Strain identifier

BacDive ID: 3200

Type strain: No

Species: Corynebacterium aurimucosum

Strain Designation: CN-1

Strain history: CIP <- 2002, S. Shukla, MMRF, Marshfield, USA, strain: CN-1, Corynebacterium nigricans

NCBI tax ID(s): 548476 (strain), 169292 (species)

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General

@ref: 12009

BacDive-ID: 3200

DSM-Number: 44827

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

description: Corynebacterium aurimucosum CN-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from human female urogenital tract.

NCBI tax id

NCBI tax idMatching level
548476strain
169292species

strain history

@refhistory
12009<- CIP <- S. K. Shukla, Marshfield,USA; CN-1
67770CIP 107346 <-- S. K. Shukla CN-1.
116635CIP <- 2002, S. Shukla, MMRF, Marshfield, USA, strain: CN-1, Corynebacterium nigricans

doi: 10.13145/bacdive3200.20230509.8.1

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 aurimucosum
  • full scientific name: Corynebacterium aurimucosum Yassin et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Corynebacterium nigricans

@ref: 12009

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium aurimucosum

full scientific name: Corynebacterium aurimucosum Yassin et al. 2002 emend. Daneshvar et al. 2004

strain designation: CN-1

type strain: no

Morphology

cell morphology

@refgram stainconfidencemotilitycell shape
69480positive100
6948097.147no
116635positivenorod-shaped

colony morphology

  • @ref: 116635

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12009TRYPTICASE 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
12009COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
33128MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
36166MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
38198MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
116635CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
116635CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12009positivegrowth37mesophilic
33128positivegrowth30mesophilic
36166positivegrowth37mesophilic
38198positivegrowth37mesophilic
67770positivegrowth37mesophilic
116635positivegrowth25-41
116635nogrowth10psychrophilic
116635nogrowth15psychrophilic
116635nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116635
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

  • @ref: 116635
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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
68371D-galactose-builds acid from12936
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
116635citrate-carbon source16947
116635esculin-hydrolysis4853
116635hippurate+hydrolysis606565
116635nitrate-reduction17632
116635nitrite-reduction16301
116635pyrazinamide+hydrolysis45285
116635nitrate-respiration17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose+fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 116635
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116635
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11663515688acetoin+
11663517234glucose+

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
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
116635oxidase-
116635beta-galactosidase-3.2.1.23
116635alcohol dehydrogenase-1.1.1.1
116635gelatinase-
116635amylase+
116635DNase-
116635caseinase-3.4.21.50
116635catalase+1.11.1.6
116635tween esterase+
116635gamma-glutamyltransferase-2.3.2.2
116635lecithinase-
116635lipase-
116635lysine decarboxylase-4.1.1.18
116635ornithine decarboxylase-4.1.1.17
116635phenylalanine ammonia-lyase-4.3.1.24
116635tryptophan deaminase-
116635urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
12009------------+---+---+
12009------------+---+---+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116635--++-+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116635+/----+/------+++--------+/------+--+/----------------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116635++-++--+-++-+-++---+--+--+-+---+-+-+---+--++-+-+-+---------+++---------+-+++-++++--+-----++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
12009human female urogenital tractMarshfieldUSAUSANorth America44.6689-90.1718
58020Human vaginal swabWI,MarshfieldUSAUSANorth America
67770Female urogenital tractMarshfield, WIUSAUSANorth America
116635Uro-genital tractMarshfield, WisconsinUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human#Female
#Host Body-Site#Urogenital tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_1226.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_322;97_835;98_971;99_1226&stattab=map
  • Last taxonomy: Corynebacterium
  • 16S sequence: AF220220
  • Sequence Identity:
  • Total samples: 26558
  • soil counts: 1053
  • aquatic counts: 1398
  • animal counts: 23824
  • plant counts: 283

Safety information

risk assessment

  • @ref: 116635
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium aurimucosum strain ATCC 700975 16S ribosomal RNA gene, partial sequenceAY5364261440ena548476
12009Corynebacterium aurimucosum strain CN-1 16S ribosomal RNA gene, partial sequenceAF2202201437ena548476

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium aurimucosum ATCC 700975 DSM 44827; ATCC 700975GCA_000022905completencbi548476
66792Corynebacterium aurimucosum ATCC 700975 DE0412GCA_007672675scaffoldncbi548476
66792Corynebacterium aurimucosum ATCC 700975 DE0414GCA_007672635scaffoldncbi548476
66792Corynebacterium aurimucosum ATCC 700975 DE0410GCA_007672725scaffoldncbi548476
66792Corynebacterium aurimucosum ATCC 700975548476.3completepatric548476
66792Corynebacterium aurimucosum ATCC 700975 (Prj:31451)548476.7wgspatric548476
66792Corynebacterium aurimucosum ATCC 700975 strain DE0410548476.21wgspatric548476
66792Corynebacterium aurimucosum ATCC 700975 strain DE0412548476.20wgspatric548476
66792Corynebacterium aurimucosum ATCC 700975 strain DE0414548476.19wgspatric548476
66792Corynebacterium aurimucosum ATCC 700975 strain DSM 44827 strain DSM 44827; ATCC 700975548476.11plasmidpatric548476
66792Corynebacterium aurimucosum strain FDAARGOS_1110169292.148completepatric169292
66792Corynebacterium aurimucosum CN-1, ATCC 700975645951870draftimg548476
66792Corynebacterium aurimucosum CN-1, ATCC 700975643692018completeimg548476
67770Corynebacterium aurimucosum ATCC 700975GCA_000174695contigncbi548476

GC content

  • @ref: 67770
  • GC-content: 60.6
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.304no
flagellatedno97.499no
gram-positiveyes94.882no
anaerobicno98.987no
aerobicno63.528no
halophileyes74.643no
spore-formingno95.043no
thermophileno94.357yes
glucose-utilyes88.057no
glucose-fermentyes73.868yes

External links

@ref: 12009

culture collection no.: DSM 44827, ATCC 700975, CCUG 48176, CIP 107346, JCM 12684, ATCC 700795

straininfo link

  • @ref: 72716
  • straininfo: 47372

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12958268Corynebacterium nigricans sp. nov.: proposed name for a black-pigmented Corynebacterium species recovered from the human female urogenital tract.Shukla SK, Bernard KA, Harney M, Frank DN, Reed KDJ Clin Microbiol10.1128/JCM.41.9.4353-4358.20032003Adult, Corynebacterium/*classification/genetics/isolation & purification, DNA, Ribosomal/genetics, Fatty Acids/analysis, Female, Humans, Phenotype, Phylogeny, Pregnancy, Pregnancy Complications/microbiology, RNA, Ribosomal, 16S/genetics, Vagina/*microbiologyPathogenicity
Genetics20137072Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion.Trost E, Gotker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehoever P, Arnold W, Bekel T, Blom J, Gartemann KH, Linke B, Goesmann A, Puhler A, Shukla SK, Tauch ABMC Genomics10.1186/1471-2164-11-912010Abortion, Spontaneous, Adult, Computational Biology, Corynebacterium/*genetics/growth & development, Corynebacterium Infections/microbiology, DNA, Bacterial/genetics, Female, Genes, Bacterial, *Genome, Bacterial, Humans, Multigene Family, Pregnancy, Sequence Analysis, DNA, Vagina/*microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12009Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44827)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44827
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
33128Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4871
36166Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5107
38198Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4771
58020Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48176)https://www.ccug.se/strain?id=48176
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/
68371Automatically annotated from API 50CH acid
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
72716Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47372.1StrainInfo: A central database for resolving microbial strain identifiers
116635Curators of the CIPCollection of Institut Pasteur (CIP 107346)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107346