Name: Rodentibacter heidelbergensis 996025094
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140302

Type strain:

Species: Rodentibacter heidelbergensis

Strain Designation: 996025094, Ac69

Culture col. no.: DSM 103978, CCUG 69667

Strain history: <- H. Christensen, University of Copenhagen,Veterinary Disease Biology <- R. Boot, Laboratory for Infectious Disease and Screening, Bilthoven, Netherlands <- W. Nicklas

NCBI tax ID(s): 1908258 (species)

SI-ID 400849

DSM 103978, CCUG 69667

Section

Rodentibacter heidelbergensis 996025094 is a microaerophile, mesophilic, Gram-negative animal pathogen that forms circular colonies and was isolated from rat, lung.

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 heidelbergensis**
	Full Scientific Name (LPSN)	Rodentibacter heidelbergensis Adhikary et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43243]	Gram stain	negative

[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

[Ref.: #63642]	Incubation period	1 day

[Ref.: #43243]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43243]

Culture medium

Bovine blood agar

[Ref.: #43243]

Culture medium growth

[Ref.: #42909]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #42909]

Culture medium growth

[Ref.: #42909]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42909]

Culture medium composition

expand / minimize

[Ref.: #43243]

Culture medium

MacConkey agar

[Ref.: #43243]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #42909]			growth	37 °C
[Ref.: #63642]			growth	37 °C

[Ref.: #42909]	Temperature range	mesophilic
[Ref.: #63642]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63642]

Oxygen tolerance

microaerophile

	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-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]	inulin ChEBI	-	builds acid from
[Ref.: #43243]	L-arabinose 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]	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]	tween 80 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.: #42909]	Sample type/isolated from	rat, lung
[Ref.: #42909]	Country	Germany
[Ref.: #42909]	Country ISO 3 Code	DEU
[Ref.: #42909]	Continent	Europe

[Ref.: #43243]	Sample type/isolated from	rats samples

[Ref.: #63642]	Sample type/isolated from	Rat,lung
[Ref.: #63642]	Country	Netherlands
[Ref.: #63642]	Country ISO 3 Code	NLD
[Ref.: #63642]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Oral cavity and airways	#Lung

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX858081 (>99% sequence identity) for Rodentibacter heidelbergensis from Microbeatlas

Aquatic Samples	1
Soil Samples
Animal Samples	92
Plant Samples
Total Samples	93

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

[Ref.: #42909]	Pathogenicity (animal)	yes, in single cases
[Ref.: #42909]	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.: #42909]	Rodentibacter heidelbergensis strain 1996025094 16S ribosomal RNA gene, partial sequence	KX858081	1510	ENA	1908258 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rodentibacter heidelbergensis Ac69	GCA_002000125	contig	GenBank	1908258 tax ID	*
[Ref.: #66792]	Rodentibacter heidelbergensis Ac69	2788500309	draft	JGI IMG/M	1908258 tax ID	*

[Ref.: #43243]	GC-content	40.4 mol%
[Ref.: #42909]	GC-content	40.4 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #42909]

Culture collection no.

DSM 103978, CCUG 69667

[Ref.: #96607]

SI-ID 400849

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 )

#42909

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103978

#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 )

#63642 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 69667

#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 .

#96607

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-ID400849.1 )

* These data were automatically processed and therefore are not curated

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