Name: Rodentibacter ratti F75
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140301

Type strain:

Species: Rodentibacter ratti

Strain Designation: F75

Culture col. no.: DSM 103977, CCUG 69665

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

NCBI tax ID(s): 1906745 (species)

SI-ID 400364

DSM 103977, CCUG 69665

Section

Rodentibacter ratti F75 is a microaerophile, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from chicken, respiratory tract.

colony-forming
Gram-negative
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 ratti**
	Full Scientific Name (LPSN)	Rodentibacter ratti 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

MacConkey agar

[Ref.: #43243]

Culture medium growth

[Ref.: #43243]

Culture medium

Bovine blood agar

[Ref.: #43243]

Culture medium growth

[Ref.: #42908]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #42908]

Culture medium growth

[Ref.: #42908]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42908]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #42908]			growth	37 °C
[Ref.: #63640]			growth	37 °C

[Ref.: #42908]	Temperature range	mesophilic
[Ref.: #63640]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63640]

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.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	amygdalin ChEBI	-	builds acid from
[Ref.: #43243]	arbutin ChEBI	-	builds acid from
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[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.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #43243]	D-mannitol ChEBI	-	builds acid from
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	D-mannose ChEBI	+	builds acid from
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #43243]	D-xylose ChEBI	+/-	builds acid from
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	dextrin ChEBI	+/-	builds acid from
[Ref.: #43243]	erythritol ChEBI	-	builds acid from
[Ref.: #43243]	esculin ChEBI	-	builds acid from
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43243]	galactarate ChEBI	+	builds acid from
[Ref.: #43243]	galactitol ChEBI	-	builds acid from
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43243]	gentiobiose ChEBI	-	builds acid from
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[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.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	L-fucose ChEBI	+/-	builds acid from
[Ref.: #43243]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #43243]	lactose ChEBI	+/-	builds acid from
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	malonate ChEBI	+	builds base from
[Ref.: #43243]	maltose ChEBI	+	builds acid from
[Ref.: #43243]	maltose ChEBI	-	builds gas from
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43243]	melezitose ChEBI	-	builds acid from
[Ref.: #43243]	melibiose ChEBI	-	builds acid from
[Ref.: #43243]	myo-inositol ChEBI	+/-	builds acid from
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[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.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #43243]	beta-galactosidase	+	3.2.1.23
[Ref.: #43243]	beta-glucosidase	-	3.2.1.21
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #43243]	beta-xylosidase	-
[Ref.: #43243]	catalase	+	1.11.1.6
[Ref.: #43243]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #43243]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[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
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #42908]	25457	+	+/-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

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

[Ref.: #42908]	Sample type/isolated from	chicken, respiratory tract
[Ref.: #42908]	Country	Denmark
[Ref.: #42908]	Country ISO 3 Code	DNK
[Ref.: #42908]	Continent	Europe

[Ref.: #43243]	Sample type/isolated from	chicken samples
[Ref.: #43243]	Geographic location (country and/or sea, region)	Denmark
[Ref.: #43243]	Country	Denmark
[Ref.: #43243]	Country ISO 3 Code	DNK
[Ref.: #43243]	Continent	Europe

[Ref.: #63640]	Sample type/isolated from	Chicken
[Ref.: #63640]	Country	Denmark
[Ref.: #63640]	Country ISO 3 Code	DNK
[Ref.: #63640]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Birds	#Chicken
#Host Body-Site	#Oral cavity and airways	#Airways

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY172726 (>99% sequence identity) for Rodentibacter ratti from Microbeatlas

Aquatic Samples	5
Soil Samples
Animal Samples	203
Plant Samples
Total Samples	208

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.: #42908]	Rodentibacter ratti strain F75 16S ribosomal RNA gene, partial sequence	AY172726	1451	ENA	1906745 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rodentibacter ratti F75	GCA_002000485	contig	GenBank	1906745 tax ID	*
[Ref.: #66792]	Rodentibacter ratti F75	2788500311	draft	JGI IMG/M	1906745 tax ID	*

[Ref.: #43243]	GC-content	40.2 mol%
[Ref.: #42908]	GC-content	40.2 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #42908]

Culture collection no.

DSM 103977, CCUG 69665

[Ref.: #96606]

SI-ID 400364

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 )

#42908

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103977

#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 )

#63640 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 69665

#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) .

#68369

Automatically annotated from API 20NE .

#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 .

#96606

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-ID400364.1 )

* These data were automatically processed and therefore are not curated

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