Strain identifier

BacDive ID: 2236

Type strain: Yes

Species: Dichelobacter nodosus

Strain Designation: 11342

Strain history: CIP <- 2001, CCUG <- 2001, ATCC <- L.V. Holdeman, VPI, USA <- L.DS. Smith <- W.I.B. Beveridge

NCBI tax ID(s): 870 (species)

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General

@ref: 16680

BacDive-ID: 2236

DSM-Number: 23057

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

description: Dichelobacter nodosus 11342 is an anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from foot rot in sheep.

NCBI tax id

  • NCBI tax id: 870
  • Matching level: species

strain history

@refhistory
16680<- CCUG; CCUG 27824 <- R. Gherna, ATCC; ATCC 25549 <- L. V. Holdeman; VPI 2340 <- L. DS. Smith; 11342 <- W. I. B. Beveridge;
121323CIP <- 2001, CCUG <- 2001, ATCC <- L.V. Holdeman, VPI, USA <- L.DS. Smith <- W.I.B. Beveridge

doi: 10.13145/bacdive2236.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cardiobacteriales
  • family: Cardiobacteriaceae
  • genus: Dichelobacter
  • species: Dichelobacter nodosus
  • full scientific name: Dichelobacter nodosus (Beveridge 1941) Dewhirst et al. 1990

  • synonyms

    @refsynonym
    20215Bacteroides nodosus
    20215Fusiformis nodosus

@ref: 16680

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cardiobacteriales

family: Cardiobacteriaceae

genus: Dichelobacter

species: Dichelobacter nodosus

full scientific name: Dichelobacter nodosus (Beveridge 1941) Dewhirst et al. 1990

strain designation: 11342

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.995
121323negativerod-shapedno

colony morphology

@refincubation period
166803-7 days
489693 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16680COLUMBIA 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
16680CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
39641MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121323CIP Medium 564yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=564
121323CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
16680positivegrowth37mesophilic
39641positivegrowth37mesophilic
48969positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16680anaerobe
48969anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380glutamyl-glutamate arylamidase-
68380alanine arylamidase+3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16680----------+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16680------------+---++---+--++/----
16680-----------------+---+/---++/----
16680--+++/-+++--------++-+/-+/-+-++++/--+
16680-+--------------++-+++-++++-+

Isolation, sampling and environmental information

isolation

@refsample type
16680foot rot in sheep
48969Foot rot in sheep
121323Animal, Foot rot in sheep

isolation source categories

Cat1Cat2Cat3
#Infection
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body-Site#Limb#Foot

taxonmaps

  • @ref: 69479
  • File name: preview.99_3611.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_183;96_1873;97_2250;98_2762;99_3611&stattab=map
  • Last taxonomy: Dichelobacter nodosus subclade
  • 16S sequence: JN175347
  • Sequence Identity:
  • Total samples: 932
  • soil counts: 80
  • aquatic counts: 154
  • animal counts: 686
  • plant counts: 12

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
16680yes2Risk group (German classification)
1213231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16680
  • description: Dichelobacter nodosus strain CIP 107042 16S ribosomal RNA gene, complete sequence
  • accession: JN175347
  • length: 1460
  • database: ena
  • NCBI tax ID: 870

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dichelobacter nodosus VPI 2340GCA_001263335contigncbi870
66792Dichelobacter nodosus strain VPI 2340870.8wgspatric870
66792Dichelobacter nodosus VPI 23402654587739draftimg870

GC content

  • @ref: 16680
  • GC-content: 45.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.378no
flagellatedno97.887no
gram-positiveno98.94no
anaerobicno74.841no
halophileyes70.262no
spore-formingno98.032no
thermophileno96.583yes
glucose-utilyes64.182no
aerobicno96.085no
glucose-fermentno60.37no

External links

@ref: 16680

culture collection no.: DSM 23057, ATCC 25549, CCUG 27824, CIP 107042, VPI 2340, KCTC 15031

straininfo link

  • @ref: 71798
  • straininfo: 38592

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics26404593Draft Genome Sequence of Dichelobacter nodosus ATCC 25549, Strain VPI 2340 [11342], a Bacterium Causing Footrot in Sheep.Jackson A, Humbert MV, Pandey A, Bratcher H, Christodoulides MGenome Announc10.1128/genomeA.01002-152015
Phylogeny34228610Ostreibacterium oceani gen. nov., sp. nov., isolated from oyster, and description of Ostreibacteriaceae fam. nov.Wang CN, Wang FQ, Liu Y, Wang MY, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0048552021Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Ostreidae/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
16680Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23057)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23057
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
39641Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19239
48969Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27824)https://www.ccug.se/strain?id=27824
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)
68367Automatically annotated from API 20A
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.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
71798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38592.1StrainInfo: A central database for resolving microbial strain identifiers
121323Curators of the CIPCollection of Institut Pasteur (CIP 107042)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107042