Strain identifier

BacDive ID: 1644

Type strain: Yes

Species: Bartonella silvatica

Strain history: CIP <- 2008, H.J. Boulouis, ENVA, Maisons Alfort, France: strain Fuji 23-1 <- LVPH, Nihon Univ., Kanagawa, Japan

NCBI tax ID(s): 357760 (species)

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General

@ref: 17324

BacDive-ID: 1644

DSM-Number: 23649

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

description: Bartonella silvatica DSM 23649 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from Blood of Apodemus speciosus mice.

NCBI tax id

  • NCBI tax id: 357760
  • Matching level: species

strain history

@refhistory
17324<- JCM <- K. Inoue; Fuji 23-1
67770K. Inoue Fuji 23-1.
122607CIP <- 2008, H.J. Boulouis, ENVA, Maisons Alfort, France: strain Fuji 23-1 <- LVPH, Nihon Univ., Kanagawa, Japan

doi: 10.13145/bacdive1644.20230509.8.1

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 silvatica
  • full scientific name: Bartonella silvatica Inoue et al. 2010

@ref: 17324

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Bartonellaceae

genus: Bartonella

species: Bartonella silvatica

full scientific name: Bartonella silvatica Inoue et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23362negative1.16 µm0.43 µmrod-shaped
122607negativerod-shapedno

colony morphology

@reftype of hemolysiscolony sizecolony colorincubation periodmedium used
17324gamma
233621-2 mmgrey-whitish14 daysHIA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17324COLUMBIA 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
23362HIAyes
37863MEDIUM 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)
122607CIP Medium 70yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=70
122607CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
17324positivegrowth35mesophilic
23362positivegrowth35mesophilic
37863positivegrowth37mesophilic
67770positivegrowth35mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 17324
  • oxygen tolerance: microaerophile

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23362903434-nitrophenyl N-acetyl-beta-D-glucosaminide-hydrolysis
2336226271proline-other
233623122bis-4-nitrophenyl phosphate+hydrolysis
2336229016arginine+other
2336215428glycine+other
2336225017leucine+other
2336225094lysine+other
2336216811methionine+other
2336227897tryptophan+other
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
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
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
12260717632nitrate-reduction
12260716301nitrite-reduction

metabolite production

  • @ref: 122607
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
17324catalase-1.11.1.6
17324cytochrome-c oxidase-1.9.3.1
23362catalase-1.11.1.6
23362cytochrome oxidase-1.9.3.1
23362pyrrolidonyl arylamidase-3.4.19.3
23362urease-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
122607oxidase-
122607catalase+1.11.1.6
122607urease-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
122607---+-+---------+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122607----------------------------+/-----------+/---------+/-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
17324Blood of Apodemus speciosus miceApodemus speciosusJapanJPNAsia
67770Blood of Apodemus speciosus miceApodemus speciosus
122607Animal, Apodemus speciosus mice, bloodJapanJPNAsiaMount Fuji2003

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1245.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_247;97_656;98_758;99_1245&stattab=map
  • Last taxonomy: Bartonella
  • 16S sequence: AB440636
  • Sequence Identity:
  • Total samples: 172
  • soil counts: 29
  • aquatic counts: 22
  • animal counts: 118
  • plant counts: 3

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
17324yes2Risk group (German classification)
1226072Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17324
  • description: Bartonella silvatica gene for 16S rRNA, partial sequence
  • accession: AB440636
  • length: 1349
  • database: ena
  • NCBI tax ID: 357760

Genome sequences

  • @ref: 66792
  • description: Bartonella silvatica DSM 23649
  • accession: 2928179098
  • assembly level: draft
  • database: img
  • NCBI tax ID: 357760

GC content

  • @ref: 17324
  • GC-content: 40.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 17324

culture collection no.: DSM 23649, CIP 109862, JCM 15566, Fuji 23-1

straininfo link

  • @ref: 71291
  • straininfo: 369416

literature

  • topic: Phylogeny
  • Pubmed-ID: 19656930
  • title: Bartonella japonica sp. nov. and Bartonella silvatica sp. nov., isolated from Apodemus mice.
  • authors: Inoue K, Kabeya H, Shiratori H, Ueda K, Kosoy MY, Chomel BB, Boulouis HJ, Maruyama S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.011528-0
  • year: 2009
  • mesh: Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Bartonella/*classification/genetics/*isolation & purification/physiology, Bartonella Infections/microbiology/*veterinary, Base Composition, Blood/*microbiology, DNA, Ribosomal/analysis/genetics, Genes, rRNA, Japan, Molecular Sequence Data, Murinae/*microbiology, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17324Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23649)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23649
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
23362Kai Inoue, Hidenori Kabeya, Hatsumi Shiratori, Kenji Ueda, Michael Y. Kosoy, Bruno B. Chomel, Henri-Jean Boulouis, Soichi Maruyama10.1099/ijs.0.011528-0Bartonella japonica sp. nov. and Bartonella silvatica sp. nov., isolated from Apodemus miceIJSEM 60: 759-763 201019656930
37863Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7654
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71291Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID369416.1StrainInfo: A central database for resolving microbial strain identifiers
122607Curators of the CIPCollection of Institut Pasteur (CIP 109862)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109862