Lactobacillus rodentium (DSM 24759, CCM 7945, KCTC 21049)

Name: Lactobacillus rodentium (DSM 24759, CCM 7945, KCTC 21049)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24141

Type strain

Strain Designation MYMRS/TLU1

Culture col. no. DSM 24759 CCM 7945 KCTC 21049 MYMRS/TLU1

NCBI tax ID(s) 947835

Special Collections DSMZ KCTC Mouse

History DSMZ <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; MYMRS-TLU1 KCTC <- DSM <- J Killer, Inst Animal Physiol and Genetics, Czech Acad Sci, Prague, MYMRS-TLU1

Links

Lactobacillus rodentium MYMRS/TLU1 is a microaerophile, rod-shaped bacterium that was isolated from colon of a wild mouse Mus musculus).

rod-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397556

LMG 31156,KCTC 21049,DSM 24759

@ref 20215

Last LPSN update 2026-05-29 08:30:33

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Lactobacillus

Species Lactobacillus rodentium

Full scientific name Lactobacillus rodentium Killer et al. 2014

Morphology

Cell morphology

@ref	Confidence	Cell shape	Gram stain
67771		rod-shaped
67771			positive
125438	93
125438	94.304		positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21001	MRS MEDIUM (DSMZ Medium 11)		Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21001	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21001	microaerophile
67771	anaerobe
125439	facultative anaerobe	90.571

Spore formation

@ref	Spore formation	Confidence
125438		90.463

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	acetoin degradation	100	3 of 3
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	sulfopterin metabolism	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	photosynthesis	64.29	9 of 14
66794	ketogluconate metabolism	62.5	5 of 8
66794	factor 420 biosynthesis	60	3 of 5
66794	starch degradation	60	6 of 10
66794	propanol degradation	57.14	4 of 7
66794	NAD metabolism	55.56	10 of 18
66794	pentose phosphate pathway	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	vitamin B1 metabolism	53.85	7 of 13
66794	oxidative phosphorylation	51.65	47 of 91
66794	gluconeogenesis	50	4 of 8
66794	suberin monomers biosynthesis	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	coenzyme A metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	flavin biosynthesis	46.67	7 of 15
66794	phenylalanine metabolism	46.15	6 of 13
66794	d-mannose degradation	44.44	4 of 9
66794	valine metabolism	44.44	4 of 9
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	serine metabolism	44.44	4 of 9
66794	mevalonate metabolism	42.86	3 of 7
66794	non-pathway related	42.11	16 of 38
66794	lipid metabolism	41.94	13 of 31
66794	purine metabolism	41.49	39 of 94
66794	methylglyoxal degradation	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	glutamate and glutamine metabolism	39.29	11 of 28
66794	methionine metabolism	38.46	10 of 26
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	C4 and CAM-carbon fixation	37.5	3 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	isoleucine metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	degradation of pentoses	35.71	10 of 28
66794	pyrimidine metabolism	35.56	16 of 45
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	nitrate assimilation	33.33	3 of 9
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of sugar alcohols	31.25	5 of 16
66794	propionate fermentation	30	3 of 10
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	alanine metabolism	27.59	8 of 29
66794	vitamin B6 metabolism	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	arginine metabolism	25	6 of 24
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	tryptophan metabolism	23.68	9 of 38
66794	leucine metabolism	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	glutathione metabolism	21.43	3 of 14
66794	lysine metabolism	21.43	9 of 42
66794	citric acid cycle	21.43	3 of 14

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
21001	-	-	-	-	-	+/-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	+	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
21001	colon of a wild mouse Mus musculus)	Mus musculus	Central Bohemia, Jesetice	Czech Republic	CZE	Europe
67771	From colon of a wild mouse, `Mus musculus`	Mus musculus	Central Bohemia, Jesetice	Czech Republic	CZE	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21001	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2462242v1 assembly for Lactobacillus rodentium DSM 24759	contig	GCA_024622425	947835.14	8114430327	947835	73.3
66792	ASM342366v1 assembly for Lactobacillus rodentium DSM 24759	scaffold	GCA_003423665	947835.3	2916469829	947835	67.73
124043	ASM4243271v1 assembly for Lactobacillus rodentium CCM 7945	scaffold	GCA_042432715			947835	67.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21001	Lactobacillus rodentium strain MYMRS/TLU1 16S ribosomal RNA gene, partial sequence	HQ851022	1436		947835
124043	Lactobacillus rodentium strain MYMRS/TLU1 16S ribosomal RNA gene, partial sequence 16S-23S ribosomal RNA intergenic spacer, complete sequence and 23S ribosomal RNA gene, partial sequence.	JQ363710	531		947835

GC content

@ref	GC-content (mol%)	Method
21001	43.7	high performance liquid chromatography (HPLC)
67771	43.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2462242v1 assembly for Lactobacillus rodentium DSM 24759
NCBI: GCA_024622425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.57	no
125439	gram_stain	BacteriaNetⓘ	positive	76.91	no
125439	spore_formation	BacteriaNetⓘ	yes	35.87	no
125439	motility	BacteriaNetⓘ	no	74.49	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus rodentium DSM 24759
NCBI: GCA_003423665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.30	yes
125438	anaerobic	anaerobicⓘ	no	69.46	no
125438	aerobic	aerobicⓘ	no	95.88	yes
125438	spore-forming	spore-formingⓘ	no	90.46	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	93.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents.	Killer J, Havlik J, Vlkova E, Rada V, Pechar R, Benada O, Kopecny J, Kofronova O, Sechovcova H	Int J Syst Evol Microbiol	10.1099/ijs.0.054924-0	2014

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 )
#21001	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24759
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68371	Automatically annotated from API 50CH acid .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Lactobacillus rodentium (DSM 24759, CCM 7945, KCTC 21049)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Pathway annotation

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_024622425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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