Rodentibacter ratti (DSM 103977, CCUG 69665, F75)

Name: Rodentibacter ratti (DSM 103977, CCUG 69665, F75)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140301

Type strain

Strain Designation F75

Culture col. no. DSM 103977 CCUG 69665 F75

NCBI tax ID(s) 1906745

Special Collections DSMZ CCUG Literature strains

History DSMZ <- H. Christensen, Veterinary Disease Biology, University of Copenhagen, Denmark <- M. Bisgaard, Institute of Avian Diseases, Langaa, Denmark

Links

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

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

Name and taxonomic classification

SI-ID 400364

DSM 103977,CCUG 69665

@ref 20215

Last LPSN update 2026-05-29 08:39:41

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Rodentibacter

Species Rodentibacter ratti

Full scientific name Rodentibacter ratti Adhikary et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
43243	negative
125439	negative		90.287

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Colony size	Colony shape	Incubation period	Medium used
43243	gamma	0	1-2 mm	circular	1 day	Bovine blood agar

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43243	MacConkey agar
43243	Bovine blood agar
42908	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
42908	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42908	positive	growth	37
63640	positive	growth	37

Physiology and metabolism

Oxygen tolerance

63640

Oxygen tolerancemicroaerophile

Spore formation

@ref	Spore formation	Confidence
125439		99.806

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		(+)-D-glycogen	-	builds acid from
43243	48095 ChEBI	(-)-D-fructose	+	builds acid from
43243	48095 ChEBI	(-)-D-fructose	-	builds gas from
43243	65328 ChEBI	(-)-L-xylose	-	builds acid from
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
43243	27613 ChEBI	amygdalin	-	builds acid from
43243	18305 ChEBI	arbutin	-	builds acid from
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
43243	17057 ChEBI	cellobiose	-	builds acid from
43243	17108 ChEBI	D-arabinose	+	builds acid from
43243	12936 ChEBI	D-galactose	+	builds acid from
43243	12936 ChEBI	D-galactose	-	builds gas from
43243	17634 ChEBI	D-glucose	+	builds acid from
43243	17634 ChEBI	D-glucose	-	builds gas from
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
43243	16899 ChEBI	D-mannitol	-	builds acid from
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
43243	16024 ChEBI	D-mannose	+	builds acid from
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
43243	16988 ChEBI	D-ribose	+	builds acid from
43243	17924 ChEBI	D-sorbitol	+	builds acid from
43243	65327 ChEBI	D-xylose	+/-	builds acid from
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
43243	23652 ChEBI	dextrin	+/-	builds acid from
43243	17113 ChEBI	erythritol	-	builds acid from
43243	4853 ChEBI	esculin	-	builds acid from
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
43243	16537 ChEBI	galactarate	+	builds acid from
43243	16813 ChEBI	galactitol	-	builds acid from
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
43243	28066 ChEBI	gentiobiose	-	builds acid from
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
43243	17234 ChEBI	glucose	-	fermentation
43243	17754 ChEBI	glycerol	+	builds acid from
43243	15443 ChEBI	inulin	-	builds acid from
43243	30849 ChEBI	L-arabinose	+	builds acid from
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
43243	18287 ChEBI	L-fucose	+/-	builds acid from
43243	62345 ChEBI	L-rhamnose	-	builds acid from
43243	17266 ChEBI	L-sorbose	-	builds acid from
43243	17716 ChEBI	lactose	+/-	builds acid from
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
43243	15792 ChEBI	malonate	+	builds base from
43243	17306 ChEBI	maltose	+	builds acid from
43243	17306 ChEBI	maltose	-	builds gas from
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
43243	6731 ChEBI	melezitose	-	builds acid from
43243	28053 ChEBI	melibiose	-	builds acid from
43243	17268 ChEBI	myo-inositol	+/-	builds acid from
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
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
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
43243	beta-galactosidase	+	3.2.1.23
43243	beta-glucosidase	-	3.2.1.21
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
43243	beta-xylosidase	-
43243	catalase	+	1.11.1.6
43243	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
43243	gelatinase	-
68369	gelatinase	-		from API 20NE
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
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
42908	+	+/-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	#Chicken
#Host Body-Site	#Oral cavity and airways	#Airways

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
42908	chicken, respiratory tract		Denmark	DNK	Europe
43243	chicken samples	Denmark	Denmark	DNK	Europe
63640	Chicken		Denmark	DNK	Europe

Taxonmaps

69479

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

Aquatic Samples	5
Soil Samples	0
Animal Samples	203
Plant Samples	0
Total Samples	208

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM200048v1 assembly for Rodentibacter ratti F75	contig	GCA_002000485	2788500311	1906745	74.71

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42908	Rodentibacter ratti strain F75 16S ribosomal RNA gene, partial sequence	AY172726	1451		1906745

GC content

@ref	GC-content (mol%)	Method
43243	40.2
42908	40.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM200048v1 assembly for Rodentibacter ratti F75
NCBI: GCA_002000485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.84	no
125439	motility	BacteriaNetⓘ	no	76.83	no
125439	gram_stain	BacteriaNetⓘ	negative	90.29	no
125439	spore_formation	BacteriaNetⓘ	no	99.81	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 )
#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 .
#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 ratti (DSM 103977, CCUG 69665, F75)

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

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002000485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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