Strain identifier

BacDive ID: 12662

Type strain: Yes

Species: Propioniferax innocua

Strain Designation: L60

Strain history: CIP <- 2009, DSMZ <- NCTC <- D.G. Pictcher: strain L60

NCBI tax ID(s): 1753 (species)

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General

@ref: 3219

BacDive-ID: 12662

DSM-Number: 8251

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

description: Propioniferax innocua L60 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human skin.

NCBI tax id

  • NCBI tax id: 1753
  • Matching level: species

strain history

@refhistory
3219<- NCTC <- D.G. Pitcher, L60
67770CCUG 33480 <-- NCTC 11082 <-- W. C. Noble L60.
120131CIP <- 2009, DSMZ <- NCTC <- D.G. Pictcher: strain L60

doi: 10.13145/bacdive12662.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Propioniferax
  • species: Propioniferax innocua
  • full scientific name: Propioniferax innocua (Pitcher and Collins 1992) Yokota et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Propionibacterium innocuum

@ref: 3219

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Propioniferax

species: Propioniferax innocua

full scientific name: Propioniferax innocua (Pitcher and Collins 1992) Yokota et al. 1994

strain designation: L60

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120131positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20203Cream (9001)10-14 days5006
20203Cream (9001)10-14 days5425
20203Cream (9001)10-14 days5428
20203Cream (9001)10-14 days5530
20203Cream (9001)10-14 daysISP 2
515422 days

multicellular morphology

@refforms multicellular complexmedium name
20203noISP 2
20203no5006
20203no5425
20203no5428
20203no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3219TRYPTICASE 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
20203ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
202035006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
202035425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
202035428yes
202035530yes
40598MEDIUM 719 - for - Propioniferaxyes
120131CIP Medium 719yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=719

culture temp

@refgrowthtypetemperaturerange
20203positiveoptimum37mesophilic
3219positivegrowth37mesophilic
40598positivegrowth37mesophilic
51542positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3219aerobe
51542microaerophile
120131facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.996

murein

  • @ref: 3219
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12013117632nitrate+reduction
12013116301nitrite-reduction
683794853esculin-hydrolysis
6837917634D-glucose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12013135581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
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
68379catalase+1.11.1.6
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
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
120131oxidase+
120131catalase+1.11.1.6
120131urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382alpha-chymotrypsin-3.4.21.1
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51542C15:02.215
    51542C16:01.116
    51542C17:03.817
    51542C18:00.818
    51542C13:0 3OH/C15:1 i I/H0.614.469
    51542C14:0 ISO713.618
    51542C15:0 ANTEISO25.914.711
    51542C15:0 ISO23.814.621
    51542C15:1 ω6c0.514.856
    51542C16:0 iso14.615.626
    51542C16:1 ISO H3.315.461
    51542C16:1 ω7c0.515.819
    51542C17:0 anteiso3.716.722
    51542C17:0 iso2.116.629
    51542C17:1 ω5c ISO0.316.461
    51542C17:1 ω8c1.316.792
    51542C17:1 ω9c ANTEISO0.416.525
    51542C17:1 ω9c ISO0.616.416
    51542C18:1 ω9c2.317.769
    51542C18:2 ω6,9c/C18:0 ANTE2.917.724
    51542Unidentified0.514.574
    51542Unidentified216.102
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
20203---+--+--++++/-----++
51542+--+--+----++--+-+--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20203+++-+----++---+----
51542+-+-----------+-----
120131+++-++++-++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20203-++++-+---+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
51542-----+--------+-++++++-++++-+

Isolation, sampling and environmental information

isolation

@refsample type
3219human skin
51542Human skin
67770Human skin
120131Human, Skin

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32191Risk group (German classification)
202031German classification
1201311Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Propioniferax innocua 16S ribosomal RNA gene, partial sequence
  • accession: AF227165
  • length: 1465
  • database: ena
  • NCBI tax ID: 1753

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propioniferax innocua strain DSM 82511753.3wgspatric1753
66792Propioniferax innocua DSM 82512814123534draftimg1753
67770Propioniferax innocua DSM 8251GCA_006716235contigncbi1753

GC content

@refGC-contentmethod
321962
6777062thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno93.78no
gram-positiveyes92.024no
anaerobicno98.64yes
aerobicyes83.443no
halophileno53.787no
spore-formingno91.239no
thermophileno96.018yes
glucose-utilyes84.501no
flagellatedno98.385no
glucose-fermentno78.359no

External links

@ref: 3219

culture collection no.: DSM 8251, ATCC 49929, CIP 110011, NCTC 11082, CCUG 33480, LMG 16732, JCM 13395

straininfo link

  • @ref: 81874
  • straininfo: 9213

literature

  • topic: Phylogeny
  • Pubmed-ID: 1840533
  • title: Phylogenetic analysis of some LL-diaminopimelic acid-containing coryneform bacteria from human skin: description of Propionibacterium innocuum sp. nov.
  • authors: Pitcher DG, Collins MD
  • journal: FEMS Microbiol Lett
  • DOI: 10.1016/0378-1097(91)90372-h
  • year: 1991
  • mesh: Actinomycetales/chemistry/*classification/genetics, Base Sequence, Biological Evolution, Diaminopimelic Acid/analysis, Humans, Isomerism, Molecular Sequence Data, Propionibacterium/chemistry/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/*genetics, Skin/*microbiology, Species Specificity
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3219Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8251)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8251
20203Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8251.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
40598Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7821
51542Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33480)https://www.ccug.se/strain?id=33480
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
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
81874Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9213.1StrainInfo: A central database for resolving microbial strain identifiers
120131Curators of the CIPCollection of Institut Pasteur (CIP 110011)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110011