Strain identifier

BacDive ID: 5488

Type strain: Yes

Species: Capnocytophaga ochracea

Strain Designation: SS31

Strain history: CIP <- 1990, ATCC <- W.E.C. Moore, VPI: strain 2845, Bacteroides ochraceus <- W. Loesch: strain SS31

NCBI tax ID(s): 521097 (strain), 1018 (species)

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General

@ref: 3088

BacDive-ID: 5488

DSM-Number: 7271

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

description: Capnocytophaga ochracea SS31 is an anaerobe, mesophilic bacterium that was isolated from human oral cavity.

NCBI tax id

NCBI tax idMatching level
521097strain
1018species

strain history

@refhistory
3088<- ATCC; ATCC 27872 <- W. E. C. Moore; VPI 2845 (Bacteroides ochraceus) <- W. J. Loesche; SS31
67770DSM 7271 <-- ATCC 27872 <-- W. E. C. Moore VPI 2845 <-- W. Loesche SS31.
121384CIP <- 1990, ATCC <- W.E.C. Moore, VPI: strain 2845, Bacteroides ochraceus <- W. Loesch: strain SS31

doi: 10.13145/bacdive5488.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Capnocytophaga
  • species: Capnocytophaga ochracea
  • full scientific name: Capnocytophaga ochracea (Prévot et al. 1956) Leadbetter et al. 1982

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides ochraceus

@ref: 3088

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Capnocytophaga

species: Capnocytophaga ochracea

full scientific name: Capnocytophaga ochracea (Prévot et al. 1956) Leadbetter et al. 1982

strain designation: SS31

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.798
6948099.994negative
121384nonegativerod-shaped

colony morphology

  • @ref: 3088
  • incubation period: 2-3 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_7271_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3088CAPNOCYTOPHAGA MEDIUM (DSMZ Medium 340)yeshttps://mediadive.dsmz.de/medium/340Name: CAPNOCYTOPHAGA MEDIUM (DSMZ Medium 340) Composition: Trypticase 17.0 g/l KNO3 3.0 g/l NaCl 3.0 g/l Glucose 3.0 g/l Yeast extract 3.0 g/l Haemin 0.003 g/l Distilled water
40645MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
3088COLUMBIA 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
121384CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
3088positivegrowth37mesophilic
40645positivegrowth37mesophilic
45232positivegrowth37mesophilic
67770positivegrowth37mesophilic
121384positivegrowth30-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3088anaerobe
45232microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.991

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12138417632nitrate-reduction
12138416301nitrite-reduction
6837717634D-glucose+builds acid from
6837715824D-fructose-builds acid from
6837717306maltose+builds acid from
6837717992sucrose-builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source
6838029016arginine-hydrolysis
6838029985L-glutamate-degradation
6838027897tryptophan-energy source
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose+builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12138435581indoleno
6838035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-
6837735581indole-

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
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase+3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase+3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
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
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase+3.4.11.5
68377beta-galactosidase+3.2.1.23
68377alkaline phosphatase+3.1.3.1
68377lipase+
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
121384oxidase-
121384alcohol dehydrogenase-1.1.1.1
121384gelatinase-
121384lysine decarboxylase-4.1.1.18
121384ornithine decarboxylase-4.1.1.17
121384urease-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
45232-+-+-+++--++-+-+-+--

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
45232-+-+---++++--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
3088---++++--+------++++++-++++++
3088+--++++--++/-+--+-++++++-++++++

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
45232-++--+-----++----++-++----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121384---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
3088human oral cavity
45232Human oral cavity
67770Human oral cavity
121384Human, Oral cavity

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways
#Host Body-Site#Oral cavity and airways#Mouth

taxonmaps

  • @ref: 69479
  • File name: preview.99_1970.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15818;96_615;97_718;98_1541;99_1970&stattab=map
  • Last taxonomy: Capnocytophaga
  • 16S sequence: U41350
  • Sequence Identity:
  • Total samples: 161
  • soil counts: 1
  • aquatic counts: 7
  • animal counts: 152
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30882Risk group (German classification)
1213841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Capnocytophaga ochracea gene for 16S ribosomal RNA, partial sequence, strain: JCM 12966AB6717611477ena1018
20218Capnocytophaga ochracea ATCC 27872 T 16S ribosomal RNA gene, partial sequenceU413501455ena521097

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Capnocytophaga ochracea DSM 7271GCA_000023285completencbi521097
66792Capnocytophaga ochracea DSM 7271521097.5completepatric521097
66792Capnocytophaga ochracea strain FDAARGOS_14681018.112completepatric1018
66792Capnocytophaga ochracea VPI 2845, DSM 7271644736338completeimg521097
66792Capnocytophaga ochracea strain FDAARGOS_14681018.114completepatric1018
66792Capnocytophaga ochracea strain FDAARGOS_14681018.116completepatric1018
66792Capnocytophaga ochracea strain FDAARGOS_14681018.113completepatric1018

GC content

  • @ref: 67770
  • GC-content: 39
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.054no
flagellatedno94.42no
gram-positiveno98.476no
anaerobicno83.618no
aerobicno94.928no
halophileno65.642no
spore-formingno95.424no
thermophileno99.057yes
glucose-utilyes87.603no
glucose-fermentno66.92no

External links

@ref: 3088

culture collection no.: CCUG 9716, NCTC 12371, CIP 103448, DSM 7271, ATCC 27872, JCM 12966, VPI 2845, KCTC 5787

straininfo link

  • @ref: 74975
  • straininfo: 302633

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics21304645Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845).Mavrommatis K, Gronow S, Saunders E, Land M, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Bruce D, Goodwin L, Pitluck S, Pati A, Ivanova N, Chen A, Palaniappan K, Chain P, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Bristow J, Goker M, Rohde M, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz PStand Genomic Sci10.4056/sigs.151952009
26800339Involvement of luxS in Biofilm Formation by Capnocytophaga ochracea.Hosohama-Saito K, Kokubu E, Okamoto-Shibayama K, Kita D, Katakura A, Ishihara KPLoS One10.1371/journal.pone.01471142016Bacterial Proteins/genetics/*physiology, *Biofilms, Capnocytophaga/genetics/*physiology, Carbon-Sulfur Lyases/genetics/*physiology, Homologous Recombination, Microscopy, Confocal, Microscopy, Electron, Scanning, Mutation
Phylogeny29181783Capnocytophaga endodontalis sp. nov., Isolated from a Human Refractory Periapical Abscess.Jo E, Park SN, Lim YK, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Chang YH, Kook JKCurr Microbiol10.1007/s00284-017-1397-52017Bacterial Typing Techniques, Base Composition, Capnocytophaga/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Gram-Negative Bacterial Infections/*microbiology, Humans, Periapical Abscess/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
33994426Role of Hyalin-like Protein in Gliding and Biofilm Formation by Capnocytophaga Ochracea.Okamoto-Shibayama K, Warita T, Kokubu E, Kita D, Kikuchi Y, Ishihara KBull Tokyo Dent Coll10.2209/tdcpublication.2020-00512021Bacterial Proteins/genetics, Bacteroidetes/genetics, Biofilms, *Capnocytophaga/genetics, *Hyalin

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3088Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7271)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7271
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
40645Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15247
45232Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 9716)https://www.ccug.se/strain?id=9716
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
68377Automatically annotated from API NH
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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
74975Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302633.1StrainInfo: A central database for resolving microbial strain identifiers
121384Curators of the CIPCollection of Institut Pasteur (CIP 103448)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103448