Strain identifier
BacDive ID: 10462
Type strain:
Species: Kingella denitrificans
Strain Designation: A358/72
Strain history: CIP <- 1991, NCTC <- R.E. Weaver, CDC: strain A358/72
NCBI tax ID(s): 888741 (strain), 502 (species)
General
@ref: 3848
BacDive-ID: 10462
DSM-Number: 10202
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped
description: Kingella denitrificans A358/72 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from pharynx.
NCBI tax id
NCBI tax id | Matching level |
---|---|
888741 | strain |
502 | species |
strain history
@ref | history |
---|---|
3848 | <- ATCC <- NCTC <- J. J. S. Snell <- R. E. Weaver |
118899 | CIP <- 1991, NCTC <- R.E. Weaver, CDC: strain A358/72 |
doi: 10.13145/bacdive10462.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Neisseriales
- family: Neisseriaceae
- genus: Kingella
- species: Kingella denitrificans
- full scientific name: Kingella denitrificans Snell and Lapage 1976 (Approved Lists 1980)
@ref: 3848
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Neisseriales
family: Neisseriaceae
genus: Kingella
species: Kingella denitrificans
full scientific name: Kingella denitrificans Snell and Lapage 1976
strain designation: A358/72
type strain: yes
Morphology
cell morphology
- @ref: 118899
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 118899
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3848 | COLUMBIA BLOOD AGAR (DSMZ Medium 429) | yes | https://mediadive.dsmz.de/medium/429 | Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base |
35554 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
118899 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3848 | positive | growth | 37 | mesophilic |
35554 | positive | growth | 30 | mesophilic |
118899 | positive | growth | 30-37 | mesophilic |
118899 | no | growth | 5 | psychrophilic |
118899 | no | growth | 22 | psychrophilic |
118899 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 118899
- oxygen tolerance: obligate aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
118899 | NaCl | positive | growth | 0 % |
118899 | NaCl | no | growth | 2 % |
118899 | NaCl | no | growth | 4 % |
118899 | NaCl | no | growth | 6 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
118899 | citrate | - | carbon source | 16947 |
118899 | nitrate | + | reduction | 17632 |
118899 | nitrite | + | reduction | 16301 |
antibiotic resistance
- @ref: 118899
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 118899
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
118899 | oxidase | + | |
118899 | beta-galactosidase | - | 3.2.1.23 |
118899 | alcohol dehydrogenase | - | 1.1.1.1 |
118899 | amylase | - | |
118899 | catalase | - | 1.11.1.6 |
118899 | gamma-glutamyltransferase | - | 2.3.2.2 |
118899 | lysine decarboxylase | - | 4.1.1.18 |
118899 | ornithine decarboxylase | - | 4.1.1.17 |
118899 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118899 | - | - | - | - | - | - | - | - | - | +/- | + | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | +/- | - | - | - | - | +/- | + | - | - | +/- | - | - | - | - | - | - | - | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
3848 | pharynx |
118899 | Human, Pharynx |
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Oral cavity and airways
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3848 | 2 | Risk group (German classification) |
118899 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Kingella denitrificans 16S ribosomal RNA, complete sequence
- accession: M22516
- length: 1475
- database: ena
- NCBI tax ID: 888741
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Kingella denitrificans NCTC10995 | GCA_900451365 | contig | ncbi | 502 |
66792 | Kingella denitrificans ATCC 33394 | GCA_000190695 | scaffold | ncbi | 888741 |
66792 | Kingella denitrificans ATCC 33394 | 888741.3 | wgs | patric | 888741 |
66792 | Kingella denitrificans strain FDAARGOS_1060 | 502.40 | complete | patric | 502 |
66792 | Kingella denitrificans strain NCTC10995 | 502.6 | wgs | patric | 502 |
66792 | Kingella denitrificans ATCC 33394 | 649989956 | draft | img | 888741 |
66792 | Kingella denitrificans NCTC 10995 | 2844173828 | draft | img | 502 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.6 | no |
anaerobic | no | 96.514 | no |
halophile | no | 74.976 | no |
spore-forming | no | 97.046 | no |
glucose-util | no | 52.751 | no |
aerobic | no | 97.625 | no |
thermophile | no | 97.975 | yes |
motile | no | 90.079 | no |
flagellated | no | 97.346 | no |
glucose-ferment | no | 88.847 | no |
External links
@ref: 3848
culture collection no.: DSM 10202, ATCC 33394, NCTC 10995, CIP 103473, CCUG 6516
straininfo link
- @ref: 79739
- straininfo: 40476
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 8945537 | Identification of four complete type 4 pilin genes in a single Kingella denitrificans genome. | Weir S, Lee LW, Marrs CF | Infect Immun | 10.1128/iai.64.12.4993-4999.1996 | 1996 | Amino Acid Sequence, Bacterial Outer Membrane Proteins/*genetics, Base Sequence, Cloning, Molecular, DNA, Bacterial/analysis/*genetics, Fimbriae Proteins, *Genes, Bacterial, *Genome, Bacterial, Kingella/*genetics, Molecular Sequence Data, Sequence Alignment | Enzymology |
Phenotype | 9224888 | Type-4 pili of Kingella denitrificans. | Weir S, Lee LW, Marrs CF | Gene | 10.1016/s0378-1119(96)00828-1 | 1997 | Bacterial Outer Membrane Proteins/*genetics, Blotting, Southern, Blotting, Western, DNA Probes, Fimbriae Proteins, Fimbriae, Bacterial/*chemistry/genetics, Gene Dosage, Gene Expression Regulation, Bacterial, *Genes, Bacterial, Kingella/*chemistry/genetics/pathogenicity, Microscopy, Electron, Phenotype |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3848 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10202) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10202 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
35554 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15274 | ||||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68371 | Automatically annotated from API 50CH acid | |||||
79739 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID40476.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118899 | Curators of the CIP | Collection of Institut Pasteur (CIP 103473) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103473 |