Name: Helicobacter muridarum ST1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6104

Type strain:

Species: Helicobacter muridarum

Strain Designation: ST1

Culture col. no.: DSM 22221, ATCC 49282, CCUG 29262, CIP 104248, LMG 13646, NCTC 12714

Strain history: CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- J.G. Fox, Cambridge, USA <- A. Lee, Sydney, Australia: strain ST1

NCBI tax ID(s): 216 (species)

SI-ID 7689

LMG 13646, ATCC 49282, CCUG 29262, LMG 12685, CIP 104248, NCTC 12714, DSM 22221

Section

Helicobacter muridarum ST1 is a microaerophile, mesophilic, Gram-negative animal pathogen that was isolated from intestinal mucosa of rats and mice.

Gram-negative
motile
rod-shaped
animal pathogen
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	*Epsilonproteobacteria*
	Order	*Campylobacterales*
	Family	*Helicobacteraceae*
	Genus	*Helicobacter*
	Species	**Helicobacter muridarum**
	Full Scientific Name (LPSN)	Helicobacter muridarum Lee et al. 1992

Information on morphological and physiological properties Morphology

[Ref.: #121194]	Gram stain	negative

[Ref.: #121194]	Cell shape	rod-shaped

[Ref.: #121194]	Motility	yes

[Ref.: #49563]

Incubation period

4-6 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16211]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #16211]

Culture medium growth

[Ref.: #16211]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16211]

Culture medium composition

expand / minimize

[Ref.: #41070]

Culture medium

MEDIUM 45 - for Columbia agar with sheep blood

[Ref.: #41070]

Culture medium growth

[Ref.: #41070]

Culture medium composition

expand / minimize

[Ref.: #121194]

Culture medium

CIP Medium 45

[Ref.: #121194]

Culture medium growth

[Ref.: #121194]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #16211]		growth	37 °C
[Ref.: #41070]		growth	37 °C
[Ref.: #121194]		growth	30-37 °C
[Ref.: #121194]	no	growth	25 °C
[Ref.: #121194]	no	growth	41 °C

[Ref.: #16211]	Temperature range	mesophilic
[Ref.: #41070]	Temperature range	mesophilic
[Ref.: #121194]	Temperature range	mesophilic
[Ref.: #121194]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16211]	Oxygen tolerance	microaerophile
[Ref.: #49563]	Oxygen tolerance	microaerophile

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68373]	acetate ChEBI	-	assimilation	* from API CAM
[Ref.: #68373]	D-glucose ChEBI	-	assimilation	* from API CAM
[Ref.: #121194]	hippurate ChEBI	-	hydrolysis
[Ref.: #68373]	hippurate ChEBI	-	hydrolysis	* from API CAM
[Ref.: #68373]	malate ChEBI	-	assimilation	* from API CAM
[Ref.: #121194]	nitrate ChEBI	-	reduction
[Ref.: #68373]	nitrate ChEBI	-	reduction	* from API CAM
[Ref.: #121194]	nitrite ChEBI	-	reduction
[Ref.: #68373]	propionate ChEBI	-	assimilation	* from API CAM
[Ref.: #68373]	triphenyltetrazolium chloride ChEBI	+	reduction	* from API CAM
[Ref.: #68373]	urea ChEBI	+	hydrolysis	* from API CAM
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #68373]	cefazolin ChEBI	yes	224	µg	* from API CAM
[Ref.: #68373]	erythromycin ChEBI	yes	14	µg	* from API CAM
[Ref.: #68373]	nalidixic acid ChEBI	yes	84	µg	* from API CAM

	Metabolite production	Metabolite	Production
[Ref.: #121194]		indole ChEBI	no
[Ref.: #68373]		hydrogen sulfide ChEBI	no	* from API CAM

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68373]	alkaline phosphatase	+	3.1.3.1	* from API CAM
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121194]	catalase	+	1.11.1.6
[Ref.: #68373]	catalase	+	1.11.1.6	* from API CAM
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68373]	gamma-glutamyltransferase	+	2.3.2.2	* from API CAM
[Ref.: #68373]	L-aspartate arylamidase	-	3.4.11.21	* from API CAM
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #121194]	oxidase	+
[Ref.: #68373]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API CAM
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121194]	urease	+	3.5.1.5
[Ref.: #68373]	urease	+	3.5.1.5	* from API CAM
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® CAM:

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

	API ID	Urease/urea hydrolysisURE	Reduction of nitrateNIT	EsteraseEST	Hippuric acidHIP	gamma-Glutamyl transferaseGGT	Reduction of Triphenyl tetrazolium chlorideTTC	Pyrrolidonyl arylamidasePYRA	L-arginine arylamidaseArgA	L-aspartic acid arylamidaseAspA	Alkaline phosphatasePAL	H2S productionH2S	Assimilation of D-glucoseGLU	Assimilation of succinateSUT	Growth inhibitionNAL	Growth inhibitionCFZ	Assimilation of acetateACE	Assimilation of propionic acidPROP	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Erythromycin resistance (+) sensitivity (-)ERO	CatalaseCAT
[Ref.: #16211]	3944	+	-	-	-	+	+	-	+/-	-	+	-	-	+	-	-	-	-	-	+/-	-	+
[Ref.: #16211]	3782	+	-	+/-	-	+	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	+

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121194]	7858	-	-	+	+	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	acetoin degradation	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]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	heme metabolism	50	7 of 14
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	oxidative phosphorylation	49.45	45 of 91
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	glycolysis	41.18	7 of 17
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[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.: #16211]	Sample type/isolated from	intestinal mucosa of rats and mice

[Ref.: #49563]	Sample type/isolated from	Rat ileum

[Ref.: #121194]	Sample type/isolated from	Animal, Rat, ileum
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence M80205 (>99% sequence identity) for Helicobacter muridarum subclade from Microbeatlas

Aquatic Samples	20
Soil Samples	10
Animal Samples	918
Plant Samples	5
Total Samples	953

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

[Ref.: #16211]	Pathogenicity (animal)	yes
[Ref.: #16211]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #121194]	Biosafety level	2	Risk group (French classification)

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.: #16211]	Helicobacter muridarum strain ST1 16S ribosomal RNA gene, complete sequence	M80205	1478	ENA	216 tax ID
[Ref.: #20218]	Helicobacter muridarum 16S ribosomal RNA gene, partial sequence	AF302104	1440	ENA	216 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Helicobacter muridarum NCTC12714	GCA_900450885	contig	GenBank	216 tax ID	*
[Ref.: #66792]	Helicobacter muridarum ST1	GCA_000765805	contig	GenBank	216 tax ID	*
[Ref.: #66792]	Helicobacter muridarum strain NCTC12714	216.15	wgs	PATRIC	216 tax ID	*
[Ref.: #66792]	Helicobacter muridarum ST1	2663763499	draft	JGI IMG/M	216 tax ID	*
[Ref.: #66792]	Helicobacter muridarum NCTC 12714	2808606664	draft	JGI IMG/M	216 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Helicobacter muridarum strain NCTC12714 PATRIC: 216.15
[Ref.: #69480]	motile	yes	90.211	no
[Ref.: #69480]	gram-positive	no	98.953	no
[Ref.: #69480]	anaerobic	no	65.941	no
[Ref.: #69480]	aerobic	no	96.264	yes
[Ref.: #69480]	halophile	no	79.661	no
[Ref.: #69480]	spore-forming	no	95.996	no
[Ref.: #69480]	glucose-util	no	87.625	yes
[Ref.: #69480]	flagellated	yes	57.929	no
[Ref.: #69480]	thermophile	no	76.546	yes
[Ref.: #69480]	glucose-ferment	no	82.891	no

Availability in culture collections External links

[Ref.: #16211]

Culture collection no.

DSM 22221, ATCC 49282, CCUG 29262, CIP 104248, LMG 13646, NCTC 12714

[Ref.: #75592]

SI-ID 7689

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Helicobacter muridarum sp. nov., a microaerophilic helical bacterium with a novel ultrastructure isolated from the intestinal mucosa of rodents.	Lee A, Phillips MW, O'Rourke JL, Paster BJ, Dewhirst FE, Fraser GJ, Fox JG, Sly LI, Romaniuk PJ, Trust TJ, et al.	Int J Syst Bacteriol	10.1099/00207713-42-1-27	1992	*

References

#16211

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22221

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#41070 ; Curators of the CIP;
#49563 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 29262

#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 )

#68373

Automatically annotated from API CAM .

#68382

Automatically annotated from API zym .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#75592

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-ID7689.1 )

#121194 Collection of Institut Pasteur ; Curators of the CIP; CIP 104248
* These data were automatically processed and therefore are not curated

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Helicobacter muridarum strain NCTC12714

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