Strain identifier

BacDive ID: 12645

Type strain: Yes

Species: Cutibacterium granulosum

Strain history: CIP <- 1988, ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 050

NCBI tax ID(s): 1160719 (strain), 33011 (species)

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General

@ref: 8778

BacDive-ID: 12645

DSM-Number: 20700

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, oval-shaped, human pathogen

description: Cutibacterium granulosum DSM 20700 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from culture contaminant.

NCBI tax id

NCBI tax idMatching level
33011species
1160719strain

strain history

@refhistory
8778<- ATCC; ATCC 25564 <- W. E. C. Moore; VPI 0507
67770Y. Benno <-- T. Mitsuoka <-- ATCC 25564 <-- W. E. C. Moore VPI 0507.
119731CIP <- 1988, ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 050

doi: 10.13145/bacdive12645.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Cutibacterium
  • species: Cutibacterium granulosum
  • full scientific name: Cutibacterium granulosum (Prévot 1938) Scholz and Kilian 2016

  • synonyms

    @refsynonym
    20215Propionibacterium granulosum
    20215Corynebacterium granulosum

@ref: 8778

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Cutibacterium

species: Cutibacterium granulosum

full scientific name: Cutibacterium granulosum (Prévot 1938) Scholz and Kilian 2016 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119731positiveoval-shapedno
125438no93
125439no96.6
125439positive99.6

colony morphology

@refincubation period
513032 days
119731

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8778PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
42200MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
8778COLUMBIA 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
119731CIP Medium 187yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=187
119731CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
8778positivegrowth37
42200positivegrowth37
51303positivegrowth37
67770positivegrowth37
119731positivegrowth30-37
119731nogrowth10
119731nogrowth22
119731nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8778anaerobe
51303anaerobe
119731anaerobe
125439anaerobe90.8

spore formation

  • @ref: 119731
  • spore formation: no

murein

  • @ref: 8778
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838029016arginine-hydrolysis
6838029985L-glutamate-degradation
1197314853esculin-hydrolysis
11973117632nitrate-reduction
11973116301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117754glycerol-builds acid from
6838016199urea-hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

antibiotic resistance

  • @ref: 119731
  • ChEBI: 6909
  • metabolite: metronidazole
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
11973135581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
11973115688acetoin-

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
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)+
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
119731oxidase-
119731gelatinase-
119731caseinase-3.4.21.50
119731catalase+1.11.1.6
119731lecithinase+
119731urease-3.5.1.5
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68382cystine arylamidase-3.4.11.3
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380proline-arylamidase+3.4.11.5
68380alpha-fucosidase-3.2.1.51
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-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
119731-++++-----++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119731-------------------------------------------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8778-----+-----------+/-++/-----++--+
8778-----+------------+-----++---
8778-----+----++/-------+-----++---

Isolation, sampling and environmental information

isolation

@refsample type
8778culture contaminant
51303Culture contaminant
67770Culture contaminant
119731Other, Contaminant culture

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4358.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_2184;97_2643;98_3276;99_4358&stattab=map
  • Last taxonomy: Cutibacterium granulosum subclade
  • 16S sequence: KF906605
  • Sequence Identity:
  • Total samples: 50562
  • soil counts: 2637
  • aquatic counts: 5453
  • animal counts: 40825
  • plant counts: 1647

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8778yesyes2Risk group (German classification)
1197311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Propionibacterium granulosum strain ATCC 25564 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceAF386070232nuccore1160719
20218Propionibacterium granulosum ATCC 25564 16S rRNA gene, partial sequenceU02906385nuccore1160719
20218Propionibacterium granulosum strain CCUG 32987 clone 1 16S-23S ribosomal RNA intergenic spacer, partial sequenceGQ496475245nuccore1160719
20218Propionibacterium granulosum strain CIP 103262 16S ribosomal RNA gene, partial sequenceAY883046462nuccore1160719
20218Propionibacterium granulosum DSM 20700 16S rRNA geneAJ0030571514nuccore1160719
20218Propionibacterium granulosum DSM 20700 16S ribosomal RNA gene, partial sequenceKF9066051463nuccore1160719
20218Propionibacterium granulosum gene for 16S ribosomal RNA, partial sequence, strain: JCM 6498AB6384441485nuccore1160719
124043Cutibacterium granulosum DSM 20700 gene for 16S rRNA, partial sequence.LC752449570nuccore1160719

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cutibacterium granulosum NCTC11865GCA_900186975completencbi33011
66792Cutibacterium granulosum DSM 20700GCA_001700755contigncbi1160719
66792Cutibacterium granulosum strain NCTC1186533011.21completepatric33011
66792Propionibacterium granulosum DSM 207001160719.4wgspatric1160719
66792Propionibacterium granulosum DSM 207001160719.7wgspatric1160719
66792Cutibacterium granulosum VPI 05072602041680draftimg1160719
66792Cutibacterium granulosum ATCC 255642518285595draftimg1160719
66792Cutibacterium granulosum NCTC 118652814123075completeimg33011
66792Cutibacterium granulosum VPI 05072512047045draftimg1160719
67770Cutibacterium granulosum DSM 20700GCA_000463665contigncbi1160719

GC content

@refGC-contentmethod
877863.0
6777063thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe90.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.6
125439BacteriaNetmotilityAbility to perform movementno96.6
125439BacteriaNetspore_formationAbility to form endo- or exosporesno87.5
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.634no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes50.809yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no78.961no
125438spore-formingspore-formingAbility to form endo- or exosporesno75.407no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno90.375yes
125438motile2+flagellatedAbility to perform flagellated movementno93no

External links

@ref: 8778

culture collection no.: DSM 20700, ATCC 25564, CIP 110009, JCM 6498, LMG 16726, NCTC 11865, CCUG 32987, VPI 0507, BCRC 17368, CIP 103262, GIFU 7612, IFO 15672, NBRC 15672, NCFB 2586, NCIMB 702586, NCDO 2586, VPI 050

straininfo link

  • @ref: 81858
  • straininfo: 118626

literature

  • topic: Phylogeny
  • Pubmed-ID: 824484
  • title: Mitogenic activity of the cell walls of mycobacteria, nocardia, corynebacteria and anaerobic coryneforms.
  • authors: Azuma I, Taniyama T, Sugimura K, Aladin A, Yamamura Y
  • journal: Jpn J Microbiol
  • DOI: 10.1111/j.1348-0421.1976.tb00987.x
  • year: 1976
  • mesh: Animals, B-Lymphocytes/immunology, *BCG Vaccine, Bacterial Proteins/analysis, Cell Wall/immunology, Corynebacterium diphtheriae/*immunology, Female, *Lymphocyte Activation, Male, Mice, *Mitogens, Mucoproteins, Mycobacterium bovis/*immunology, Mycolic Acids/immunology, Nocardia/*immunology, Polysaccharides, Bacterial, Propionibacterium/*immunology, Species Specificity, Spleen/immunology, T-Lymphocytes/immunology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8778Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20700)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20700
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
42200Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15040
51303Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32987)https://www.ccug.se/strain?id=32987
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
68380Automatically annotated from API rID32A
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
81858Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID118626.1StrainInfo: A central database for resolving microbial strain identifiers
119731Curators of the CIPCollection of Institut Pasteur (CIP 103262)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103262
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1