Rodentibacter heidelbergensis (DSM 103978, CCUG 69667, 996025094)

Name: Rodentibacter heidelbergensis (DSM 103978, CCUG 69667, 996025094)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140302

Type strain

Strain Designation 996025094, Ac69

Culture col. no. DSM 103978 CCUG 69667 996025094 Ac69

NCBI tax ID(s) 1908258

Special Collections DSMZ CCUG Literature strains

Links

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

Gram-negative colony-forming microaerophile mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400849

DSM 103978,CCUG 69667

@ref 20215

Last LPSN update 2025-12-16 10:03:33

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Rodentibacter

Species Rodentibacter heidelbergensis

Full scientific name Rodentibacter heidelbergensis Adhikary et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
43243	negative
125439	negative		96.1

Colony morphology

@ref	Type of hemolysis	Colony size	Colony shape	Incubation period	Medium used
43243	gamma	1-2 mm	circular	1 day	Bovine blood agar
63642				1 day

Pigmentation

43243

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43243	Bovine blood agar
42909	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
43243	MacConkey agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
42909	positive	growth	37	mesophilic
63642	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
63642	microaerophile
125439	microaerophile	93.6

Spore formation

@ref	Spore formation	Confidence
125439		97.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43243	18333 ChEBI	(+)-D-arabitol	-	builds acid from
43243	28847 ChEBI	(+)-D-fucose	-	builds acid from
43243	17634 ChEBI	(+)-D-glucose	+	builds acid from
43243	17634 ChEBI	(+)-D-glucose	-	builds gas from
43243		(+)-D-glycogen	-	builds acid from
43243	48095 ChEBI	(-)-D-fructose	+	builds acid from
43243	48095 ChEBI	(-)-D-fructose	-	builds gas from
43243	16988 ChEBI	(-)-D-ribose	-	builds acid from
43243	17266 ChEBI	(-)-L-sorbose	-	builds acid from
43243	65328 ChEBI	(-)-L-xylose	-	builds acid from
43243	27613 ChEBI	amygdalin	-	builds acid from
43243	18305 ChEBI	arbutin	-	builds acid from
43243	17057 ChEBI	cellobiose	-	builds acid from
43243	12936 ChEBI	D-galactose	+	builds acid from
43243	12936 ChEBI	D-galactose	-	builds gas from
43243	16899 ChEBI	D-mannitol	-	builds acid from
43243	16024 ChEBI	D-mannose	+	builds acid from
43243	17924 ChEBI	D-sorbitol	+	builds acid from
43243	65327 ChEBI	D-xylose	-	builds acid from
43243	23652 ChEBI	dextrin	+	builds acid from
43243	17113 ChEBI	erythritol	-	builds acid from
43243	4853 ChEBI	esculin	-	builds acid from
43243	16537 ChEBI	galactarate	+	builds acid from
43243	16813 ChEBI	galactitol	-	builds acid from
43243	28066 ChEBI	gentiobiose	-	builds acid from
43243	17234 ChEBI	glucose	-	fermentation
43243	15443 ChEBI	inulin	-	builds acid from
43243	30849 ChEBI	L-arabinose	-	builds acid from
43243	62345 ChEBI	L-rhamnose	-	builds acid from
43243	17716 ChEBI	lactose	+/-	builds acid from
43243	15792 ChEBI	malonate	+	builds base from
43243	17306 ChEBI	maltose	+	builds acid from
43243	17306 ChEBI	maltose	-	builds gas from
43243	6731 ChEBI	melezitose	-	builds acid from
43243	28053 ChEBI	melibiose	-	builds acid from
43243	17268 ChEBI	myo-inositol	-	builds acid from
43243	16634 ChEBI	raffinose	+	builds acid from
43243	15963 ChEBI	ribitol	-	builds acid from
43243	17814 ChEBI	salicin	-	builds acid from
43243	17992 ChEBI	sucrose	+	builds acid from
43243	15226 ChEBI	tetrathionate	-	reduction
43243	27082 ChEBI	trehalose	-	builds acid from
43243	32528 ChEBI	turanose	-	builds acid from
43243	53424 ChEBI	tween 20	-	hydrolysis
43243	53426 ChEBI	tween 80	-	hydrolysis
43243	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43243	15688 ChEBI	acetoin

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
43243	15688 ChEBI	acetoin	-
43243	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
43243	alkaline phosphatase	+	3.1.3.1
43243	alpha-fucosidase	-	3.2.1.51
43243	alpha-galactosidase	-	3.2.1.22
43243	alpha-glucosidase	-	3.2.1.20
43243	alpha-mannosidase	-	3.2.1.24
43243	arginine dihydrolase	-	3.5.3.6
43243	beta-galactosidase	+	3.2.1.23
43243	beta-glucosidase	-	3.2.1.21
43243	beta-xylosidase	-
43243	catalase	+	1.11.1.6
43243	cytochrome oxidase	+	1.9.3.1
43243	gelatinase	-
43243	lysine decarboxylase	-	4.1.1.18
43243	ornithine decarboxylase	-	4.1.1.17
43243	phenylalanine deaminase	-	4.3.1.5
43243	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Oral cavity and airways	#Lung

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
42909	rat, lung	Germany	DEU	Europe
43243	rats samples
63642	Rat,lung	Netherlands	NLD	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
42909	yes, in single cases	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM200012v1 assembly for Rodentibacter heidelbergensis Ac69	contig	GCA_002000125	2788500309	1908258	72.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42909	Rodentibacter heidelbergensis strain 1996025094 16S ribosomal RNA gene, partial sequence	KX858081	1510		1908258

GC content

@ref	GC-content (mol%)	Method
43243	40.4
42909	40.4	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rodentibacter heidelbergensis Ac69
NCBI: GCA_002000125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.60	no
125439	motility	BacteriaNetⓘ	no	69.40	no
125439	gram_stain	BacteriaNetⓘ	negative	96.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	93.60	no

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 .
#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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Rodentibacter heidelbergensis (DSM 103978, CCUG 69667, 996025094)

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

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002000125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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