Strain identifier

BacDive ID: 379

Type strain: Yes

Species: Bordetella trematum

Strain Designation: 1779, 22-93

Strain history: CIP <- 1997, CCUG <- 1993, P. Vandamme, Ghent Univ., Ghent, Belgium <- 1993, K.H. Hinz: strain 22-93 <- C.H. Wirsing von Konig <- E. Becker-Boost, Krefeld, Germany

NCBI tax ID(s): 123899 (species)

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General

@ref: 4304

BacDive-ID: 379

DSM-Number: 11334

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Bordetella trematum 1779 is a microaerophile, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from ear swab of patient suffering from chronic otitis media.

NCBI tax id

  • NCBI tax id: 123899
  • Matching level: species

strain history

@refhistory
4304<- LMG <- K.H. Hinz, poultry hospital Hannover (Bordetella avium-like strain 22-39) <- E. Becker-Boost, Krefeld
123579CIP <- 1997, CCUG <- 1993, P. Vandamme, Ghent Univ., Ghent, Belgium <- 1993, K.H. Hinz: strain 22-93 <- C.H. Wirsing von Konig <- E. Becker-Boost, Krefeld, Germany

doi: 10.13145/bacdive379.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Bordetella
  • species: Bordetella trematum
  • full scientific name: Bordetella trematum Vandamme et al. 1996

@ref: 4304

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Bordetella

species: Bordetella trematum

full scientific name: Bordetella trematum Vandamme et al. 1996

strain designation: 1779, 22-93

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
22905negative1-1.8 µm0.5-0.6 µmrod-shapedyesperitrichous
69480yes92.157
69480negative99.992
123579negativerod-shapedyes

colony morphology

@refcolony colorcolony shapeincubation periodmedium used
22905greyish cream whitecircular1 dayblood agar
123579

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4304CASO 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
32670MEDIUM 21 - for BordetellayesDistilled water make up to (1000.000 ml);Horse blood (250.000 ml);Bordetgengou agar (30.000 g)
22905blood agaryes
22905MacConkey agaryes
123579CIP Medium 21yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=21

culture temp

@refgrowthtypetemperaturerange
4304positivegrowth37mesophilic
22905positivegrowth42thermophilic
22905inconsistentgrowth25mesophilic
22905positiveoptimum37mesophilic
32670positivegrowth30mesophilic
123579positivegrowth25-41
123579nogrowth5psychrophilic
123579nogrowth15psychrophilic
123579nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
22905microaerophile
123579obligate aerobe

spore formation

@refspore formationconfidence
22905no
69481no100
69480no99.978

halophily

@refsaltgrowthtested relationconcentration
123579NaClpositivegrowth0-8 %
123579NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22905168082-dehydro-D-gluconate-assimilation
2290515963ribitol-assimilation
2290527613amygdalin-assimilation
2290518305arbutin-assimilation
2290527689decanoate-assimilation
2290517057cellobiose-assimilation
2290517108D-arabinose-assimilation
2290518333D-arabitol-assimilation
2290528847D-fucose-assimilation
229058391D-gluconate-assimilation
2290517634D-glucose-assimilation
2290562318D-lyxose-assimilation
2290516443D-tagatose-assimilation
2290532528turanose-assimilation
2290565327D-xylose-assimilation
2290516813galactitol-assimilation
2290517113erythritol-assimilation
2290528757fructose-assimilation
2290528260galactose-assimilation
2290528066gentiobiose-assimilation
2290517754glycerol-assimilation
2290528087glycogen-assimilation
2290517268myo-inositol-assimilation
2290515443inulin-assimilation
2290530849L-arabinose-assimilation
2290518403L-arabitol-assimilation
2290518287L-fucose-assimilation
2290565328L-xylose-assimilation
2290517716lactose-assimilation
2290517306maltose-assimilation
2290529864mannitol-assimilation
2290537684mannose-assimilation
229056731melezitose-assimilation
2290528053melibiose-assimilation
22905320061methyl alpha-D-glucopyranoside-assimilation
2290543943methyl alpha-D-mannoside-assimilation
2290574863methyl beta-D-xylopyranoside-assimilation
22905506227N-acetylglucosamine-assimilation
2290516634raffinose-assimilation
2290526546rhamnose-assimilation
2290533942ribose-assimilation
2290517992sucrose-assimilation
2290517814salicin-assimilation
2290530911sorbitol-assimilation
2290527922sorbose-assimilation
2290528017starch-assimilation
2290527082trehalose-assimilation
2290517151xylitol-assimilation
22905174265-dehydro-D-gluconate-builds acid from
2290515963ribitol-builds acid from
2290517057cellobiose-builds acid from
2290518333D-arabitol-builds acid from
2290524175galacturonate-builds acid from
2290517234glucose-builds acid from
2290517268myo-inositol-builds acid from
2290530849L-arabinose-builds acid from
2290518403L-arabitol-builds acid from
2290517306maltose-builds acid from
2290529864mannitol-builds acid from
2290518394palatinose-builds acid from
2290526546rhamnose-builds acid from
2290517992sucrose-builds acid from
2290530911sorbitol-builds acid from
2290527082trehalose-builds acid from
2290515428glycine-builds base from
2290517234glucose-fermentation
229054853esculin-hydrolysis
229055291gelatin-hydrolysis
2290517128adipate+assimilation
229054853esculin+assimilation
2290515589L-malate+assimilation
2290518401phenylacetate+assimilation
2290517128adipate+builds base from
2290548537malonamide+builds base from
2290515792malonate+builds base from
2290545422propionamide+builds base from
2290578021tetrazolium+reduction
22905174265-dehydro-D-gluconate+/-assimilation
2290528044phenylalanine+/-assimilation
2290527856acetamide+/-builds base from
2290531011valerate+/-builds base from
2290517632nitrate+/-reduction
68371Potassium 5-ketogluconate-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
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
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
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-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
6837116988D-ribose-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
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
12357916947citrate-carbon source
1235794853esculin+hydrolysis
123579606565hippurate+hydrolysis
12357917632nitrate-builds gas from
12357917632nitrate-reduction
12357916301nitrite-builds gas from
12357916301nitrite-reduction
12357915792malonate+assimilation
12357917234glucose-degradation
12357917632nitrate-respiration

antibiotic resistance

  • @ref: 123579
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2290535581indoleno
2290515688acetoinno
6836935581indoleno
12357935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
2290515688acetoin-
6836935581indole-
12357915688acetoin-
12357917234glucose-

enzymes

@refvalueactivityec
22905alkaline phosphatase+3.1.3.1
22905alpha-fucosidase-3.2.1.51
22905alpha-galactosidase-3.2.1.22
22905alpha-glucosidase-3.2.1.20
22905alpha-mannosidase-3.2.1.24
22905arginine dihydrolase-3.5.3.6
22905beta-galactosidase-3.2.1.23
22905beta-glucosidase-3.2.1.21
22905beta-glucuronidase-3.2.1.31
22905chymotrypsin+/-3.4.4.5
22905cystine arylamidase-3.4.11.3
22905cytochrome oxidase-1.9.3.1
22905esterase lipase (C 8)+
22905glutamyl-glutamate arylamidase+/-
22905histidine arylamidase-
22905L-arginine arylamidase+/-
22905L-aspartate arylamidase+3.4.11.21
22905leucyl glycin arylamidase+3.4.11.1
22905lipase (C 14)+/-
22905lysine decarboxylase-4.1.1.18
22905N-acetyl-beta-glucosaminidase-3.2.1.52
22905naphthol-AS-BI-phosphohydrolase+
22905ornithine decarboxylase-4.1.1.17
22905proline-arylamidase-3.4.11.5
22905pyroglutamic acid arylamidase-
22905serine arylamidase+
22905trypsin-3.4.21.4
22905tyrosine arylamidase+/-
22905urease-3.5.1.5
22905valine arylamidase+
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
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123579oxidase-
123579beta-galactosidase-3.2.1.23
123579alcohol dehydrogenase-1.1.1.1
123579gelatinase-
123579amylase-
123579DNase-
123579caseinase-3.4.21.50
123579catalase+1.11.1.6
123579tween esterase-
123579gamma-glutamyltransferase-2.3.2.2
123579lecithinase-
123579lipase-
123579lysine decarboxylase-4.1.1.18
123579ornithine decarboxylase-4.1.1.17
123579phenylalanine ammonia-lyase-4.3.1.24
123579protease-
123579tryptophan deaminase-
123579urease-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
123579-+++-+----++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4304----------------+++++/-
4304-------------+/---+++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123579-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123579-------------------------------------------+----+++--+-------+-----------+-+---+++-----++++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4304ear swab of patient suffering from chronic otitis mediaGermanyDEUEurope
50983Human otitis media,chronicGermanyDEUEurope
123579Human, OtitisGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host Body-Site#Organ#Ear

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43042Risk group (German classification)
1235792Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bordetella trematum partial 16S rRNA gene, strain DSM 11334 (T)AJ2777981521ena123899
20218Bordetella trematum strain LMG 13506 16S ribosomal RNA gene, partial sequenceKF6019061376ena123899

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bordetella trematum strain NCTC12995123899.5wgspatric123899
66792Bordetella trematum LMG 13506GCA_900078335scaffoldncbi123899

GC content

  • @ref: 22905
  • GC-content: 65.00
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.94yes
gram-positiveno98.734no
anaerobicno98.875no
aerobicyes81.609yes
halophileno79.237no
spore-formingno95.764no
thermophileno99.469no
glucose-utilno81.912no
flagellatedyes64.598yes
glucose-fermentno89.934yes

External links

@ref: 4304

culture collection no.: DSM 11334, CCUG 32381, LMG 13506, CIP 105351

straininfo link

  • @ref: 70059
  • straininfo: 386955

literature

  • topic: Phylogeny
  • Pubmed-ID: 19749028
  • title: Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field.
  • authors: Srinivasan S, Kim MK, Sathiyaraj G, Kim YJ, Yang DC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018358-0
  • year: 2009
  • mesh: Alcaligenaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4304Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11334)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11334
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
22905P. VANDAMME, M. HEYNDRICKX, M. VANCANNEYT, B. HOSTE, P. DE VOS, E. FALSEN, K. KERSTERS, K.-H. HINZ10.1099/00207713-46-4-849Bordetella trematum sp. nov., Isolated from Wounds and Ear Infections in Humans, and Reassessment of Alcaligenes denitrificans Rüger and Tan 1983IJSEM 46: 849-858 19968863408
32670Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17361
50983Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32381)https://www.ccug.se/strain?id=32381
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70059Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID386955.1StrainInfo: A central database for resolving microbial strain identifiers
123579Curators of the CIPCollection of Institut Pasteur (CIP 105351)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105351