Name: Rodentibacter trehalosifermentans H1987082031
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140303

Type strain:

Species: Rodentibacter trehalosifermentans

Strain Designation: H1987082031

Culture col. no.: DSM 104075, CCUG 69668

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

NCBI tax ID(s): 1908263 (species)

SI-ID 407757

DSM 104075, CCUG 69668

Special Collections

Section

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

colony-forming
Gram-negative
animal pathogen
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 trehalosifermentans**
	Full Scientific Name (LPSN)	Rodentibacter trehalosifermentans 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

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43243]

Culture medium

Bovine blood agar

[Ref.: #43243]

Culture medium growth

[Ref.: #42910]

Culture medium

CHOCOLATE AGAR (DSMZ Medium 429b)

[Ref.: #42910]

Culture medium growth

[Ref.: #42910]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42910]

Culture medium composition

expand / minimize

[Ref.: #42910]

Culture medium

BHI/3 MEDIUM (DSMZ Medium 218)

[Ref.: #42910]

Culture medium growth

[Ref.: #42910]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42910]

Culture medium composition

expand / minimize

[Ref.: #42910]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #42910]

Culture medium growth

[Ref.: #42910]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42910]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #42910]			growth	37 °C
[Ref.: #63643]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63643]

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]	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-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.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	metabolism of amino sugars and derivatives	100	5 of 5
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glutamate and glutamine metabolism	50	14 of 28
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	NAD metabolism	33.33	6 of 18
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid metabolism	32.26	10 of 31
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		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.: #42910]	Sample type/isolated from	laboratory rat, trachea
[Ref.: #42910]	Country	Germany
[Ref.: #42910]	Country ISO 3 Code	DEU
[Ref.: #42910]	Continent	Europe

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

[Ref.: #63643]	Sample type/isolated from	Laboratory rat,trachea
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #42910]	Pathogenicity (animal)	yes, in single cases
[Ref.: #42910]	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.: #42910]	Rodentibacter trehalosifermentans strain H1987082031 16S ribosomal RNA gene, partial sequence	KX858172	1428	GenBank ENA	1908263 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rodentibacter trehalosifermentans H1987082031	GCA_002000545	contig	GenBank ENA	1908263 tax ID	*
[Ref.: #66792]	Rodentibacter trehalosifermentans H1987082031	2791354947	draft	JGI IMG/M	1908263 tax ID	*

[Ref.: #43243]	GC-content	40.9 mol%
[Ref.: #42910]	GC-content	40.9 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #42910]

Culture collection no.

DSM 104075, CCUG 69668

[Ref.: #96608]

SI-ID 407757

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 )

#96608

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-ID407757.1 )

* These data were automatically processed and therefore are not curated

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