Strain identifier

BacDive ID: 12515

Type strain: Yes

Species: Dysgonomonas gadei

Strain history: CIP <- 2000, CCUG <- CDC group DF-3

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16530

BacDive-ID: 12515

DSM-Number: 22811

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

description: Dysgonomonas gadei DSM 22811 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from gall bladder .

NCBI tax id

NCBI tax idMatching level
742766strain
156974species

strain history

@refhistory
16530<- CIP <- CCUG <- T. Hofstad
67770CCUG 42882 <-- T. Hofstad 1145589.
119501CIP <- 2000, CCUG <- CDC group DF-3

doi: 10.13145/bacdive12515.20230509.8.1

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 gadei
  • full scientific name: Dysgonomonas gadei Hofstad et al. 2000

@ref: 16530

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Dysgonomonadaceae

genus: Dysgonomonas

species: Dysgonomonas gadei

full scientific name: Dysgonomonas gadei Hofstad et al. 2000 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 119501
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation period
165302-3 days
119501

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16530COLUMBIA 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
16530PYG 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
32967MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119501CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
16530positivegrowth37mesophilic
32967positivegrowth37mesophilic
67770positivegrowth37mesophilic
119501positivegrowth25-37mesophilic
119501nogrowth15psychrophilic
119501nogrowth41thermophilic
119501nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16530anaerobe
16530microaerophile
55590microaerophile
119501facultative anaerobe

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
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
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
68367L-rhamnose+builds acid from62345
68367sorbitol-builds acid from30911
68367raffinose+builds acid from16634
68367D-mannose+builds acid from16024
68367esculin+hydrolysis4853
68367gelatin-hydrolysis5291
68367L-arabinose+builds acid from30849
68367D-xylose+builds acid from65327
68367maltose+builds acid from17306
68367sucrose+builds acid from17992
68367D-mannitol-builds acid from16899
68367D-glucose+builds acid from17634
68367urea-hydrolysis16199
68367tryptophan-energy source27897
119501esculin+hydrolysis4853
119501hippurate-hydrolysis606565
119501nitrate-reduction17632
119501nitrite-reduction16301
119501nitrate+respiration17632
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose+builds acid from17306
68377ornithine-degradation18257
68377tryptophan-energy source27897
68380urea-hydrolysis16199
68380D-mannose+fermentation16024
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897

antibiotic resistance

  • @ref: 119501
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
6836735581indoleno
11950135581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6837735581indole-
6836735581indole-

enzymes

@refvalueactivityec
16530catalase+1.11.1.6
68380serine 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
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
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
68380urease-3.5.1.5
68377tryptophan deaminase-4.1.99.1
68377ornithine decarboxylase-4.1.1.17
68367catalase+1.11.1.6
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5
119501oxidase-
119501beta-galactosidase+3.2.1.23
119501alcohol dehydrogenase-1.1.1.1
119501catalase+1.11.1.6
119501gamma-glutamyltransferase-2.3.2.2
119501lysine decarboxylase-4.1.1.18
119501ornithine decarboxylase-4.1.1.17
119501urease-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
119501-+++----++++---+++-+

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
16530--+-+/-++-++-++/--++/-+-++/-
16530--+-++++++-+-++++-+++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119501+-++-+---++++-+----+/-+/-++++++/-++++++++++-++---+-----

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
16530++++--+++-+--
16530++++--++/-+-+--
16530-++++--+++-+-
16530-++++--++/-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16530--++-+++/--++-----+--+----+--+/--
16530-+++-+++++++-+--+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16530gall bladder (68-year-old male patient)BergenNorwayNOREurope
55590Human gall bladder,68-yr-old manBergenNorwayNOREurope
67770Human infected gall bladder
119501Human, Gall bladderBergenNorwayNOREurope

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Gastrointestinal tract
#Host#Human#Male

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
16530yes, in single cases1Risk group (German classification)
1195011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16530Dysgonomonas gadei gene for 16S ribosomal RNA, partial sequence, strin: JCM 16698AB5486751488ena742766
67770Dysgonomonas gadei strain 1145589 16S rRNA geneY185301464ena742766

Genome sequences

  • @ref: 67770
  • description: Dysgonomonas gadei ATCC BAA-286
  • accession: GCA_000213555
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 742766

GC content

  • @ref: 16530
  • GC-content: 39.6
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno88.419no
flagellatedno97.376no
gram-positiveno94.35no
anaerobicyes90.23no
aerobicno93.167yes
halophileno95.293no
spore-formingno92.482no
thermophileno99.492no
glucose-utilyes88.772no
glucose-fermentyes65.059no

External links

@ref: 16530

culture collection no.: DSM 22811, ATCC BAA 286, CCUG 42882, CIP 106420, JCM 16698

straininfo link

  • @ref: 81734
  • straininfo: 44343

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155996Dysgonomonas gen. nov. to accommodate Dysgonomonas gadei sp. nov., an organism isolated from a human gall bladder, and Dysgonomonas capnocytophagoides (formerly CDC group DF-3).Hofstad T, Olsen I, Eribe ER, Falsen E, Collins MD, Lawson PAInt J Syst Evol Microbiol10.1099/00207713-50-6-21892000Aged, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/analysis, Culture Media, Fatty Acids/analysis, Gallbladder/*microbiology, Gallbladder Diseases/*microbiology, Genes, rRNA, Gram-Negative Anaerobic Bacteria/*classification/drug effects/genetics/*isolation & purification/physiology, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
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
Phylogeny25428419Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus.Pramono AK, Sakamoto M, Iino T, Hongoh Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.070391-02014Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Isoptera/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny30656513Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description.Bilen M, Fonkou MDM, Dubourg G, Tomei E, Richez M, Delerce J, Levasseur A, Daoud Z, Raoult D, Cadoret FAntonie Van Leeuwenhoek10.1007/s10482-019-01227-12019Adult, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Feces/*microbiology, Gastrointestinal Microbiome, Humans, Male, Phylogeny, RNA, Ribosomal, 16S/geneticsPathogenicity

Reference

@idauthorscataloguedoi/urltitle
16530Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22811)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22811
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
32967Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18549
55590Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42882)https://www.ccug.se/strain?id=42882
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
81734Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44343.1StrainInfo: A central database for resolving microbial strain identifiers
119501Curators of the CIPCollection of Institut Pasteur (CIP 106420)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106420