Strain identifier

BacDive ID: 5492

Type strain: Yes

Species: Capnocytophaga granulosa

Strain Designation: B0611

Strain history: CIP <- 1994, F. Escande, Inst. Pasteur, Paris, France <- T. Watanabe, Okayama Univ., Japan: strain B0611 <- T. Yamamoto, Japan

NCBI tax ID(s): 641143 (strain), 45242 (species)

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General

@ref: 4371

BacDive-ID: 5492

DSM-Number: 11449

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

description: Capnocytophaga granulosa B0611 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from supragingival dental plaque.

NCBI tax id

NCBI tax idMatching level
641143strain
45242species

strain history

@refhistory
4371<- JCM <- T. Yamamoto, B0611
67770T. Yamamoto B0611.
119730CIP <- 1994, F. Escande, Inst. Pasteur, Paris, France <- T. Watanabe, Okayama Univ., Japan: strain B0611 <- T. Yamamoto, Japan

doi: 10.13145/bacdive5492.20250331.9.3

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 granulosa
  • full scientific name: Capnocytophaga granulosa Yamamoto et al. 1994

@ref: 4371

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Capnocytophaga

species: Capnocytophaga granulosa

full scientific name: Capnocytophaga granulosa Yamamoto et al. 1994

strain designation: B0611

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119730negativerod-shapedno
125438no91.5
125438negative96.702
125439negative99.1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4371CAPNOCYTOPHAGA II MEDIUM (DSMZ Medium 779)yeshttps://mediadive.dsmz.de/medium/779Name: CAPNOCYTOPHAGA II MEDIUM (DSMZ Medium 779) Composition: Agar 15.0 g/l Proteose peptone no. 3 10.0 g/l Yeast extract 5.0 g/l Na2HPO4 4.0 g/l Lab-Lemco beef extract 2.4 g/l Glucose 1.5 g/l L-Cysteine HCl x H2O 0.5 g/l Starch 0.5 g/l Horse blood Distilled water
41003MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
119730CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperature
4371positivegrowth37
41003positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4371facultative anaerobe
119730anaerobe

spore formation

@refspore formationconfidence
125438no91.554
125439no99.9

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11973017632nitrate-reduction
11973016301nitrite-reduction
119730132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 119730
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119730oxidase-
119730beta-galactosidase+3.2.1.23
119730alcohol dehydrogenase-1.1.1.1
119730gelatinase-
119730catalase-1.11.1.6
119730lysine decarboxylase+4.1.1.18
119730ornithine decarboxylase-4.1.1.17
119730urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
4371supragingival dental plaqueJapanJPNAsia
67770Supragingival dental plaque
119730Human, Supragingival dental plaqueJapanJPNAsia1992

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Subgingival plaque
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_332.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15818;96_232;97_254;98_283;99_332&stattab=map
  • Last taxonomy: Capnocytophaga granulosa subclade
  • 16S sequence: X97248
  • Sequence Identity:
  • Total samples: 5552
  • soil counts: 52
  • aquatic counts: 96
  • animal counts: 5351
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43712Risk group (German classification)
1197301Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.granulosa 16S rRNA geneX972481417nuccore641143
20218Capnocytophaga granulosa LMG16022 T 16S ribosomal RNA gene, partial sequenceU413471429nuccore641143
67770Capnocytophaga granulosa gene for 16S ribosomal RNA, partial sequence, strain: JCM 8566LC0372221473nuccore45242

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Capnocytophaga granulosa ATCC 51502641143.3wgspatric641143
66792Capnocytophaga granulosa strain DSM 1144945242.154wgspatric45242
66792Capnocytophaga granulosa strain NCTC1294845242.4wgspatric45242
66792Capnocytophaga granulosa ATCC 515022541046980draftimg641143
66792Capnocytophaga granulosa NCTC 129482808606723draftimg45242
66792Capnocytophaga granulosa DSM 114492693429885draftimg45242
67770Capnocytophaga granulosa ATCC 51502GCA_000411115scaffoldncbi641143
67770Capnocytophaga granulosa DSM 11449GCA_900106575scaffoldncbi45242
67770Capnocytophaga granulosa NCTC12948GCA_900446675contigncbi45242

GC content

  • @ref: 4371
  • GC-content: 42
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.702no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no82.454no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no78.38yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.554no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.134yes
125438motile2+flagellatedAbility to perform flagellated movementno91.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.9
125439BacteriaNetmotilityAbility to perform movementno73.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe62.2

External links

@ref: 4371

culture collection no.: DSM 11449, ATCC 51502, JCM 8566, CCUG 32991, CIP 104128, LMG 16022, NCTC 12948, KCTC 5785

straininfo link

  • @ref: 74979
  • straininfo: 43075

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186098Capnocytophaga haemolytica sp. nov. and Capnocytophaga granulosa sp. nov., from human dental plaque.Yamamoto T, Kajiura S, Hirai Y, Watanabe TInt J Syst Bacteriol10.1099/00207713-44-2-3241994Adult, Aged, Bacterial Typing Techniques, Capnocytophaga/*classification/genetics/growth & development/ultrastructure, Carbohydrate Metabolism, DNA, Bacterial/genetics, Dental Plaque/*microbiology, Fatty Acids/analysis, Female, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Nucleic Acid Hybridization, Vitamin K/analogs & derivatives/analysis, *Vitamin K 2/*analogs & derivativesPathogenicity
Enzymology15720565Isolation and characterization of aminopeptidase from Capnocytophaga granulosa ATCC 51502.Ohishi K, Yamamoto T, Tomofuji T, Tamaki N, Watanabe TOral Microbiol Immunol10.1111/j.1399-302X.2005.00183.x2005Amino Acids, Aminopeptidases/antagonists & inhibitors/*chemistry/*isolation & purification, Capnocytophaga/*enzymology, Chemical Fractionation, Chromatography, Ion Exchange, Dental Calculus/microbiology, Electrophoresis, Polyacrylamide Gel, Isoelectric Point, Molecular Weight, Protease Inhibitors/metabolism, Substrate SpecificityPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4371Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11449)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11449
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
41003Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16003
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
74979Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43075.1StrainInfo: A central database for resolving microbial strain identifiers
119730Curators of the CIPCollection of Institut Pasteur (CIP 104128)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104128
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