Strain identifier
BacDive ID: 10494
Type strain:
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)
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
@ref | history |
---|---|
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 |
124034 | CIP <- 1994, F. Escande, Inst. Pasteur, Paris, France: strain CNPE12 <- B. Holmes, London, UK <- CDC: strain D5986 <- Honolulu Hosp., Hawaii |
doi: 10.13145/bacdive10494.20230509.8.1
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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
31732 | negative | rod-shaped | no | |
69480 | negative | 99.987 | ||
124034 | negative | rod-shaped | no |
pigmentation
- @ref: 31732
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15862 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
40672 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
124034 | CIP Medium 118-b | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b | |
124034 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15862 | positive | growth | 37 | mesophilic |
31732 | positive | growth | 18-37 | |
31732 | positive | optimum | 18-22 | psychrophilic |
40672 | positive | growth | 37 | mesophilic |
124034 | positive | growth | 25-41 | |
124034 | no | growth | 15 | psychrophilic |
124034 | no | growth | 45 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31732 | positive | growth | 7 |
31732 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31732 | facultative anaerobe |
124034 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31732 | no | |
69481 | no | 100 |
69480 | no | 99.998 |
observation
- @ref: 31732
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31732 | 30089 | acetate | + | carbon source |
31732 | 17234 | glucose | + | carbon source |
31732 | 17632 | nitrate | + | reduction |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
124034 | 16947 | citrate | - | carbon source |
124034 | 4853 | esculin | - | hydrolysis |
124034 | 17234 | glucose | + | fermentation |
124034 | 606565 | hippurate | + | hydrolysis |
124034 | 17716 | lactose | - | fermentation |
124034 | 17632 | nitrate | + | reduction |
124034 | 16301 | nitrite | + | reduction |
124034 | 132112 | sodium thiosulfate | - | builds gas from |
124034 | 17234 | glucose | - | degradation |
124034 | 17632 | nitrate | - | respiration |
68377 | 15824 | D-fructose | - | builds acid from |
68377 | 17306 | maltose | - | builds acid from |
68377 | 17992 | sucrose | - | builds acid from |
68377 | 18257 | ornithine | - | degradation |
68377 | 16199 | urea | - | hydrolysis |
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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
124034 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | - | ||
124034 | 15688 | acetoin | - | ||
124034 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31732 | catalase | + | 1.11.1.6 |
31732 | cytochrome oxidase | + | 1.9.3.1 |
68377 | proline-arylamidase | + | 3.4.11.5 |
68377 | alkaline phosphatase | - | 3.1.3.1 |
68377 | lipase | - | |
68377 | urease | - | 3.5.1.5 |
68377 | ornithine decarboxylase | - | 4.1.1.17 |
68377 | beta-lactamase | + | 3.5.2.6 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
124034 | oxidase | + | |
124034 | beta-galactosidase | - | 3.2.1.23 |
124034 | alcohol dehydrogenase | - | 1.1.1.1 |
124034 | gelatinase | - | |
124034 | catalase | + | 1.11.1.6 |
124034 | gamma-glutamyltransferase | + | 2.3.2.2 |
124034 | lysine decarboxylase | - | 4.1.1.18 |
124034 | ornithine decarboxylase | - | 4.1.1.17 |
124034 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
124034 | tryptophan deaminase | - | |
124034 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
124034 | - | - | + | + | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15862 | + | - | - | - | - | - | +/- | - | + | - | - | - | - | - | - | - | - | - | - | - | + |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
124034 | - | - | - | - | +/- | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API NH
@ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT | IND |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
15862 | + | - | - | - | - | - | - | - | - | + | + | - | + |
15862 | + | + | - | - | - | - | - | - | - | - | + | + | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
124034 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | + | - | - | - | - | - | - | - | - | - | + | - | - | + | - | - | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15862 | dog-bite wound | Hawaii | USA | USA | North America |
124034 | Human, Dog bite | Hawaii | United States of America | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
15862 | 2 | Risk group (German classification) |
124034 | 1 | Risk 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: ena
- NCBI tax ID: 326523
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Neisseria zoodegmatis NCTC12230 | GCA_900187305 | complete | ncbi | 326523 |
66792 | Neisseria zoodegmatis DSM 21643 | GCA_002108575 | contig | ncbi | 326523 |
66792 | Neisseria zoodegmatis strain DSM 21643 | 326523.3 | wgs | patric | 326523 |
66792 | Neisseria zoodegmatis strain NCTC12230 | 326523.5 | complete | patric | 326523 |
66792 | Neisseria zoodegmatis NCTC 12230 | 2765235960 | complete | img | 326523 |
GC content
@ref | GC-content | method |
---|---|---|
15862 | 50.5 | high performance liquid chromatography (HPLC) |
31732 | 50 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 86.945 | yes |
flagellated | no | 95.048 | no |
gram-positive | no | 98.617 | yes |
anaerobic | no | 97.182 | yes |
aerobic | no | 90.544 | no |
halophile | no | 78.859 | no |
spore-forming | no | 97.053 | yes |
thermophile | no | 99.128 | yes |
glucose-util | yes | 72.885 | yes |
glucose-ferment | no | 89.431 | yes |
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
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15862 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21643) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21643 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31732 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28008 | 28776041 | |
40672 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16020 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68369 | Automatically annotated from API 20NE | |||||
68371 | Automatically annotated from API 50CH acid | |||||
68377 | Automatically annotated from API NH | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
79771 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39765.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
124034 | Curators of the CIP | Collection of Institut Pasteur (CIP 104144) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104144 |