Bartonella pachyuromydis (DSM 28563, JCM 17714, KCTC 23657)

Name: Bartonella pachyuromydis (DSM 28563, JCM 17714, KCTC 23657)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23784

Type strain

Strain Designation FN15-2

Culture col. no. DSM 28563 JCM 17714 KCTC 23657 FN15-2

NCBI tax ID(s) 931097

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- KCTC <- S. Sato; FN15-2 JCM <-- S. Sato FN15-2. KCTC <- S Maruyama, Nihon Univ., Japan

Links

Bartonella pachyuromydis FN15-2 is an aerobe, Gram-negative, ovoid-shaped bacterium that was isolated from blood of fat-tailed gerbil Pachyuromys duprasi; imported pet.

Gram-negative ovoid-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399896

KCTC 23657,JCM 17714,DSM 28563

@ref 20215

Last LPSN update 2026-05-29 08:30:29

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Bartonellaceae

Genus Bartonella

Species Bartonella pachyuromydis

Full scientific name Bartonella pachyuromydis Sato et al. 2013

BacDive ID	Other strains from **Bartonella pachyuromydis** (1)	Type strain
162085	B. pachyuromydis JCM 17715, KCTC 23911

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30683	negative	1.35 µm	0.59 µm	ovoid-shaped
67771
67771	negative
125439	negative				94.866

Colony morphology

20454

Incubation period3-7 days

Pigmentation

30683

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20454	COLUMBIA BLOOD AGAR (DSMZ Medium 429)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429; with strain-specific modifications) Composition: Horse blood 100.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)
20454	positive	growth	37
30683	positive	optimum	35
67770	positive	growth	35
67771	positive	growth	35

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30683	aerobe
67771	microaerophile
125439	facultative anaerobe	99.062

Spore formation

@ref	Spore formation	Confidence
125439		99.982

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30683	29016 ChEBI	arginine	+	carbon source
30683	16296 ChEBI	D-tryptophan	+	carbon source
30683	15428 ChEBI	glycine	+	carbon source
30683	25017 ChEBI	leucine	+	carbon source
30683	26271 ChEBI	proline	+	carbon source

Enzymes

@ref	Value	Activity	Ec
20454	catalase	-	1.11.1.6
20454	cytochrome-c oxidase	-	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
20454	blood of fat-tailed gerbil Pachyuromys duprasi; imported pet	Pachyuromys duprasi	Japan	JPN	Asia
67770	Blood of fat-tail gerbil (Pachyuromys duprasi)	Pachyuromys duprasi
67771	From blood of fat-tailed gerbil, `Pachyuromys duprasi`		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB602531 (>99% sequence identity) for Bartonella from Microbeatlas

Aquatic Samples	22
Soil Samples	29
Animal Samples	118
Plant Samples	3
Total Samples	172

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
20454	yes, in single cases	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3954306v1 assembly for Bartonella pachyuromydis JCM 17714	scaffold	GCA_039543065	931097	61.91

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20454	Bartonella pachyuromydis gene for 16S rRNA, partial sequence, strain: FN15-2	AB602531	1350		931097

GC content

20454

GC-content (mol%)35.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3954306v1 assembly for Bartonella pachyuromydis JCM 17714
NCBI: GCA_039543065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	94.87	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	99.06	no
125439	motility	BacteriaNetⓘ	yes	43.20	no
125439	spore_formation	BacteriaNetⓘ	no	99.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov., isolated from wild Rodentia.	Sato S, Kabeya H, Fujinaga Y, Inoue K, Une Y, Yoshikawa Y, Maruyama S	Int J Syst Evol Microbiol	10.1099/ijs.0.041939-0	2012

References

#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20454	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28563
#27014	IJSEM 1734 2013 ( DOI 10.1099/ijs.0.041939-0 , PubMed 22941296 )
#30683	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27014
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#69479	João 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 beta .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Bartonella pachyuromydis (DSM 28563, JCM 17714, KCTC 23657)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039543065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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