Name: Rodentibacter rarus 2325/79
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140304

Type strain:

Species: Rodentibacter rarus

Strain Designation: 2325/79

Culture col. no.: DSM 103980, CCUG 17206, HPA 41

Strain history: <- H. Christensen, Veterinary Disease Biology, University of Copenhagen <- Institute of Avian Diseases, Langaa, Denmark

NCBI tax ID(s): 1908260 (species)

SI-ID 51978

CCUG 17206, DSM 103980

Section

Rodentibacter rarus 2325/79 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from rat.

colony-forming
Gram-negative
animal pathogen
mesophilic
microaerophile
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pasteurellales*
	Family	*Pasteurellaceae*
	Genus	*Rodentibacter*
	Species	**Rodentibacter rarus**
	Full Scientific Name (LPSN)	Rodentibacter rarus Adhikary et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43243]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.939

[Ref.: #43243]	Motility	no

[Ref.: #43243]	Type of hemolysis	gamma
[Ref.: #43243]	Colony size	1-2 mm
[Ref.: #43243]	Colony shape	circular
[Ref.: #43243]	Incubation period	1 day
[Ref.: #43243]	Cultivation medium used	Bovine blood agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43243]

Culture medium

Bovine blood agar

[Ref.: #43243]

Culture medium growth

[Ref.: #42911]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #42911]

Culture medium growth

[Ref.: #42911]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42911]

Culture medium composition

expand / minimize

[Ref.: #43243]

Culture medium

Bovine blood agar

[Ref.: #43243]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #42911]			growth	37 °C
[Ref.: #46562]			growth	37 °C

[Ref.: #42911]	Temperature range	mesophilic
[Ref.: #46562]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #46562]

Oxygen tolerance

microaerophile

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43243]	(+)-D-arabitol ChEBI	-	builds acid from
[Ref.: #43243]	(+)-D-fucose ChEBI	-	builds acid from
[Ref.: #43243]	(+)-D-glucose ChEBI	+	builds acid from
[Ref.: #43243]	(+)-D-glucose ChEBI	-	builds gas from
[Ref.: #43243]	(+)-D-glycogen	-	builds acid from
[Ref.: #43243]	(-)-D-fructose ChEBI	+	builds acid from
[Ref.: #43243]	(-)-D-fructose ChEBI	-	builds gas from
[Ref.: #43243]	(-)-D-ribose ChEBI	-	builds acid from
[Ref.: #43243]	(-)-L-sorbose ChEBI	-	builds acid from
[Ref.: #43243]	(-)-L-xylose ChEBI	-	builds acid from
[Ref.: #43243]	amygdalin ChEBI	-	builds acid from
[Ref.: #43243]	arbutin ChEBI	-	builds acid from
[Ref.: #43243]	cellobiose ChEBI	-	builds acid from
[Ref.: #43243]	D-arabinose ChEBI	-	builds acid from
[Ref.: #43243]	D-galactose ChEBI	+	builds acid from
[Ref.: #43243]	D-galactose ChEBI	-	builds gas from
[Ref.: #43243]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43243]	D-mannose ChEBI	+	builds acid from
[Ref.: #43243]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43243]	D-xylose ChEBI	-	builds acid from
[Ref.: #43243]	dextrin ChEBI	+	builds acid from
[Ref.: #43243]	erythritol ChEBI	-	builds acid from
[Ref.: #43243]	esculin ChEBI	-	builds acid from
[Ref.: #43243]	galactarate ChEBI	+	builds acid from
[Ref.: #43243]	galactitol ChEBI	-	builds acid from
[Ref.: #43243]	gentiobiose ChEBI	-	builds acid from
[Ref.: #43243]	glucose ChEBI	-	fermentation
[Ref.: #43243]	glycerol ChEBI	+	builds acid from
[Ref.: #43243]	inulin ChEBI	-	builds acid from
[Ref.: #43243]	L-arabinose ChEBI	-	builds acid from
[Ref.: #43243]	L-fucose ChEBI	+	builds acid from
[Ref.: #43243]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43243]	lactose ChEBI	+	builds acid from
[Ref.: #43243]	malonate ChEBI	+	builds base from
[Ref.: #43243]	maltose ChEBI	+	builds acid from
[Ref.: #43243]	maltose ChEBI	-	builds gas from
[Ref.: #43243]	melezitose ChEBI	-	builds acid from
[Ref.: #43243]	melibiose ChEBI	+	builds acid from
[Ref.: #43243]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43243]	nad ChEBI	-	required for growth
[Ref.: #43243]	raffinose ChEBI	-	builds acid from
[Ref.: #43243]	ribitol ChEBI	-	builds acid from
[Ref.: #43243]	salicin ChEBI	-	builds acid from
[Ref.: #43243]	sucrose ChEBI	+	builds acid from
[Ref.: #43243]	tetrathionate ChEBI	-	reduction
[Ref.: #43243]	trehalose ChEBI	+	builds acid from
[Ref.: #43243]	turanose ChEBI	-	builds acid from
[Ref.: #43243]	tween 20 ChEBI	-	hydrolysis
[Ref.: #43243]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43243]		acetoin ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43243]		acetoin ChEBI	-
[Ref.: #43243]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #43243]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43243]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43243]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43243]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43243]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43243]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43243]	beta-galactosidase	+	3.2.1.23
[Ref.: #43243]	beta-glucosidase	-	3.2.1.21
[Ref.: #43243]	beta-xylosidase	-
[Ref.: #43243]	catalase	+	1.11.1.6
[Ref.: #43243]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43243]	gelatinase	-
[Ref.: #43243]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43243]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43243]	phenylalanine deaminase	-	4.3.1.5
[Ref.: #43243]	urease	+	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #42911]	Sample type/isolated from	rat

[Ref.: #43243]	Sample type/isolated from	rat samples
[Ref.: #43243]	Geographic location (country and/or sea, region)	USA
[Ref.: #43243]	Country	USA
[Ref.: #43243]	Country ISO 3 Code	USA
[Ref.: #43243]	Continent	North America

[Ref.: #46562]	Sample type/isolated from	Mouse
[Ref.: #46562]	Country	USA
[Ref.: #46562]	Country ISO 3 Code	USA
[Ref.: #46562]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host

#Mammals

#Muridae (Mouse/Rat)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF024529 (>99% sequence identity) for Rodentibacter rarus subclade from Microbeatlas

Aquatic Samples	9
Soil Samples	2
Animal Samples	775
Plant Samples	1
Total Samples	787

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #42911]	Pathogenicity (animal)	yes, in single cases
[Ref.: #42911]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #42911]	Rodentibacter rarus strain CCUG 17206 16S ribosomal RNA gene, complete sequence	AF024529	1480	ENA	1908260 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rodentibacter rarus CCUG 17206	GCA_001998965	contig	GenBank	1908260 tax ID	*
[Ref.: #66792]	Rodentibacter rarus strain CCUG17206	1908260.3	wgs	PATRIC	1908260 tax ID	*
[Ref.: #66792]	Rodentibacter rarus CCUG17206	2791354952	draft	JGI IMG/M	1908260 tax ID	*

[Ref.: #43243]

GC-content

40.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rodentibacter rarus strain CCUG17206 PATRIC: 1908260.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rodentibacter rarus strain CCUG17206 PATRIC: 1908260.3
[Ref.: #69480]	motile	no	90.128	no
[Ref.: #69480]	gram-positive	no	98.042	yes
[Ref.: #69480]	anaerobic	no	93.284	no
[Ref.: #69480]	aerobic	no	94.526	yes
[Ref.: #69480]	halophile	no	59.936	no
[Ref.: #69480]	spore-forming	no	98.812	no
[Ref.: #69480]	glucose-util	no	51.839	no
[Ref.: #69480]	flagellated	no	94.579	yes
[Ref.: #69480]	thermophile	no	98.923	no
[Ref.: #69480]	glucose-ferment	yes	55.043	no

Availability in culture collections External links

[Ref.: #42911]

Culture collection no.

DSM 103980, CCUG 17206, HPA 41

[Ref.: #96609]

SI-ID 51978

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies.	Adhikary S, Nicklas W, Bisgaard M, Boot R, Kuhnert P, Waberschek T, Aalbaek B, Korczak B, Christensen H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001866	2017	*

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 )

#42911

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103980

#43243

Sadhana Adhikary, Werner Nicklas, Magne Bisgaard, Ron Boot, Peter Kuhnert, Torsten Waberschek, Bent Aalbaek, Bozena Korczak and Henrik Christensen: Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies. IJSEM 67: 1793 - 1806 2017 ( DOI 10.1099/ijsem.0.001866 , PubMed 28629498 )

#46562 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 17206

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#96609

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID51978.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Rodentibacter rarus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Rodentibacter rarus strain CCUG17206

Rodentibacter rarus strain CCUG17206

Change proposal

Change proposal