Strain identifier

BacDive ID: 12658

Type strain: Yes

Species: Propionibacterium cyclohexanicum

Strain Designation: TA-12

Strain history: CIP <- 1998, K. Kusano, Tokyo Univ. Agriculture, Tokyo, Japan: strain TA-12 <- Kirin Beverage Corp., Kanagawa, Japan

NCBI tax ID(s): 1122996 (strain), 64702 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6638

BacDive-ID: 12658

DSM-Number: 16859

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

description: Propionibacterium cyclohexanicum TA-12 is an anaerobe, mesophilic bacterium that was isolated from spoiled orange juice.

NCBI tax id

NCBI tax idMatching level
1122996strain
64702species

strain history

@refhistory
6638<- CIP <- <- K. Kusano, Tokyo Univ. Agric., Japan; TA-12 <- R & D Office Kirin Beverage Co, Japan
67770IAM 14535 <-- K. Kusano TA-12.
118829CIP <- 1998, K. Kusano, Tokyo Univ. Agriculture, Tokyo, Japan: strain TA-12 <- Kirin Beverage Corp., Kanagawa, Japan

doi: 10.13145/bacdive12658.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Propionibacterium
  • species: Propionibacterium cyclohexanicum
  • full scientific name: Propionibacterium cyclohexanicum Kusano et al. 1997

@ref: 6638

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Propionibacterium

species: Propionibacterium cyclohexanicum

full scientific name: Propionibacterium cyclohexanicum Kusano et al. 1997

strain designation: TA-12

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.838
69480100positive
118829nopositiverod-shaped

colony morphology

  • @ref: 118829

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6638BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
32705MEDIUM 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)
118829CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
6638positivegrowth37mesophilic
32705positivegrowth37mesophilic
58382positivegrowth37mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6638anaerobe
6638microaerophile
58382anaerobe
69480anaerobe91.093
118829facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.993

observation

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

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
118829D-arabinose-degradation17108
118829D-fructose-degradation15824
118829D-glucose-degradation17634
118829D-xylose-degradation65327
118829cellobiose-degradation17057
118829lactose-degradation17716
118829maltose-degradation17306
118829salicin-degradation17814
118829sucrose-degradation17992
118829esculin+hydrolysis4853
118829nitrate-reduction17632
118829nitrite-reduction16301
118829nitrate+respiration17632
68380urea+hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

metabolite production

@refChebi-IDmetaboliteproduction
11882935581indoleno
6838035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68380glutamyl-glutamate 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
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
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380arginine dihydrolase-3.5.3.6
68380urease+3.5.1.5
118829oxidase-
118829beta-galactosidase+3.2.1.23
118829gelatinase-
118829amylase-
118829DNase-
118829caseinase-3.4.21.50
118829catalase-1.11.1.6
118829tween esterase-
118829lecithinase-
118829lipase-
118829protease-
118829urease+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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    58382C14:00.414
    58382C15:06.715
    58382C16:04.416
    58382C17:02.517
    58382C18:01.718
    58382C19:00.419
    58382C14:0 2OH0.515.205
    58382C14:0 3OH/C16:1 ISO I1.915.485
    58382C15:0 ANTEISO23.714.711
    58382C15:0 ISO4.814.621
    58382C16:0 aldehyde0.514.949
    58382C16:0 iso0.615.626
    58382C16:1 ω11c1.415.757
    58382C16:1 ω7c0.715.819
    58382C17:0 anteiso3.216.722
    58382C17:0 iso116.629
    58382C17:1 ISO I/C16:0 DMA2.116.481
    58382C18:1 ISO H0.817.46
    58382C18:1 ω7c /12t/9t29.417.824
    58382C18:1 ω9c2.617.769
    58382C18:2 ω6,9c/C18:0 ANTE617.724
    58382C19:1 ISO I0.618.473
    58382Unidentified0.613.93
    58382Unidentified0.517.19
    58382Unidentified3.218.307
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118829--++-+-+--+-++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118829+-+++++-+++++---------+++++++-++-+----++----+-+-+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6638+-+/-+-+/-+---+------+/-++/-++-++/-+/-+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
6638spoiled orange juiceJapanJPNAsia
58382Spoiled orange juiceJapanJPNAsia1991
67770Spoiled orange juice
118829Spoiled orange juiceJapanJPNAsia1991

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Beverage
#Environmental#Microbial community

taxonmaps

  • @ref: 69479
  • File name: preview.99_63247.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_27581;97_34716;98_44774;99_63247&stattab=map
  • Last taxonomy: Propionibacterium cyclohexanicum subclade
  • 16S sequence: D82046
  • Sequence Identity:
  • Total samples: 687
  • soil counts: 12
  • aquatic counts: 268
  • animal counts: 401
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66381Risk group (German classification)
1188291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Propionibacterium cyclohexanicum strain CIP 105414 16S ribosomal RNA gene, partial sequenceAY883039459ena64702
6638Propionibacterium cyclohexanicum gene for 16S rRNAD820461471ena64702
67770Propionibacterium cyclohexanicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 21245AB6391451480ena64702

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propionibacterium cyclohexanicum strain DSM 1685964702.3wgspatric64702
66792Propionibacterium cyclohexanicum DSM 168592675903216draftimg64702
67770Propionibacterium cyclohexanicum DSM 16859GCA_900111365scaffoldncbi64702

GC content

@refGC-contentmethod
663866.8
6777066.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno83no
gram-positiveyes93.763no
anaerobicno66.487no
halophileno84.168no
spore-formingno93.514no
glucose-utilyes85.855no
thermophileno90.888yes
flagellatedno98.25no
aerobicno77.09no
motileno94.252no
glucose-fermentyes70.966no

External links

@ref: 6638

culture collection no.: DSM 16859, CIP 105414, IAM 14535, NRIC 0247, CCUG 48885, ATCC 700429, JCM 21245, NBRC 103082, NCIMB 13575

straininfo link

  • @ref: 81870
  • straininfo: 46235

literature

  • topic: Phylogeny
  • Pubmed-ID: 9226913
  • title: Propionibacterium cyclohexanicum sp. nov., a new acid-tolerant omega-cyclohexyl fatty acid-containing propionibacterium isolated from spoiled orange juice.
  • authors: Kusano K, Yamada H, Niwa M, Yamasato K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-47-3-825
  • year: 1997
  • mesh: Acids/metabolism, Fatty Acids/analysis/metabolism, *Food Microbiology, Fruit/*microbiology, Molecular Sequence Data, Phylogeny, Propionibacterium/chemistry/*classification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6638Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16859)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16859
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
32705Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17431
58382Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48885)https://www.ccug.se/strain?id=48885
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
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)
81870Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46235.1StrainInfo: A central database for resolving microbial strain identifiers
118829Curators of the CIPCollection of Institut Pasteur (CIP 105414)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105414