Strain identifier

BacDive ID: 12641

Type strain: Yes

Species: Cutibacterium avidum

Strain Designation: 1689B

Strain history: CIP <- 1988, ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 0179 <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 1689B

NCBI tax ID(s): 997355 (strain), 33010 (species)

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

@ref: 1868

BacDive-ID: 12641

DSM-Number: 4901

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Cutibacterium avidum 1689B is an anaerobe, mesophilic, Gram-positive bacterium of the family Propionibacteriaceae.

NCBI tax id

NCBI tax idMatching level
33010species
997355strain

strain history

@refhistory
1868<- ATCC <- W.E.C. Moore, VPI 0179 <- A.R. Prévot, 1689B
116665CIP <- 1988, ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 0179 <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 1689B

doi: 10.13145/bacdive12641.20230509.8.1

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 avidum
  • full scientific name: Cutibacterium avidum (Eggerth 1935) Scholz and Kilian 2016
  • synonyms

    @refsynonym
    20215Bacteroides avidus
    20215Propionibacterium avidum

@ref: 1868

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Cutibacterium

species: Cutibacterium avidum

full scientific name: Cutibacterium avidum (Eggerth 1935) Scholz and Kilian 2016 emend. Nouioui et al. 2018

strain designation: 1689B

type strain: yes

Morphology

cell morphology

  • @ref: 116665
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 53372
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1868PYG 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
42202MEDIUM 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)
1868COLUMBIA 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
116665CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
1868positivegrowth37mesophilic
42202positivegrowth37mesophilic
53372positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1868anaerobe
53372anaerobe
53372microaerophile
116665anaerobe

compound production

  • @ref: 1868
  • compound: LL diaminopimelic acid

murein

  • @ref: 1868
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

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
68371maltose+builds acid from17306
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
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
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol+builds acid from17113
68371glycerol+builds acid from17754
116665nitrate-reduction17632
116665nitrite-reduction16301
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

@refChebi-IDmetaboliteproduction
11666535581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380proline-arylamidase+3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
116665oxidase-
116665catalase+1.11.1.6
116665urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116665-++-------++-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116665++-++--+-++++---+----+-----+--++-+-----+----+++--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
1868---+/--++/-+--+------+/-++/-----++--+
1868---+/--++/-+-+/-+-------++/-----+/-+/---+/-

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_868.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_410;97_598;98_687;99_868&stattab=map
  • Last taxonomy: Cutibacterium avidum subclade
  • 16S sequence: KF906606
  • Sequence Identity:
  • Total samples: 29908
  • soil counts: 847
  • aquatic counts: 1592
  • animal counts: 27061
  • plant counts: 408

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
18682Risk group (German classification)
1166651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Propionibacterium avidum strain ATCC 25577 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceAF386071284ena997355
20218Propionibacterium avidum ATCC 25577 16S rRNA gene, partial sequenceU02905385ena997355
20218Propionibacterium avidum ATCC 25577 16S ribosomal RNA gene, partial sequenceKF9066061462ena997355
1868Propionibacterium avidum DSM 4901 16S rRNA geneAJ0030551504ena997355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propionibacterium avidum ATCC 25577997355.3wgspatric997355
66792Cutibacterium avidum VPI 01792518285596draftimg997355
66792Cutibacterium avidum VPI 01792513237389draftimg997355
66792Cutibacterium avidum ATCC 25577GCA_000227295scaffoldncbi997355

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.872no
flagellatedno98.196no
gram-positiveyes92.244no
anaerobicno55.086no
aerobicno86.098yes
halophileno86.679no
spore-formingno91.912no
thermophileno84.726yes
glucose-utilyes90.7no
glucose-fermentyes78.477no

External links

@ref: 1868

culture collection no.: DSM 4901, ATCC 25577, CCUG 36754, VPI 0179, CIP 103261, NCDO 2585, NCTC 11864, PCM 2467, NBRC 15671

straininfo link

  • @ref: 81854
  • straininfo: 38601

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
1868Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4901)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4901
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
42202Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15039
53372Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 36754)https://www.ccug.se/strain?id=36754
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)
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
81854Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38601.1StrainInfo: A central database for resolving microbial strain identifiers
116665Curators of the CIPCollection of Institut Pasteur (CIP 103261)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103261