales/*classification/genetics, Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nematoda/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny22349954Leucobacter margaritiformis sp. nov., isolated from bamboo extract.Lee JH, Lee SSCurr Microbiol10.1007/s00284-012-0089-42012Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Bambusa/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Extracts/*chemistry, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny22367952Leucobacter denitrificans sp. nov., isolated from cow dung.Weon HY, Anandham R, Tamura T, Hamada M, Kim SJ, Kim YS, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-012-1324-12012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aminobutyrates/analysis, Animals, Bacterial Typing Techniques, Cattle, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNAGenetics
Phylogeny25921298Leucobacter humi sp. nov., Isolated from Forest Soil.Her J, Lee SSCurr Microbiol10.1007/s00284-015-0820-z2015Actinomycetales/classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3409Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8803)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8803
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
41479Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17063
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128560.1StrainInfo: A central database for resolving microbial strain identifiers
120459Curators of the CIPCollection of Institut Pasteur (CIP 105084)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105084