Intestinimonas butyriciproducens (DSM 26588, CCUG 63529, KCTC 15744)

Name: Intestinimonas butyriciproducens (DSM 26588, CCUG 63529, KCTC 15744)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24772

Type strain

Strain Designation SRB-521-5-l

Culture col. no. DSM 26588 CCUG 63529 KCTC 15744 SRB-521-5-l JCM 32124

NCBI tax ID(s) 1297617

Special Collections DSMZ CCUG JCM KCTC Mouse Literature strains

History DSMZ <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; SRB-521-5-l <- K. Kläring {2012} JCM <-- CCUG 63529 <-- T. Clavel; Tech. Univ. of Munich, Germany; SRB-521-5-I. KCTC <- DSM <- T Clavel, TU Munich, Freising-Weihenstephan, Germany, SRB-521-5-l <- K Klaring(2012)

Links

Intestinimonas butyriciproducens SRB-521-5-l is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from caecal content of a 17-week-old female heterozygous TNF ^deltaARE mouse.

spore-forming Gram-positive rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404444

KCTC 15744,DSM 26588,CCUG 63529

@ref 20215

Last LPSN update 2026-05-29 08:30:41

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Intestinimonas

Species Intestinimonas butyriciproducens

Full scientific name Intestinimonas butyriciproducens Kläring et al. 2013

BacDive ID	Other strains from **Intestinimonas butyriciproducens** (4)	Type strain
132161	I. butyriciproducens Sanger_35, DSM 102175
140057	I. butyriciproducens AP4, DSM 26097
159587	I. butyriciproducens 27-5-10, DSM 104946
169637	I. butyriciproducens afr 2-1.1, AF211, DSM 26243

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31076	positive	3.5 µm	0.5 µm	rod-shaped
67771				rod-shaped
67771	positive

Colony morphology

62991

Incubation period2 days

Pigmentation

31076

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21298	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21298	positive	growth	37
31076	positive	growth	25-45
62991	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21298	anaerobe
31076	anaerobe
62991	anaerobe
67771	anaerobe
125439	obligate anaerobe	99.943

Spore formation

@ref	Type of spore	Spore formation
31076
67771	spore

Compound production

21298

Compoundbutyrate

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31076	23652 ChEBI	dextrin	+	carbon source
31076	28260 ChEBI	galactose	+	carbon source
31076	17234 ChEBI	glucose	+	carbon source
31076	17596 ChEBI	inosine	+	carbon source
31076	24996 ChEBI	lactate	+	carbon source
31076	51850 ChEBI	methyl pyruvate	+	carbon source
31076	506227 ChEBI	N-acetylglucosamine	+	carbon source
31076	15361 ChEBI	pyruvate	+	carbon source
31076	17822 ChEBI	serine	+	carbon source
31076	30911 ChEBI	sorbitol	+	carbon source
31076	26986 ChEBI	threonine	+	carbon source
31076	17748 ChEBI	thymidine	+	carbon source
31076	16704 ChEBI	uridine	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	aspartate and asparagine metabolism	100	9 of 9
66794	gluconeogenesis	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	isoleucine metabolism	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	propanol degradation	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	purine metabolism	84.04	79 of 94
66794	pyrimidine metabolism	82.22	37 of 45
66794	glycine betaine biosynthesis	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	cellulose degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	methionine metabolism	73.08	19 of 26
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	alanine metabolism	68.97	20 of 29
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	methane metabolism	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	NAD metabolism	61.11	11 of 18
66794	tryptophan metabolism	60.53	23 of 38
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	arginine metabolism	58.33	14 of 24
66794	oxidative phosphorylation	58.24	53 of 91
66794	citric acid cycle	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	degradation of hexoses	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	non-pathway related	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	pentose phosphate pathway	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	vitamin B1 metabolism	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	tyrosine metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phenylpropanoid biosynthesis	23.08	3 of 13

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	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
21298	caecal content of a 17-week-old female heterozygous TNF ^deltaARE mouse			Germany	DEU	Europe
62991	Mouse caecum	2012-08-01	Weihenstephan,Freising	Germany	DEU	Europe
67770	Cecal content of a TNF^deltaARE mouse
67771	From caecal content of a 17-week-old female heterozygous TNF deltaARE mouse			Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KC311367 (>99% sequence identity) for Intestinimonas butyriciproducens subclade from Microbeatlas

Aquatic Samples	463
Soil Samples	249
Animal Samples	72859
Plant Samples	120
Total Samples	73691

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21298	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM415495v1 assembly for Intestinimonas butyriciproducens SRB-521-5-I	complete	GCA_004154955	1297617.82	2837229570	1297617	97.83
66792	ASM2462256v1 assembly for Intestinimonas butyriciproducens DSM 26588	contig	GCA_024622565	1297617.140	8065342644	1297617	73.86
66792	ASM309633v1 assembly for Intestinimonas butyriciproducens DSM 26588	scaffold	GCA_003096335	1297617.27	2756170247	1297617	69.16

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21298	Intestinimonas butyriciproducens strain SRB-521-5-I 16S ribosomal RNA gene, partial sequence	KC311367	1475		1297617

GC content

@ref	GC-content (mol%)	Method
21298	58.4	high performance liquid chromatography (HPLC)
31076	58.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM415495v1 assembly for Intestinimonas butyriciproducens SRB-521-5-I
NCBI: GCA_004154955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	68.74	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.94	no
125439	motility	BacteriaNetⓘ	no	64.67	no
125439	spore_formation	BacteriaNetⓘ	no	85.19	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Intestinimonas butyriciproducens strain SRB-521-5-I
PATRIC: 1297617.82

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.98	yes
125438	anaerobic	anaerobicⓘ	yes	89.61	no
125438	spore-forming	spore-formingⓘ	no	53.15	no
125438	aerobic	aerobicⓘ	no	93.86	yes
125438	thermophilic	thermophileⓘ	no	89.38	no
125438	flagellated	motile2+ⓘ	no	82.21	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.	Jin X, Cheng AG, Chanin RB, Yu FB, Dimas A, Jasper M, Weakley A, Yan J, Bhatt AS, Pollard KS.	Microbiome	10.1186/s40168-025-02052-7	2025
Metabolism	Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary heterocyclic amine biotransformation.	Zhang J, Lacroix C, Wortmann E, Ruscheweyh HJ, Sunagawa S, Sturla SJ, Schwab C.	BMC Microbiol	10.1186/s12866-019-1483-x	2019
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Phylogeny	Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.	Klaring K, Hanske L, Bui N, Charrier C, Blaut M, Haller D, Plugge CM, Clavel T	Int J Syst Evol Microbiol	10.1099/ijs.0.051441-0	2013

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 )
#21298	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26588
#27405	IJSEM 4606 2013 ( DOI 10.1099/ijs.0.051441-0 , PubMed 23918795 )
#31076	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27405
#62991	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 63529
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 )

Content

About us

Intestinimonas butyriciproducens (DSM 26588, CCUG 63529, KCTC 15744)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004154955

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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