Strain identifier

BacDive ID: 5490

Type strain: Yes

Species: Capnocytophaga sputigena

Strain Designation: 4

Strain history: CIP <- 2010, DSMZ <- ATCC <- A. Tanner strain <- S.S. Socransky: strain 4 <- S.S. Socransky

NCBI tax ID(s): 553177 (strain), 1019 (species)

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General

@ref: 3090

BacDive-ID: 5490

DSM-Number: 7273

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

description: Capnocytophaga sputigena 4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from periodontal lesions.

NCBI tax id

NCBI tax idMatching level
1019species
553177strain

strain history

@refhistory
3090<- ATCC; ATCC 33612 <- A. C. R. Tanner; <- S. C. Holt; 4 <- S. S. Socransky;
67770DSM 7273 <-- ATCC 33612 <-- A. C. R. Tanner <-- S. C. Holt 4 <-- S. S. Socransky.
123285CIP <- 2010, DSMZ <- ATCC <- A. Tanner strain <- S.S. Socransky: strain 4 <- S.S. Socransky

doi: 10.13145/bacdive5490.20250331.9.3

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 sputigena
  • full scientific name: Capnocytophaga sputigena Leadbetter et al. 1982

@ref: 3090

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Capnocytophaga

species: Capnocytophaga sputigena

full scientific name: Capnocytophaga sputigena Leadbetter et al. 1982 emend. Hahnke et al. 2016

strain designation: 4

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123285negativerod-shapedno
125438no92
125438negative96.669
125439negative99.2

colony morphology

@refincubation period
30903-7 days
452302 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3090CAPNOCYTOPHAGA 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
37924MEDIUM 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)
3090COLUMBIA 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
123285CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45
123285CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
3090positivegrowth37
37924positivegrowth37
45230positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3090anaerobe
45230microaerophile
123285facultative anaerobe

spore formation

@refspore formationconfidence
125438no93.708
125439no99.7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837716199urea-hydrolysis
6837727897tryptophan-energy source
6837717306maltose+builds acid from
6837718257ornithine-degradation
6837715824D-fructose+builds acid from
12328517632nitrate+reduction
12328516301nitrite-reduction
6837717634D-glucose+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12328535581indoleno

metabolite tests

  • @ref: 68377
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
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
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
123285oxidase-
123285catalase+1.11.1.6
123285urease+3.5.1.5
68377beta-galactosidase+3.2.1.23
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68377tryptophan deaminase-4.1.99.1
68377proline-arylamidase+3.4.11.5
68377alkaline phosphatase+3.1.3.1
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123285-+-+-+----+---------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
3090-++++---++++-
3090++++---++++--
3090-++++---++++-

Isolation, sampling and environmental information

isolation

@refsample typesampling date
3090periodontal lesions
45230Human periodontal lesion1978
67770Periodontal lesions
123285Human, Periodontal lesions

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_5500.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15818;96_2659;97_3263;98_4107;99_5500&stattab=map
  • Last taxonomy: Capnocytophaga sputigena subclade
  • 16S sequence: NR_026095
  • Sequence Identity:
  • Total samples: 63038
  • soil counts: 1170
  • aquatic counts: 1334
  • animal counts: 60103
  • plant counts: 431

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30902Risk group (German classification)
1232851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Capnocytophaga sputigena gene for 16S ribosomal RNA, partial sequence, strain: JCM 12967AB6717621477nuccore1019
20218Capnocytophaga sputigena 16S ribosomal RNAL146361465nuccore1019
20218C.sputigena gene for 16S rRNAX676091489nuccore553177
3090Capnocytophaga sputigena ATCC 33612 16S ribosomal RNA, partial sequenceNR_0260951489nuccore553177

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Capnocytophaga sputigena NCTC11653GCA_900446695contigncbi1019
66792Capnocytophaga sputigena ATCC 33612553177.6wgspatric553177
66792Capnocytophaga sputigena strain NCTC116531019.49wgspatric1019
66792Capnocytophaga sputigena Capno, ATCC 33612642979305draftimg553177
66792Capnocytophaga sputigena NCTC 116532814123397draftimg1019
67770Capnocytophaga sputigena ATCC 33612GCA_000173675contigncbi553177

GC content

@refGC-contentmethod
309038.4sequence analysis
6777034thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe66.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.2
125439BacteriaNetmotilityAbility to perform movementno64.1
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.7
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.669no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.082no
125438spore-formingspore-formingAbility to form endo- or exosporesno93.708no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no75.057no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno92no

External links

@ref: 3090

culture collection no.: CCUG 9714, NCTC 11653, LMG 11518, CIP 104301, DSM 7273, ATCC 33612, CIP 110086, DSM 3292, JCM 12967, VPI 12913

straininfo link

  • @ref: 74977
  • straininfo: 7612

literature

  • topic: Pathogenicity
  • Pubmed-ID: 28453633
  • title: Role of DNA gyrase and topoisomerase IV mutations in fluoroquinolone resistance of Capnocytophaga spp. clinical isolates and laboratory mutants.
  • authors: Ehrmann E, Jolivet-Gougeon A, Bonnaure-Mallet M, Fosse T
  • journal: J Antimicrob Chemother
  • DOI: 10.1093/jac/dkx119
  • year: 2017
  • mesh: Amino Acid Substitution, Anti-Bacterial Agents/*pharmacology, Capnocytophaga/*drug effects/*enzymology/genetics/isolation & purification, DNA Gyrase/*genetics, DNA Topoisomerase IV/*genetics, Fluoroquinolones/*pharmacology, Gram-Negative Bacterial Infections/microbiology, Humans, Microbial Sensitivity Tests, *Mutation, Missense, Polymerase Chain Reaction, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3090Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7273)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7273
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
37924Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7906
45230Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 9714)https://www.ccug.se/strain?id=9714
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/
68377Automatically annotated from API NH
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
74977Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7612.1StrainInfo: A central database for resolving microbial strain identifiers
123285Curators of the CIPCollection of Institut Pasteur (CIP 110086)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110086
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