Strain identifier

BacDive ID: 132892

Type strain: Yes

Species: Dysgonomonas hofstadii

Strain Designation: MX 1040

Strain history: CCUG 54731 <-- P. Carlson MX 1040.

NCBI tax ID(s): 1298597 (strain), 637886 (species)

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General

@ref: 24680

BacDive-ID: 132892

DSM-Number: 104969

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

description: Dysgonomonas hofstadii MX 1040 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human wound, clinical source.

NCBI tax id

NCBI tax idMatching level
637886species
1298597strain

strain history

@refhistory
24680<- CCM; CCM 7606 <- CCUG; CCUG 54731 <- P. Carlson; MX 1040
67770CCUG 54731 <-- P. Carlson MX 1040.

doi: 10.13145/bacdive132892.20230509.8.1

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 hofstadii
  • full scientific name: Dysgonomonas hofstadii Lawson et al. 2010

@ref: 24680

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Dysgonomonadaceae

genus: Dysgonomonas

species: Dysgonomonas hofstadii

full scientific name: Dysgonomonas hofstadii Lawson et al. 2010

strain designation: MX 1040

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.993

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24680TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
24680COLUMBIA 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
24680FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24680positivegrowth37mesophilic
60297positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
60297anaerobe
60297microaerophile
69480anaerobe98.747

spore formation

@refspore formationconfidence
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol-builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose-builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose-builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose+builds acid from
6837462345L-rhamnose-builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose+builds acid from
6837430911sorbitol-builds acid from
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6837435581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
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-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
68380urease-3.5.1.5
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase+
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase+3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase+3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
60297---------+-+-----++----+++--+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24680--++-++--+++/--+/--++--+--+/--+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
24680human wound, clinical sourceHelsinkiFinlandFINEurope
60297Human wound,72-yr-old man,abdominal surgeryHelsinkiFinlandFINEurope2007-03-19
67770Human clinical specimen

isolation source categories

Cat1Cat2Cat3
#Infection#Medical environment#Clinic
#Host#Human
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_38869.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_77;96_18325;97_22629;98_28481;99_38869&stattab=map
  • Last taxonomy: Dysgonomonas hofstadii subclade
  • 16S sequence: FN356023
  • Sequence Identity:
  • Total samples: 123
  • soil counts: 21
  • aquatic counts: 19
  • animal counts: 71
  • plant counts: 12

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
24680Dysgonomonas hofstadii partial 16S rRNA gene, type strain MX 1040TFN3560231504ena1298597
67770Dysgonomonas hofstadii gene for 16S ribosomal RNA, partial sequence, strain: JCM 17038AB5880221474ena1298597

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dysgonomonas hofstadii DSM 104969GCA_014196915scaffoldncbi637886
66792Dysgonomonas hofstadii JCM 170381298597.3wgspatric1298597
66792Dysgonomonas hofstadii strain DSM 104969637886.6wgspatric637886
66792Dysgonomonas hofstadii JCM 170382734481905draftimg1298597
66792Dysgonomonas hofstadii DSM 1049692830022421draftimg637886
67770Dysgonomonas hofstadii JCM 17038GCA_001312525contigncbi1298597

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.729no
gram-positiveno96.474no
anaerobicyes91.1no
aerobicno93.802yes
halophileno94.711no
spore-formingno94.075no
thermophileno98.986no
glucose-utilyes88.309no
flagellatedno97.778no
glucose-fermentyes57.584no

External links

@ref: 24680

culture collection no.: DSM 104969, CCM 7606, CCUG 54731, JCM 17038

straininfo link

  • @ref: 91172
  • straininfo: 406864

literature

  • topic: Phylogeny
  • Pubmed-ID: 19576289
  • title: Dysgonomonas hofstadii sp. nov., isolated from a human clinical source.
  • authors: Lawson PA, Carlson P, Wernersson S, Moore ER, Falsen E
  • journal: Anaerobe
  • DOI: 10.1016/j.anaerobe.2009.06.005
  • year: 2009
  • mesh: Aged, Anaerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Surgical Wound Infection/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24680Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104969Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104969)
60297Curators of the CCUGhttps://www.ccug.se/strain?id=54731Culture Collection University of Gothenburg (CCUG) (CCUG 54731)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68374Automatically annotated from API ID32E
68380Automatically annotated from API rID32A
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91172Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID406864.1