Strain identifier

BacDive ID: 138801

Type strain: Yes

Species: Bartonella phoceensis

Strain Designation: 16120

Strain history: CIP <- 2002, B. La Scola, CNRS, Medicine Fac., Marseille, France: strain 16120

NCBI tax ID(s): 270249 (species)

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General

@ref: 40716

BacDive-ID: 138801

keywords: genome sequence, Bacteria, microaerophile, mesophilic, Gram-negative

description: Bartonella phoceensis 16120 is a microaerophile, mesophilic, Gram-negative bacterium of the family Bartonellaceae.

NCBI tax id

  • NCBI tax id: 270249
  • Matching level: species

strain history

@refhistory
407162002, B. La Scola, CNRS, Medecine Fac., Marseille, France: strain 16120
40716CIP <- 2002, B. La Scola, CNRS, Medicine Fac., Marseille, France: strain 16120

doi: 10.13145/bacdive138801.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Bartonellaceae
  • genus: Bartonella
  • species: Bartonella phoceensis
  • full scientific name: Bartonella phoceensis Gundi et al. 2004

@ref: 40716

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Bartonellaceae

genus: Bartonella

species: Bartonella phoceensis

strain designation: 16120

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shape
69480negative99.984
40716negativerod-shaped

colony morphology

@refincubation period
591094 days
40716

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40716MEDIUM 70 - columbia agar with horse blood and hemin for BartonellayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);Hemin solution - M00149 (10.000 ml)
40716CIP Medium 70yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=70

culture temp

@refgrowthtypetemperaturerange
40716positivegrowth37mesophilic
40716positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 59109
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
40716NaClpositivegrowth0 %
40716NaClnogrowth2 %
40716NaClnogrowth4 %
40716NaClnogrowth6 %
40716NaClnogrowth8 %
40716NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose+builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose-builds acid from32528
68371glycogen-builds acid from28087
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-mannitol-builds acid from16899
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
40716esculin-hydrolysis4853
40716hippurate+hydrolysis606565
40716nitrate-reduction17632
40716nitrite-reduction16301

metabolite production

  • @ref: 40716
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4071615688acetoin-
4071617234glucose-

enzymes

@refvalueactivityec
40716oxidase+
40716beta-galactosidase-3.2.1.23
40716alcohol dehydrogenase-1.1.1.1
40716gelatinase-
40716catalase-1.11.1.6
40716gamma-glutamyltransferase+2.3.2.2
40716lysine decarboxylase-4.1.1.18
40716ornithine decarboxylase-4.1.1.17
40716phenylalanine ammonia-lyase-4.3.1.24
40716tryptophan deaminase-
40716urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
40716--++-+--+------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
40716----+/-----+/-------+/--+/---+/-+/-+/-+-++--+/-+/--+/--+/--+/-+/--++------+

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
40716MarseilleFranceFRAEurope
59109MarseilleFranceFRAEuropeRat,wild (Rattus norvegicus)
40716MarseilleFranceFRAEuropeAnimal, Rat, blood

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Muridae (Mouse/Rat)

Safety information

risk assessment

  • @ref: 40716
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bartonella phoceensis CIP107707GCA_902825145scaffoldncbi270249
66792Bartonella phoceensis strain CIP107707270249.3wgspatric270249

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.509no
gram-positiveno98.166no
anaerobicno97.164yes
aerobicno95.746yes
halophileno56.271no
spore-formingno97.461no
thermophileno90.047yes
glucose-utilyes51.765no
motileno89.286no
glucose-fermentno77.154no

External links

@ref: 40716

culture collection no.: CIP 107707, CCUG 51222

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
40716Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107707Collection of Institut Pasteur (CIP 107707)
59109Curators of the CCUGhttps://www.ccug.se/strain?id=51222Culture Collection University of Gothenburg (CCUG) (CCUG 51222)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1