Strain identifier

BacDive ID: 131133

Type strain: Yes

Species: Bartonella doshiae

Strain Designation: R18

Strain history: CIP <- 2001, B. La Scola, NRC, Fac. Medicine, Marseille, France <- R. Birtles: strain R18

NCBI tax ID(s): 1094553 (strain), 33044 (species)

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General

@ref: 22425

BacDive-ID: 131133

DSM-Number: 102055

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, animal pathogen

description: Bartonella doshiae R18 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from blood of Microtus agrestis.

NCBI tax id

NCBI tax idMatching level
33044species
1094553strain

strain history

@refhistory
22425<- NCTC <- R. J. Birtles; R18
118967CIP <- 2001, B. La Scola, NRC, Fac. Medicine, Marseille, France <- R. Birtles: strain R18

doi: 10.13145/bacdive131133.20230509.8.1

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 doshiae
  • full scientific name: Bartonella doshiae Birtles et al. 1995

@ref: 22425

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Bartonellaceae

genus: Bartonella

species: Bartonella doshiae

full scientific name: Bartonella doshiae Birtles et al. 1995

strain designation: R18

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.977
118967negativerod-shapedno

colony morphology

@refincubation period
224252-3 days
118967

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22425COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429; with strain-specific modifications) Composition: Horse blood 100.0 g/l Columbia agar base
33038MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
118967CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
22425positivegrowth37mesophilic
33038positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118967
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
118967NaClpositivegrowth8-10 %
118967NaClnogrowth0 %
118967NaClnogrowth2 %
118967NaClnogrowth4 %
118967NaClnogrowth6 %

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
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
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
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118967esculin-hydrolysis4853
118967hippurate+hydrolysis606565
118967nitrate-reduction17632
118967nitrite-reduction16301

antibiotic resistance

  • @ref: 118967
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118967
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11896715688acetoin-
11896717234glucose-

enzymes

@refvalueactivityec
118967oxidase-
118967beta-galactosidase-3.2.1.23
118967alcohol dehydrogenase-1.1.1.1
118967gelatinase-
118967catalase-1.11.1.6
118967gamma-glutamyltransferase+2.3.2.2
118967lysine decarboxylase-4.1.1.18
118967ornithine decarboxylase-4.1.1.17
118967phenylalanine ammonia-lyase-4.3.1.24
118967tryptophan deaminase-
118967urease-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
118967--++-+--+--+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118967------------------------------------------------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
22425blood of Microtus agrestisMicrotus agrestisUnited KingdomGBREurope
58983Microtus agrestis blood
118967Microtus agrestis, blood

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_972.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_247;97_656;98_758;99_972&stattab=map
  • Last taxonomy: Bartonella
  • 16S sequence: Z31351
  • Sequence Identity:
  • Total samples: 1497
  • soil counts: 187
  • aquatic counts: 669
  • animal counts: 589
  • plant counts: 52

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
22425yes2Risk group (German classification)
1189672Risk group (French classification)

Sequence information

16S sequences

  • @ref: 22425
  • description: B.doshiae (R18 gene) for 16S ribosomal RNA
  • accession: Z31351
  • length: 1399
  • database: ena
  • NCBI tax ID: 33044

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bartonella doshiae NCTC12862GCA_900445535contigncbi33044
66792Bartonella doshiae DSM 102055GCA_014201435scaffoldncbi33044
66792Bartonella doshiae CCUG 50770GCA_902728115contigncbi33044
66792Bartonella doshiae NCTC 12862 = ATCC 700133GCA_000278155scaffoldncbi1094553
66792Bartonella doshiae NCTC 12862 = ATCC 700133GCA_000526895contigncbi1094553
66792Bartonella doshiae NCTC 128621094553.3wgspatric1094553
66792Bartonella doshiae strain CCUG 5077033044.10wgspatric33044
66792Bartonella doshiae strain DSM 10205533044.6wgspatric33044
66792Bartonella doshiae strain NCTC1286233044.5wgspatric33044
66792Bartonella doshiae NCTC 128622808606804draftimg1094553
66792Bartonella doshiae NCTC 128622519899787draftimg1094553
66792Bartonella doshiae DSM 1020552861153995draftimg33044

GC content

  • @ref: 22425
  • GC-content: 41
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.454no
flagellatedno98.142no
gram-positiveno97.412no
anaerobicno97.766no
aerobicno94.17no
halophileno58.048no
spore-formingno97.076no
thermophileno91.578yes
glucose-utilyes53.204no
glucose-fermentno73.546no

External links

@ref: 22425

culture collection no.: DSM 102055, NCTC 12862, CCUG 50770, CIP 107026, NCTC 12682

straininfo link

  • @ref: 89587
  • straininfo: 46215

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
22425Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102055Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102055)
33038Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19221
58983Curators of the CCUGhttps://www.ccug.se/strain?id=50770Culture Collection University of Gothenburg (CCUG) (CCUG 50770)
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
89587Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID46215.1
118967Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107026Collection of Institut Pasteur (CIP 107026)