Strain identifier

BacDive ID: 12516

Type strain: Yes

Species: Dysgonomonas capnocytophagoides

Strain history: CIP <- 2001, CCUG <- 1985, W. Frederiksen, SSI, Copenhagen, Denmark

NCBI tax ID(s): 1121485 (strain), 45254 (species)

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General

@ref: 16540

BacDive-ID: 12516

DSM-Number: 22835

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

description: Dysgonomonas capnocytophagoides DSM 22835 is an anaerobe, Gram-negative bacterium that was isolated from human, cutaneous abscess.

NCBI tax id

NCBI tax idMatching level
45254species
1121485strain

strain history

@refhistory
16540<- CIP; CIP 107043 <- CCUG <- W. Frederiksen, SSI, Copenhagen, Denmark
67770CCUG 17996 <-- W. Frederiksen SSI Fsk10268.
117152CIP <- 2001, CCUG <- 1985, W. Frederiksen, SSI, Copenhagen, Denmark

doi: 10.13145/bacdive12516.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Dysgonomonadaceae
  • genus: Dysgonomonas
  • species: Dysgonomonas capnocytophagoides
  • full scientific name: Dysgonomonas capnocytophagoides Hofstad et al. 2000

@ref: 16540

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Dysgonomonadaceae

genus: Dysgonomonas

species: Dysgonomonas capnocytophagoides

full scientific name: Dysgonomonas capnocytophagoides Hofstad et al. 2000

type strain: yes

Morphology

cell morphology

  • @ref: 117152
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 117152

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16540PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
16540CHOCOLATE AGAR (DSMZ Medium 429b)yeshttps://mediadive.dsmz.de/medium/429bName: CHOCOLATE AGAR (DSMZ Medium 429b) Composition: Horse blood 100.0 g/l Sheep blood 100.0 g/l Columbia agar base
39642MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
117152CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
16540positivegrowth37
39642positivegrowth37
67770positivegrowth37
117152positivegrowth25-37
117152nogrowth15
117152nogrowth41
117152nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16540anaerobe
117152facultative anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

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
68367trehalose+builds acid from27082
68367L-rhamnose+builds acid from62345
68367sorbitol+builds acid from30911
68367raffinose+builds acid from16634
68367melezitose+builds acid from6731
68367D-mannose+builds acid from16024
68367cellobiose+builds acid from17057
68367glycerol+builds acid from17754
68367esculin+hydrolysis4853
68367gelatin-hydrolysis5291
68367L-arabinose+builds acid from30849
68367D-xylose+builds acid from65327
68367salicin+builds acid from17814
68367maltose+builds acid from17306
68367sucrose+builds acid from17992
68367lactose+builds acid from17716
68367D-mannitol+builds acid from16899
68367D-glucose+builds acid from17634
68367urea-hydrolysis16199
68367tryptophan-energy source27897
117152esculin+hydrolysis4853
117152hippurate+hydrolysis606565
117152nitrate-reduction17632
117152nitrite-reduction16301
117152nitrate+respiration17632
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose+builds acid from17306
68377ornithine-degradation18257
68377urea-hydrolysis16199
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose+fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

antibiotic resistance

  • @ref: 117152
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
11715235581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

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
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
68377beta-galactosidase-3.2.1.23
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase+3.5.2.6
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5
117152oxidase-
117152beta-galactosidase+3.2.1.23
117152alcohol dehydrogenase-1.1.1.1
117152catalase-1.11.1.6
117152gamma-glutamyltransferase+2.3.2.2
117152lysine decarboxylase-4.1.1.18
117152ornithine decarboxylase-4.1.1.17
117152urease-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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117152-+++------++++-++---

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16540--++++++++-+++++++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117152+-+++----++++-+------++++++++++-+-+++-++---+----+

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
16540++++---+--+-+
16540+++++---+--+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
65646--++++++--++----+--+----+--+-
16540---+++/-+---++----+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
16540human, cutaneous abscessDenmarkDNKEurope
67770Human clinical specimen
117152Human, Cutaneous abscessDenmarkDNKEurope1985

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8091.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_77;96_3733;97_4590;98_5892;99_8091&stattab=map
  • Last taxonomy: Dysgonomonas capnocytophagoides subclade
  • 16S sequence: U41355
  • Sequence Identity:
  • Total samples: 6908
  • soil counts: 490
  • aquatic counts: 1143
  • animal counts: 5028
  • plant counts: 247

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
165402Risk group (German classification)
1171521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16540CDC Group DF-3 16S LMG 11519 ribosomal RNA gene, partial sequenceU413551471nuccore45254
67770Dysgonomonas capnocytophagoides gene for 16S ribosomal RNA, partial sequence, strin: JCM 16697AB5486741491nuccore45254

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dysgonomonas capnocytophagoides DSM 228351121485.3wgspatric1121485
66792Dysgonomonas capnocytophagoides DSM 228352526164513draftimg1121485
67770Dysgonomonas capnocytophagoides DSM 22835GCA_000426485scaffoldncbi1121485

GC content

@refGC-content
1654038.0
6777038

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno89.822no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes61.073no
69480spore-formingspore-formingAbility to form endo- or exosporesno88.478no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no80.54no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.447no
69480flagellatedmotile2+Ability to perform flagellated movementno88no

External links

@ref: 16540

culture collection no.: DSM 22835, CCUG 17996, CIP 107043, LMG 11519, JCM 16697, CDC F9047

straininfo link

  • @ref: 81735
  • straininfo: 13931

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24899656Dysgonomonas macrotermitis sp. nov., isolated from the hindgut of a fungus-growing termite.Yang YJ, Zhang N, Ji SQ, Lan X, Zhang KD, Shen YL, Li FL, Ni JFInt J Syst Evol Microbiol10.1099/ijs.0.061739-02014Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Digestive System/microbiology, Fatty Acids/chemistry, Isoptera/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny26297040Dysgonomonas alginatilytica sp. nov., an alginate-degrading bacterium isolated from a microbial consortium.Kita A, Miura T, Okamura Y, Aki T, Matsumura Y, Tajima T, Kato J, Nakashimada YInt J Syst Evol Microbiol10.1099/ijsem.0.0004592015Alginates/*metabolism, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Japan, *Microbial Consortia, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16540Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22835)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22835
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
39642Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19240
65646Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 17996)https://www.ccug.se/strain?id=17996
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/
68367Automatically annotated from API 20A
68371Automatically annotated from API 50CH acid
68377Automatically annotated from API NH
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)
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
81735Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13931.1StrainInfo: A central database for resolving microbial strain identifiers
117152Curators of the CIPCollection of Institut Pasteur (CIP 107043)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107043