Strain identifier

BacDive ID: 354

Type strain: Yes

Species: Kerstersia gyiorum

Strain Designation: 3925, R-20010

Strain history: CIP <- 2003, CCUG <- 2002, T. Coenye, Ghent, Belgium: strain R-20010 <- D. Monget, Api, France: strain Api 184-2-84

NCBI tax ID(s): 206506 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6526

BacDive-ID: 354

DSM-Number: 16618

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped

description: Kerstersia gyiorum 3925 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from ankle wound.

NCBI tax id

  • NCBI tax id: 206506
  • Matching level: species

strain history

@refhistory
6526<- LMG <- D. Monget <- G. Gilardi, CDC
119756CIP <- 2003, CCUG <- 2002, T. Coenye, Ghent, Belgium: strain R-20010 <- D. Monget, Api, France: strain Api 184-2-84

doi: 10.13145/bacdive354.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Kerstersia
  • species: Kerstersia gyiorum
  • full scientific name: Kerstersia gyiorum Coenye et al. 2003

@ref: 6526

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Kerstersia

species: Kerstersia gyiorum

full scientific name: Kerstersia gyiorum Coenye et al. 2003

strain designation: 3925, R-20010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
23271negative1-2 µmcoccus-shaped
119756negativerod-shapedyes

colony morphology

@refcolony colormedium used
23271white to light brownnutrient agar
119756

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6526CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23271Nutrient agar (NA)yes
32904MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119756CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6526positivegrowth37mesophilic
23271positivegrowth28-42
32904positivegrowth30mesophilic
57446positivegrowth30-37mesophilic
119756positivegrowth15-41
119756nogrowth5psychrophilic
119756nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57446aerobe
119756obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119756NaClpositivegrowth0-6 %
119756NaClnogrowth8 %
119756NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2327132382(R)-mandelate-assimilation
2327132800(S)-mandelic acid-assimilation
23271194752-aminopentanoic acid-assimilation
23271168082-dehydro-D-gluconate-assimilation
23271307613-aminobenzoate-assimilation
23271879973-aminobutyrate-assimilation
23271852563-dehydro-D-gluconate-assimilation
23271161933-hydroxybenzoate-assimilation
23271178794-hydroxybenzoate-assimilation
23271158875-aminovaleric acid-assimilation
2327127856acetamide-assimilation
2327122210aconitate-assimilation
2327117128adipate-assimilation
2327115963ribitol-assimilation
2327127613amygdalin-assimilation
2327118305arbutin-assimilation
2327178208azelaate-assimilation
2327116150benzoate-assimilation
2327140538benzylamine-assimilation
2327117750betaine-assimilation
2327130719citraconate-assimilation
2327116919creatine-assimilation
2327117108D-arabinose-assimilation
2327118333D-arabitol-assimilation
2327128847D-fucose-assimilation
2327117634D-glucose-assimilation
2327115824D-fructose-assimilation
2327162318D-lyxose-assimilation
2327116024D-mannose-assimilation
232716731melezitose-assimilation
2327116443D-tagatose-assimilation
2327130927D-tartrate-assimilation
2327116296D-tryptophan-assimilation
2327132528turanose-assimilation
2327165327D-xylose-assimilation
2327133871glycerate-assimilation
2327116813galactitol-assimilation
2327117113erythritol-assimilation
232714853esculin-assimilation
2327116000ethanolamine-assimilation
2327115862ethylamine-assimilation
2327128260galactose-assimilation
232715417glucosamine-assimilation
2327117859glutaric acid-assimilation
2327115428glycine-assimilation
2327128087glycogen-assimilation
2327129805glycolate-assimilation
2327118295histamine-assimilation
2327117268myo-inositol-assimilation
2327115443inulin-assimilation
2327148944isobutyrate-assimilation
2327130803isophthalate-assimilation
2327148942isovalerate-assimilation
2327130849L-arabinose-assimilation
2327118403L-arabitol-assimilation
2327116467L-arginine-assimilation
2327116349L-citrulline-assimilation
2327117561L-cysteine-assimilation
2327118287L-fucose-assimilation
2327115971L-histidine-assimilation
2327117191L-isoleucine-assimilation
2327115603L-leucine-assimilation
2327118019L-lysine-assimilation
2327116643L-methionine-assimilation
2327162345L-rhamnose-assimilation
2327117115L-serine-assimilation
2327117266L-sorbose-assimilation
2327130924L-tartrate-assimilation
2327116857L-threonine-assimilation
2327116414L-valine-assimilation
2327165328L-xylose-assimilation
2327117716lactose-assimilation
2327125115malate-assimilation
2327115792malonate-assimilation
2327117306maltose-assimilation
2327129864mannitol-assimilation
2327128053melibiose-assimilation
2327136986mesaconate-assimilation
2327130928meso-tartrate-assimilation
23271320061methyl alpha-D-glucopyranoside-assimilation
2327143943methyl alpha-D-mannoside-assimilation
2327174863methyl beta-D-xylopyranoside-assimilation
23271506227N-acetylglucosamine-assimilation
2327130623oxalate-assimilation
2327117563phthalate-assimilation
2327117774pimelate-assimilation
2327117148putrescine-assimilation
2327116634raffinose-assimilation
2327133942ribose-assimilation
2327117814salicin-assimilation
2327115611sarcosine-assimilation
2327141865sebacic acid-assimilation
2327130911sorbitol-assimilation
2327115746spermine-assimilation
2327128017starch-assimilation
232719300suberic acid-assimilation
2327117992sucrose-assimilation
2327130043terephthalate-assimilation
2327127082trehalose-assimilation
2327118123trigonelline-assimilation
2327116199urea-assimilation
2327117151xylitol-assimilation
23271165672-aminobenzoate+assimilation
23271370543-hydroxybutyrate+assimilation
23271178364-aminobenzoate+assimilation
2327116865gamma-aminobutyric acid+assimilation
23271178794-hydroxybenzoate+assimilation
2327130089acetate+assimilation
2327117968butyrate+assimilation
2327127689decanoate+assimilation
2327125646octanoate+assimilation
2327116947citrate+assimilation
2327115570D-alanine+assimilation
2327129806fumarate+assimilation
2327132362heptanoate+assimilation
2327128683kynurenine+assimilation
2327116977L-alanine+assimilation
2327129991L-aspartate+assimilation
2327129985L-glutamate+assimilation
2327115729L-ornithine+assimilation
2327117295L-phenylalanine+assimilation
2327117203L-proline+assimilation
2327117895L-tyrosine+assimilation
2327124996lactate+assimilation
2327125115malate+assimilation
2327132361nonanoate+assimilation
2327174848pentan-1-amine+assimilation
2327118401phenylacetate+assimilation
2327117272propionate+assimilation
2327115361pyruvate+assimilation
2327130031succinate+assimilation
2327131011valerate+assimilation
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
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11975616947citrate+carbon source
1197564853esculin-hydrolysis
119756606565hippurate-hydrolysis
11975617632nitrate-builds gas from
11975617632nitrate-reduction
11975616301nitrite-builds gas from
11975616301nitrite-reduction
11975615792malonate-assimilation
11975617632nitrate-respiration

antibiotic resistance

  • @ref: 119756
  • 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
11975635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11975615688acetoin-
11975617234glucose-

enzymes

@refvalueactivityec
23271beta-galactosidase-3.2.1.23
23271catalase+1.11.1.6
23271cytochrome oxidase-1.9.3.1
23271urease-3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119756oxidase-
119756beta-galactosidase-3.2.1.23
119756alcohol dehydrogenase-1.1.1.1
119756gelatinase-
119756amylase-
119756DNase-
119756caseinase-3.4.21.50
119756catalase+1.11.1.6
119756tween esterase-
119756gamma-glutamyltransferase+2.3.2.2
119756lecithinase-
119756lipase-
119756lysine decarboxylase-4.1.1.18
119756ornithine decarboxylase-4.1.1.17
119756phenylalanine ammonia-lyase+4.3.1.24
119756protease-
119756tryptophan deaminase+
119756urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119756--+--+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6526---------------+-+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119756------------------------------------------------+++--+++--+--++++---+----+-++++++----+--++++++--++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6526ankle woundUSAUSANorth America
23271human ankle wound
57446Human wound,ankle
119756Human, Wound, ankle

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Wound
#Host Body-Site#Limb#Ankle

taxonmaps

  • @ref: 69479
  • File name: preview.99_4097.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1447;97_2504;98_3098;99_4097&stattab=map
  • Last taxonomy: Kerstersia gyiorum
  • 16S sequence: AY131213
  • Sequence Identity:
  • Total samples: 2582
  • soil counts: 520
  • aquatic counts: 1161
  • animal counts: 732
  • plant counts: 169

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65262Risk group (German classification)
1197561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6526
  • description: Alcaligenes sp. LMG 5906 16S ribosomal RNA gene, partial sequence
  • accession: AY131213
  • length: 1414
  • database: ena
  • NCBI tax ID: 206506

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kerstersia gyiorum DSM 16618GCA_004216755scaffoldncbi206506
66792Kerstersia gyiorum CCUG 47000GCA_008801725contigncbi206506
66792Kerstersia gyiorum strain CCUG 47000206506.12wgspatric206506
66792Kerstersia gyiorum strain DSM 16618206506.8wgspatric206506
66792Kerstersia gyiorum DSM 166182799112210draftimg206506

GC content

  • @ref: 23271
  • GC-content: 62.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes86.314no
flagellatedno51.841no
gram-positiveno97.745yes
anaerobicno96.217no
aerobicyes75.463no
halophileno79.511no
spore-formingno95.674no
glucose-utilno81.197yes
thermophileno99.715yes
glucose-fermentno84.952no

External links

@ref: 6526

culture collection no.: DSM 16618, CCUG 47000, LMG 5906, CIP 108214, Api 184-2-84

straininfo link

  • @ref: 70034
  • straininfo: 780

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657111Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Ruger and Tan 1983 as Achromobacter denitrificans comb. nov.Coenye T, Vancanneyt M, Cnockaert MC, Falsen E, Swings J, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.02609-02003Achromobacter/*classification, Alcaligenes/*classification, Alcaligenes faecalis/*classification/isolation & purification, DNA, Bacterial/genetics, Gram-Negative Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, *PhylogenyPathogenicity
Phylogeny31025054Algicoccus marinus gen. nov. sp. nov., a marine bacterium isolated from the surface of brown seaweed Laminaria japonica.Ying JJ, Zhang SL, Huang CY, Xu L, Zhao Z, Wu M, Sun CArch Microbiol10.1007/s00203-019-01664-62019Alcaligenaceae/chemistry/*classification/genetics, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycolipids/analysis, Laminaria/*microbiology, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Species Specificity, Ubiquinone/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6526Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16618)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16618
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
23271Tom Coenye, Marc Vancanneyt, Margo C. Cnockaert, Enevold Falsen, Jean Swings, Peter Vandamme10.1099/ijs.0.02609-0Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Rüger and Tan 1983 as Achromobacter denitrificans comb. nov.IJSEM 53: 1825-1831 200314657111
32904Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5812
57446Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47000)https://www.ccug.se/strain?id=47000
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
68369Automatically annotated from API 20NE
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
70034Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID780.1StrainInfo: A central database for resolving microbial strain identifiers
119756Curators of the CIPCollection of Institut Pasteur (CIP 108214)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108214