Strain identifier

BacDive ID: 10494

Type strain: Yes

Species: Neisseria zoodegmatis

Strain Designation: CL 194/78, Vandamme R-24681, CNPE12, D5986

Strain history: CIP <- 1994, F. Escande, Inst. Pasteur, Paris, France: strain CNPE12 <- B. Holmes, London, UK <- CDC: strain D5986 <- Honolulu Hosp., Hawaii

NCBI tax ID(s): 326523 (species)

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General

@ref: 15862

BacDive-ID: 10494

DSM-Number: 21643

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

description: Neisseria zoodegmatis CL 194/78 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from dog-bite wound.

NCBI tax id

  • NCBI tax id: 326523
  • Matching level: species

strain history

@refhistory
15862<- LMG; CL 194/78 {2008} <- P. Vandamme, Univ. Ghent, Belgium; Vandamme R-24681 (CDC group EF-4b) <- NCTC <- B. Holmes <- CDC, Atlanta, USA <- Dept. Hlth. Honolulu Hawaii <- Straub Clinic Honolulu Hawaii
124034CIP <- 1994, F. Escande, Inst. Pasteur, Paris, France: strain CNPE12 <- B. Holmes, London, UK <- CDC: strain D5986 <- Honolulu Hosp., Hawaii

doi: 10.13145/bacdive10494.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Neisseriaceae
  • genus: Neisseria
  • species: Neisseria zoodegmatis
  • full scientific name: Neisseria zoodegmatis Vandamme et al. 2006

@ref: 15862

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Neisseriaceae

genus: Neisseria

species: Neisseria zoodegmatis

full scientific name: Neisseria zoodegmatis Vandamme et al. 2006

strain designation: CL 194/78, Vandamme R-24681, CNPE12, D5986

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31732negativerod-shapedno
124034negativerod-shapedno
125438negative98.97

pigmentation

  • @ref: 31732
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15862COLUMBIA 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
40672MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
124034CIP Medium 118-byeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b
124034CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
15862positivegrowth37
31732positivegrowth18-37
31732positiveoptimum18-22
40672positivegrowth37
124034positivegrowth25-41
124034nogrowth15
124034nogrowth45

culture pH

@refabilitytypepH
31732positivegrowth7
31732positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31732facultative anaerobe
124034obligate aerobe
125439obligate aerobe94.8

spore formation

@refspore formationconfidence
31732no
125439no98.8
125438no91.43

observation

  • @ref: 31732
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3173230089acetate+carbon source
3173217234glucose+carbon source
3173217632nitrate+reduction
6837716199urea-hydrolysis
6837717306maltose-builds acid from
6837717992sucrose-builds acid from
6837715824D-fructose-builds acid from
12403416947citrate-carbon source
1240344853esculin-hydrolysis
12403417234glucose+fermentation
124034606565hippurate+hydrolysis
12403417716lactose-fermentation
12403417632nitrate+reduction
12403416301nitrite+reduction
124034132112sodium thiosulfate-builds gas from
12403417234glucose-degradation
12403417632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837718257ornithine-degradation
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

antibiotic resistance

  • @ref: 124034
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12403435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12403415688acetoin-
12403417234glucose-

enzymes

@refvalueactivityec
31732catalase+1.11.1.6
31732cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
124034oxidase+
124034beta-galactosidase-3.2.1.23
124034alcohol dehydrogenase-1.1.1.1
124034gelatinase-
124034catalase+1.11.1.6
124034gamma-glutamyltransferase+2.3.2.2
124034lysine decarboxylase-4.1.1.18
124034ornithine decarboxylase-4.1.1.17
124034phenylalanine ammonia-lyase-4.3.1.24
124034tryptophan deaminase-
124034urease-3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369urease-3.5.1.5
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382cystine arylamidase+3.4.11.3
68377proline-arylamidase+3.4.11.5
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase+3.5.2.6
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124034--++-+-+--++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15862+-----+/--+-----------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
124034----+/------+/---------------------------------------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
15862+--------++-+
15862++--------++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124034+-----------------------------------------------+--------------------------+---++---------+--+--+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15862dog-bite woundHawaiiUSAUSANorth America
124034Human, Dog biteHawaiiUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Canidae (Dog)
#Host Body-Site#Other#Wound

taxonmaps

  • @ref: 69479
  • File name: preview.99_6030.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_837;97_979;98_4473;99_6030&stattab=map
  • Last taxonomy: Neisseria zoodegmatis subclade
  • 16S sequence: DQ006843
  • Sequence Identity:
  • Total samples: 1713
  • soil counts: 23
  • aquatic counts: 50
  • animal counts: 1638
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158622Risk group (German classification)
1240341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15862
  • description: Neisseria zoodegmatis strain LMG 23012 16S ribosomal RNA gene, partial sequence
  • accession: DQ006843
  • length: 1482
  • database: nuccore
  • NCBI tax ID: 326523

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neisseria zoodegmatis NCTC12230GCA_900187305completencbi326523
66792Neisseria zoodegmatis DSM 21643GCA_002108575contigncbi326523
66792Neisseria zoodegmatis strain DSM 21643326523.3wgspatric326523
66792Neisseria zoodegmatis strain NCTC12230326523.5completepatric326523
66792Neisseria zoodegmatis NCTC 122302765235960completeimg326523

GC content

@refGC-contentmethod
1586250.5high performance liquid chromatography (HPLC)
3173250

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.97yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.877yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes56.995no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.43yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.99yes
125438motile2+flagellatedAbility to perform flagellated movementno84.549yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.8
125439BacteriaNetmotilityAbility to perform movementno65.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative85.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe94.8

External links

@ref: 15862

culture collection no.: DSM 21643, ATCC 29859, CDC D5986, LMG 23012, NCTC 12230, CIP 104144

straininfo link

  • @ref: 79771
  • straininfo: 39765

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902011
  • title: Classification of Centers for Disease Control Group Eugonic Fermenter (EF)-4a and EF-4b as Neisseria animaloris sp. nov. and Neisseria zoodegmatis sp. nov., respectively.
  • authors: Vandamme P, Holmes B, Bercovier H, Coenye T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64142-0
  • year: 2006
  • mesh: Animals, Bites and Stings, DNA, Bacterial/genetics, Dogs, Humans, Molecular Sequence Data, Neisseria/*classification/genetics/metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Wounds and Injuries/microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15862Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21643)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21643
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
31732Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2800828776041
40672Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16020
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)
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
79771Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39765.1StrainInfo: A central database for resolving microbial strain identifiers
124034Curators of the CIPCollection of Institut Pasteur (CIP 104144)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104144
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