Strain identifier

BacDive ID: 10462

Type strain: Yes

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)

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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 idMatching level
888741strain
502species

strain history

@refhistory
3848<- ATCC <- NCTC <- J. J. S. Snell <- R. E. Weaver
118899CIP <- 1991, NCTC <- R.E. Weaver, CDC: strain A358/72

doi: 10.13145/bacdive10462.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Neisseriaceae
  • genus: 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

@refgram staincell shapemotilityconfidence
118899negativerod-shapedno
125438negative99.5
125439negative98.3

colony morphology

  • @ref: 118899

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3848COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
35554MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118899CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
3848positivegrowth37
35554positivegrowth30
118899positivegrowth30-37
118899nogrowth5
118899nogrowth22
118899nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 118899
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
125438no90.244
125439no99.5

halophily

@refsaltgrowthtested relationconcentration
118899NaClpositivegrowth0 %
118899NaClnogrowth2 %
118899NaClnogrowth4 %
118899NaClnogrowth6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11889916947citrate-carbon source
11889917632nitrate+reduction
11889916301nitrite+reduction
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
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
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-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
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

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

@refvalueactivityec
118899oxidase+
118899beta-galactosidase-3.2.1.23
118899alcohol dehydrogenase-1.1.1.1
118899amylase-
118899catalase-1.11.1.6
118899gamma-glutamyltransferase-2.3.2.2
118899lysine decarboxylase-4.1.1.18
118899ornithine decarboxylase-4.1.1.17
118899urease-3.5.1.5

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118899---------+/-+-+/---------------+--+/-----+/-+--+/---------+/-

Isolation, sampling and environmental information

isolation

@refsample type
3848pharynx
118899Human, Pharynx

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
38482Risk group (German classification)
1188991Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Kingella denitrificans 16S ribosomal RNA, complete sequence
  • accession: M22516
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 888741

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kingella denitrificans NCTC10995GCA_900451365contigncbi502
66792Kingella denitrificans ATCC 33394GCA_000190695scaffoldncbi888741
66792Kingella denitrificans ATCC 33394888741.3wgspatric888741
66792Kingella denitrificans strain FDAARGOS_1060502.40completepatric502
66792Kingella denitrificans strain NCTC10995502.6wgspatric502
66792Kingella denitrificans ATCC 33394649989956draftimg888741
66792Kingella denitrificans NCTC 109952844173828draftimg502

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.437no
125438spore-formingspore-formingAbility to form endo- or exosporesno90.244no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes58.422yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.33yes
125438motile2+flagellatedAbility to perform flagellated movementno85.382no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.5
125439BacteriaNetmotilityAbility to perform movementyes55.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe75.4

External links

@ref: 3848

culture collection no.: DSM 10202, ATCC 33394, NCTC 10995, CIP 103473, CCUG 6516

straininfo link

  • @ref: 79739
  • straininfo: 40476

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics8945537Identification of four complete type 4 pilin genes in a single Kingella denitrificans genome.Weir S, Lee LW, Marrs CFInfect Immun10.1128/iai.64.12.4993-4999.19961996Amino 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 AlignmentEnzymology
Phenotype9224888Type-4 pili of Kingella denitrificans.Weir S, Lee LW, Marrs CFGene10.1016/s0378-1119(96)00828-11997Bacterial 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

@idauthorscataloguedoi/urltitlejournalpubmed
3848Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10202)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10202
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35554Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15274
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
79739Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40476.1StrainInfo: A central database for resolving microbial strain identifiers
118899Curators of the CIPCollection of Institut Pasteur (CIP 103473)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103473
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