Muribaculum intestinale (DSM 100739, YL5, JCM 33112)

Name: Muribaculum intestinale (DSM 100739, YL5, JCM 33112)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158192

Type strain

Strain Designation YL5

Culture col. no. DSM 100739 YL5 JCM 33112

NCBI tax ID(s) 1796646

Special Collections DSMZ JCM Mouse DZIF

History DSMZ <- B. Stecher, Max von Pettenkofer-Inst., Munich; YL5 JCM <-- B. Abt; DSMZ, Germany; DSM 100739 (=YL5) <-- B. Stecher; Max von Pettenkofer-Inst., Germany.

Links

Muribaculum intestinale YL5 is a bacterium that was isolated from caecal content; C57BL/6J wildtype mouse.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407663

DSM 100739

@ref 20215

Last LPSN update 2026-05-29 08:43:54

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Muribaculaceae

Genus Muribaculum

Species Muribaculum intestinale

Full scientific name Muribaculum intestinale Lagkouvardos et al. 2016

BacDive ID	Other strains from **Muribaculum intestinale** (2)	Type strain
131536	M. intestinale YL27, DSM 28989, KCTC 15537 (type strain)
158193	M. intestinale YL7, DSM 100746, JCM 33113

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.775
125439	negative	95.647

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64791	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
64791	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		92.978
125439		99.908

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	glycogen metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	starch degradation	100	10 of 10
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	vitamin K metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	O-antigen biosynthesis	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	threonine metabolism	70	7 of 10
66794	Entner Doudoroff pathway	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	phenylalanine metabolism	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	purine metabolism	65.96	62 of 94
66794	degradation of sugar alcohols	62.5	10 of 16
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	methylglyoxal degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	d-xylose degradation	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	leucine metabolism	53.85	7 of 13
66794	histidine metabolism	51.72	15 of 29
66794	arginine metabolism	50	12 of 24
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	adipate degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	lipid metabolism	48.39	15 of 31
66794	lysine metabolism	47.62	20 of 42
66794	non-pathway related	47.37	18 of 38
66794	tryptophan metabolism	44.74	17 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	degradation of pentoses	39.29	11 of 28
66794	polyamine pathway	39.13	9 of 23
66794	urea cycle	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	nitrate assimilation	33.33	3 of 9
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	glutathione metabolism	28.57	4 of 14
66794	ascorbate metabolism	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	heme metabolism	21.43	3 of 14

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
64791	-	-	+	+	-	+	-	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-
64791	-	-	+	+	-	+	-	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64791	caecal content; C57BL/6J wildtype mouse	Zurich	Switzerland	CHE	Europe
67770	Mouse intestine	Munich	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence MG970329 (>99% sequence identity) for Muribaculum intestinale subclade from Microbeatlas

Aquatic Samples	230
Soil Samples	293
Animal Samples	37331
Plant Samples	154
Total Samples	38008

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64791	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
67770	ASM302484v1 assembly for Muribaculum intestinale DSM 100739	contig	GCA_003024845	2094240.3	1796646	58.03

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Muribaculum intestinale strain YL5 16S ribosomal RNA gene, partial sequence	MG970329	1530		1796646

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM302484v1 assembly for Muribaculum intestinale DSM 100739
NCBI: GCA_003024845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	73.28	no
125439	motility	BacteriaNetⓘ	yes	41.32	no
125439	gram_stain	BacteriaNetⓘ	negative	95.65	no
125439	spore_formation	BacteriaNetⓘ	no	99.91	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Muribaculaceae bacterium DSM 100739
PATRIC: 2094240.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.78	no
125438	anaerobic	anaerobicⓘ	yes	81.17	no
125438	spore-forming	spore-formingⓘ	no	92.98	no
125438	aerobic	aerobicⓘ	no	86.68	no
125438	thermophilic	thermophileⓘ	no	93.17	no
125438	flagellated	motile2+ⓘ	no	87.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.	Lagkouvardos I, Lesker TR, Hitch TCA, Galvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, Overmann J, Strowig T, Clavel T.	Microbiome	10.1186/s40168-019-0637-2	2019
	Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.	Hagihara M, Yamashita M, Ariyoshi T, Minemura A, Yoshida C, Higashi S, Oka K, Takahashi M, Ota A, Maenaka A, Iwasaki K, Hirai J, Shibata Y, Umemura T, Mori T, Kato H, Asai N, Mikamo H.	iScience	10.1016/j.isci.2025.113502	2025

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 )
#64791	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100739
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#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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Muribaculum intestinale (DSM 100739, YL5, JCM 33112)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003024845

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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