Rodentibacter caecimuris (DSM 28627, KCTC 52216, AA-424-CC-1)

Name: Rodentibacter caecimuris (DSM 28627, KCTC 52216, AA-424-CC-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131523

Type strain

Strain Designation AA-424-CC-1

Culture col. no. DSM 28627 KCTC 52216 AA-424-CC-1

NCBI tax ID(s) 1796644

Special Collections DSMZ KCTC Mouse DZIF

History DSMZ <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; AA-424-CC-1(A) KCTC <- Barbel Fosel, DSM

Links

Rodentibacter caecimuris AA-424-CC-1 is an aerobe bacterium that was isolated from caecal content; TNF^deltaARE/+ C57BL/6 mouse.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402999

KCTC 52216,DSM 28627

@ref 20215

Last LPSN update 2026-05-29 08:37:38

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pasteurellales

Family Pasteurellaceae

Genus Rodentibacter

Species Rodentibacter caecimuris

Full scientific name Rodentibacter caecimuris (Lagkouvardos et al. 2016) Li 2024

Synonyms (2)

Pasteurella caecimuris
Rodentibacter heylii

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		93.988
125438		97.415	negative

Colony morphology

22750

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
22750	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)	Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
22750	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
22750	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)
22750	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	facultative anaerobe	90.537

Spore formation

@ref	Spore formation	Confidence
125438		91.497
125439		99.015

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68381	40585 ChEBI	alpha-cyclodextrin	-	builds acid from	from API rID32STR
68381	29016 ChEBI	arginine	-	hydrolysis	from API rID32STR
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68381	18333 ChEBI	D-arabitol	-	builds acid from	from API rID32STR
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	+	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68381	16899 ChEBI	D-mannitol	-	builds acid from	from API rID32STR
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68381	16443 ChEBI	D-tagatose	-	builds acid from	from API rID32STR
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68381	28087 ChEBI	glycogen	-	builds acid from	from API rID32STR
68381	606565 ChEBI	hippurate	-	hydrolysis	from API rID32STR
68381	30849 ChEBI	L-arabinose	-	builds acid from	from API rID32STR
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68381	17306 ChEBI	maltose	+	builds acid from	from API rID32STR
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68381	6731 ChEBI	melezitose	-	builds acid from	from API rID32STR
68381	320055 ChEBI	methyl beta-D-glucopyranoside	-	builds acid from	from API rID32STR
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68381	27941 ChEBI	pullulan	-	builds acid from	from API rID32STR
68381	30911 ChEBI	sorbitol	-	builds acid from	from API rID32STR
68381	27082 ChEBI	trehalose	+	builds acid from	from API rID32STR
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
68381	16199 ChEBI	urea	+	hydrolysis	from API rID32STR

Enzymes

@ref	Value	Activity	Ec
68381	Alanyl-Phenylalanyl-Proline arylamidase	-		from API rID32STR
68381	alkaline phosphatase	+	3.1.3.1	from API rID32STR
68381	alpha-galactosidase	+	3.2.1.22	from API rID32STR
68381	arginine dihydrolase	-	3.5.3.6	from API rID32STR
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68381	beta-galactosidase	+	3.2.1.23	from API rID32STR
68381	beta-glucosidase	-	3.2.1.21	from API rID32STR
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68381	beta-glucuronidase	-	3.2.1.31	from API rID32STR
68381	beta-mannosidase	-	3.2.1.25	from API rID32STR
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68381	glycyl tryptophan arylamidase	-		from API rID32STR
68381	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32STR
68381	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32STR
68381	urease	+	3.5.1.5	from API rID32STR
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
22750	+	+/-	+	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

API rID32STR

@ref	ADH (Arg)	beta GLU	beta GAR	beta GUR	alpha GAL	PAL	RIB	MAN	SOR	LAC	TRE	RAF	SAC	LARA	DARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	HIP	GLYG	PUL	MAL	MEL	MLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	TAG	beta MAN	URE
22750	-	-	+	-	+	+	+/-	-	-	+/-	+	+/-	+/-	-	-	-	+/-	-	+	-	-	-	-	-	-	+	+/-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22750	caecal content; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe
67771	From Mouse intestine	Freising-Weihenstephan	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364783 (>99% sequence identity) for Rodentibacter heylii from Microbeatlas

Aquatic Samples	200
Soil Samples	106
Animal Samples	7753
Plant Samples	52
Total Samples	8111

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2462204v1 assembly for Rodentibacter caecimuris DSM 28627	contig	GCA_024622045	1796644.7	8111517909	1796644	70.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22750	Rodentibacter caecimuris strain AA-424-CC-1 16S ribosomal RNA gene, partial sequence	KR364783	1423		1796644

GC content

@ref	GC-content (mol%)	Method
22750	40.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2462204v1 assembly for Rodentibacter caecimuris DSM 28627
NCBI: GCA_024622045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.54	no
125439	gram_stain	BacteriaNetⓘ	negative	53.71	no
125439	motility	BacteriaNetⓘ	no	80.01	no
125439	spore_formation	BacteriaNetⓘ	no	99.02	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pasteurella caecimuris DSM 28627
NCBI: GCA_024622045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.42	no
125438	anaerobic	anaerobicⓘ	no	93.97	yes
125438	aerobic	aerobicⓘ	no	80.24	no
125438	spore-forming	spore-formingⓘ	no	91.50	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	93.99	no

Literature

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 )
#22750	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28627
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#68381	Automatically annotated from API rID32STR .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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