Name: Intestinimonas butyriciproducens SRB-521-5-l
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24772

Type strain:

Species: Intestinimonas butyriciproducens

Strain Designation: SRB-521-5-l

Culture col. no.: DSM 26588, CCUG 63529, KCTC 15744, JCM 32124

Strain history: <- DSM <- T Clavel, TU Munich, Freising-Weihenstephan, Germany, SRB-521-5-l <- K Klaring(2012)

NCBI tax ID(s): 1297617 (species)

SI-ID 404444

DSM 26588, CCUG 63529

Other strains from Intestinimonas butyriciproducens

I. butyriciproducens Sanger_35, DSM 102175
I. butyriciproducens AP4, DSM 26097
I. butyriciproducens 27-5-10, DSM 104946
I. butyriciproducens afr 2-1.1, AF211, DSM 26243

Section

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

Gram-positive
rod-shaped
spore-forming
anaerobe
mesophilic
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Oscillospiraceae*
	Genus	*Intestinimonas*
	Species	**Intestinimonas butyriciproducens**
	Full Scientific Name (LPSN)	Intestinimonas butyriciproducens Kläring et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31076]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31076]	Cell length	3.5 µm

[Ref.: #31076]	Cell width	0.5 µm

[Ref.: #31076]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31076]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #62991]

Incubation period

2 days

[Ref.: #31076]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21298]

Culture medium

WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)

[Ref.: #21298]

Culture medium growth

[Ref.: #21298]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21298]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21298]	growth	37 °C
[Ref.: #31076]	growth	25-45 °C
[Ref.: #62991]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #21298]	Temperature range	mesophilic
[Ref.: #62991]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21298]	Oxygen tolerance	anaerobe
[Ref.: #31076]	Oxygen tolerance	anaerobe
[Ref.: #62991]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #67771]	Type of spore	spore
[Ref.: #67771]	Ability of spore formation	yes
[Ref.: #31076]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.104

[Ref.: #21298]

Name of produced compound

butyrate

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31076]	dextrin ChEBI	+	carbon source
[Ref.: #31076]	galactose ChEBI	+	carbon source
[Ref.: #31076]	glucose ChEBI	+	carbon source
[Ref.: #31076]	inosine ChEBI	+	carbon source
[Ref.: #31076]	lactate ChEBI	+	carbon source
[Ref.: #31076]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #31076]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31076]	pyruvate ChEBI	+	carbon source
[Ref.: #31076]	serine ChEBI	+	carbon source
[Ref.: #31076]	sorbitol ChEBI	+	carbon source
[Ref.: #31076]	threonine ChEBI	+	carbon source
[Ref.: #31076]	thymidine ChEBI	+	carbon source
[Ref.: #31076]	uridine ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		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.: #21298]	Sample type/isolated from	caecal content of a 17-week-old female heterozygous TNF ^deltaARE mouse
[Ref.: #21298]	Country	Germany
[Ref.: #21298]	Country ISO 3 Code	DEU
[Ref.: #21298]	Continent	Europe

[Ref.: #62991]	Sample type/isolated from	Mouse caecum
[Ref.: #62991]	Sampling date	2012-08-01
[Ref.: #62991]	Geographic location (country and/or sea, region)	Weihenstephan,Freising
[Ref.: #62991]	Country	Germany
[Ref.: #62991]	Country ISO 3 Code	DEU
[Ref.: #62991]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Cecal content of a TNF^deltaARE mouse

[Ref.: #67771]	Sample type/isolated from	From caecal content of a 17-week-old female heterozygous TNF deltaARE mouse
[Ref.: #67771]	Country	Germany
[Ref.: #67771]	Country ISO 3 Code	DEU
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #21298]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #21298]	Intestinimonas butyriciproducens strain SRB-521-5-I 16S ribosomal RNA gene, partial sequence	KC311367	1475	ENA	1297617 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Intestinimonas butyriciproducens DSM 26588	GCA_003096335	scaffold	GenBank	1297617 tax ID	*
[Ref.: #66792]	Intestinimonas butyriciproducens strain DSM 26588	1297617.27	wgs	PATRIC	1297617 tax ID	*
[Ref.: #66792]	Intestinimonas butyriciproducens strain SRB-521-5-I	1297617.82	complete	PATRIC	1297617 tax ID	*
[Ref.: #66792]	Intestinimonas butyriciproducens DSM 26588	2756170247	draft	JGI IMG/M	1297617 tax ID	*
[Ref.: #66792]	Intestinimonas butyriciproducens DSM 26588	GCA_024622565	contig	GenBank	1297617 tax ID	*

[Ref.: #21298]	GC-content	58.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31076]	GC-content	58.4 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Intestinimonas butyriciproducens strain SRB-521-5-I PATRIC: 1297617.82
[Ref.: #69481]	spore-forming	yes	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Intestinimonas butyriciproducens strain SRB-521-5-I PATRIC: 1297617.82
[Ref.: #69480]	motile	no	89.97	yes
[Ref.: #69480]	gram-positive	yes	68.141	no
[Ref.: #69480]	anaerobic	yes	99.206	yes
[Ref.: #69480]	aerobic	no	96.322	yes
[Ref.: #69480]	halophile	no	92.032	no
[Ref.: #69480]	spore-forming	yes	58.14	yes
[Ref.: #69480]	thermophile	no	96.616	no
[Ref.: #69480]	glucose-util	yes	82.875	no
[Ref.: #69480]	flagellated	no	95.645	yes
[Ref.: #69480]	glucose-ferment	yes	53.703	no

Availability in culture collections External links

[Ref.: #21298]

Culture collection no.

DSM 26588, CCUG 63529, KCTC 15744, JCM 32124

[Ref.: #88598]

SI-ID 404444

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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 (see below)

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88598

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-ID404444.1 )

#27405

IJSEM 4606 2013 ( DOI 10.1099/ijs.0.051441-0 , PubMed 23918795 )

* These data were automatically processed and therefore are not curated

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Intestinimonas butyriciproducens strain SRB-521-5-I

Intestinimonas butyriciproducens strain SRB-521-5-I

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