Strain identifier

BacDive ID: 3108

Type strain: Yes

Species: Corynebacterium pilosum

Strain Designation: 46 Hara

Strain history: CIP <- 1990, ATCC <- R. Yanagawa, Japan: strain 46 Hara <- K. Hirato, Japan

NCBI tax ID(s): 1121366 (strain), 35756 (species)

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General

@ref: 8890

BacDive-ID: 3108

DSM-Number: 20521

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Corynebacterium pilosum 46 Hara is a mesophilic bacterium that was isolated from urine of cow.

NCBI tax id

NCBI tax idMatching level
35756species
1121366strain

strain history

@refhistory
8890<- H. Seiler <- ATCC <- R. Yanagawa, 46 Hara <- K.Hirato
67770R. Yanagawa strain 46 Hara.
121832CIP <- 1990, ATCC <- R. Yanagawa, Japan: strain 46 Hara <- K. Hirato, Japan

doi: 10.13145/bacdive3108.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium pilosum
  • full scientific name: Corynebacterium pilosum Yanagawa and Honda 1978 (Approved Lists 1980)

@ref: 8890

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium pilosum

full scientific name: Corynebacterium pilosum Yanagawa and Honda 1978

strain designation: 46 Hara

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no96.485
6948099.998positive

colony morphology

  • @ref: 18444
  • colony color: Colorless
  • incubation period: 10-14 days
  • medium used: ISP 6

multicellular morphology

  • @ref: 18444
  • forms multicellular complex: no
  • medium name: ISP 6

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18444ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
8890TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: 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 waterhttps://mediadive.dsmz.de/medium/92
40635MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121832CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18444positiveoptimum37mesophilic
8890positivegrowth37mesophilic
40635positivegrowth37mesophilic
48680positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

  • @ref: 18444
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

murein

  • @ref: 8890
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1844417234glucose+
1844422599arabinose-
1844417992sucrose-
1844418222xylose-
1844417268myo-inositol-
1844429864mannitol-
1844428757fructose+/-
1844426546rhamnose-
1844416634raffinose-
1844462968cellulose-
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

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
68379catalase+1.11.1.6
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18444----+----+-+-----+-
8890++--+/---+/--+-++-------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18444--+-+--+-----+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
18444------+--+-+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8890urine of cow
48680CowJapanJPNAsia
67770Urine of cow
121832Animal, CowJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_8151.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_3757;97_4622;98_5933;99_8151&stattab=map
  • Last taxonomy: Corynebacterium pilosum subclade
  • 16S sequence: X81908
  • Sequence Identity:
  • Total samples: 3320
  • soil counts: 198
  • aquatic counts: 95
  • animal counts: 2984
  • plant counts: 43

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184442German classification
88902Risk group (German classification)
1218322Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium pilosum gene for 16S rRNAD379151324ena35756
20218C.pilosum 16S rRNA gene (ATCC 29592T)X819081381ena35756
20218Corynebacterium pilosum 16S rRNA gene, strain NCTC 11862X842461440ena35756

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium pilosum DSM 205211121366.3wgspatric1121366
66792Corynebacterium pilosum strain CIP10342235756.11wgspatric35756
66792Corynebacterium pilosum strain NCTC1186235756.13wgspatric35756
66792Corynebacterium pilosum DSM 205212515154153draftimg1121366
66792Corynebacterium pilosum CIP1034222630968875draftimg35756
67770Corynebacterium pilosum DSM 20521GCA_000373805scaffoldncbi1121366
67770Corynebacterium pilosum CIP103422GCA_001044155contigncbi35756
67770Corynebacterium pilosum NCTC11862GCA_900447205contigncbi35756

GC content

@refGC-contentmethod
889059.8
6777062high performance liquid chromatography (HPLC)
6777060.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.057no
flagellatedno98.09no
gram-positiveyes92.356no
anaerobicno99.164no
aerobicno50no
halophileyes77.257no
spore-formingno94.584no
thermophileno97.118yes
glucose-utilyes87.337no
glucose-fermentyes65.466yes

External links

@ref: 8890

culture collection no.: CCUG 27193, JCM 3714, NCTC 11862, CIP 103422, CCM 6140, DSM 20521, ATCC 29592, CECT 4049, CGMCC 1.1931, IFO 15285, KCTC 3434, LMG 19068, NBRC 15285

straininfo link

  • @ref: 72626
  • straininfo: 13101

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406802Corynebacterium lubricantis sp. nov., isolated from a coolant lubricant.Kampfer P, Lodders N, Warfolomeow I, Falsen E, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.006379-02009*Air Conditioning, Bacterial Typing Techniques, Corynebacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, *Lubricants, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Genetics26958092Draft Genome Sequences of Two Pathogenic Corynebacterial Species Isolated from Cows.Guimaraes LC, Lopes T, Ramos RT, Carneiro AR, Cavalcante AL, Barreto D, de Sa PC, Veras AA, Rocha FS, Bagano P, Pereira FL, Dorella FA, Leal CA, Carvalho AF, Bizet C, Guiso N, Badell E, Figueiredo HC, Azevedo V, Silva AJ Genomics10.7150/jgen.144562016Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8890Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20521)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20521
18444Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20521.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
40635Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15218
48680Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27193)https://www.ccug.se/strain?id=27193
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
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
72626Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13101.1StrainInfo: A central database for resolving microbial strain identifiers
121832Curators of the CIPCollection of Institut Pasteur (CIP 103422)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103422