Rodentibacter trehalosifermentans (DSM 104075, CCUG 69668, H1987082031)

Name: Rodentibacter trehalosifermentans (DSM 104075, CCUG 69668, H1987082031)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140303

Type strain

Strain Designation H1987082031

Culture col. no. DSM 104075 CCUG 69668 H1987082031

NCBI tax ID(s) 1908263

Special Collections DSMZ CCUG Literature strains

History <- H. Christensen, University of Copenhagen, Frederiksberg, DENMARK; H1987082031 <-W. Nicklas, German Cancer Research Centre, Heidelberg, Germany

Links

Rodentibacter trehalosifermentans H1987082031 is a microaerophile, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from laboratory rat, trachea.

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

Name and taxonomic classification

SI-ID 407757

DSM 104075,CCUG 69668

@ref 20215

Last LPSN update 2026-02-09 11:33:35

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Rodentibacter

Species Rodentibacter trehalosifermentans

Full scientific name Rodentibacter trehalosifermentans Adhikary et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
43243	negative
125439	negative		97.7

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

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43243	Bovine blood agar
42910	CHOCOLATE AGAR (DSMZ Medium 429b)	Medium recipe at MediaDive	Name: CHOCOLATE AGAR (DSMZ Medium 429b) Composition: Horse blood 100.0 g/l Sheep blood 100.0 g/l Columbia agar base
42910	BHI/3 MEDIUM (DSMZ Medium 218)	Medium recipe at MediaDive	Name: BHI/3 MEDIUM (DSMZ Medium 218) Composition: Brain heart infusion 37.0 g/l Casein hydrolysate 10.0 g/l Starch 1.0 g/l Distilled water
42910	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
42910	positive	growth	37	mesophilic
63643	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

63643

Oxygen tolerancemicroaerophile

Spore formation

@ref	Spore formation	Confidence
125439		97.3

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	13389 ChEBI	nad	+	required for growth
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	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-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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	denitrification	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	pentose phosphate pathway	90.91	10 of 11
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	lipid A biosynthesis	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	70.21	66 of 94
66794	phenylalanine metabolism	69.23	9 of 13
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	flavin biosynthesis	66.67	10 of 15
66794	serine metabolism	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	starch degradation	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	oxidative phosphorylation	57.14	52 of 91
66794	citric acid cycle	57.14	8 of 14
66794	heme metabolism	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	methionine metabolism	53.85	14 of 26
66794	histidine metabolism	51.72	15 of 29
66794	sulfopterin metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	adipate degradation	50	1 of 2
66794	glutamate and glutamine metabolism	50	14 of 28
66794	degradation of pentoses	50	14 of 28
66794	biotin biosynthesis	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	butanoate fermentation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	lysine metabolism	47.62	20 of 42
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	propanol degradation	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	Entner Doudoroff pathway	40	4 of 10
66794	propionate fermentation	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	metabolism of disaccharids	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	NAD metabolism	33.33	6 of 18
66794	cyanate degradation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	lipid metabolism	32.26	10 of 31
66794	ascorbate metabolism	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	arachidonic acid metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
42910	laboratory rat, trachea	Germany	DEU	Europe
43243	rats samples
63643	Laboratory rat,trachea

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
42910	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	ASM200054v1 assembly for Rodentibacter trehalosifermentans H1987082031	contig	GCA_002000545	2791354947	1908263	54.31

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42910	Rodentibacter trehalosifermentans strain H1987082031 16S ribosomal RNA gene, partial sequence	KX858172	1428		1908263

GC content

@ref	GC-content (mol%)	Method
43243	40.9
42910	40.9	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rodentibacter trehalosifermentans H1987082031
NCBI: GCA_002000545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.30	no
125439	motility	BacteriaNetⓘ	no	70.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.80	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 )
#42910	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104075
#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 )
#63643	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 69668
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 )

Rate our new design

Content

About us

Rodentibacter trehalosifermentans (DSM 104075, CCUG 69668, H1987082031)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002000545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media