Name: Gordonibacter urolithinfaciens DSM 27213
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24792

Type strain:

Species: Gordonibacter urolithinfaciens

Culture col. no.: DSM 27213, CCUG 64261, KCTC 15440, CEBAS 1/15P, CEBAS 1/15

Strain history: <- CCUG <- MV Selma, CEBAS-CSIC, Espinardo, Murcia, Spain <- D Beltran, MV Selma, FA Tomas-Barberan

NCBI tax ID(s): 1335613 (species)

SI-ID 402943

DSM 27213, CCUG 64261

Other strains from Gordonibacter urolithinfaciens

G. urolithinfaciens JCM 16058, KCTC 15204

Section

Gordonibacter urolithinfaciens DSM 27213 is an anaerobe, mesophilic, motile bacterium that was isolated from human faeces of a healthy volunteer.

motile
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	*Actinomycetota*
	Class	*Coriobacteriia*
	Order	*Eggerthellales*
	Family	*Eggerthellaceae*
	Genus	*Gordonibacter*
	Species	**Gordonibacter urolithinfaciens**
	Full Scientific Name (LPSN)	Gordonibacter urolithinfaciens Selma et al. 2014

Synonym

Gordonibacter faecihominis

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	positive

[Ref.: #67771]	Motility	yes

[Ref.: #63109]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21196]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #21196]

Culture medium growth

[Ref.: #21196]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21196]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21196]	growth	37 °C
[Ref.: #63109]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #21196]	Temperature range	mesophilic
[Ref.: #63109]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21196]	Oxygen tolerance	anaerobe
[Ref.: #63109]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #67771]

Ability of spore formation

[Ref.: #21196]

Name of produced compound

urolithin

[Ref.: #67771]

Observation

quinones: MK-6, MMK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	+	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	+	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

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

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #21196]	12824	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21196]	Sample type/isolated from	human faeces of a healthy volunteer
[Ref.: #21196]	Geographic location (country and/or sea, region)	Murcia
[Ref.: #21196]	Country	Spain
[Ref.: #21196]	Country ISO 3 Code	ESP
[Ref.: #21196]	Continent	Europe

[Ref.: #63109]	Sample type/isolated from	Human feces
[Ref.: #63109]	Sampling date	2012-06-12
[Ref.: #63109]	Geographic location (country and/or sea, region)	Murcia
[Ref.: #63109]	Country	Spain
[Ref.: #63109]	Country ISO 3 Code	ESP
[Ref.: #63109]	Continent	Europe

[Ref.: #67771]	Sample type/isolated from	From human feces of a healthy volunteer
[Ref.: #67771]	Geographic location (country and/or sea, region)	Murcia
[Ref.: #67771]	Country	Spain
[Ref.: #67771]	Country ISO 3 Code	ESP
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HG000667 (>99% sequence identity) for Gordonibacter urolithinfaciens subclade from Microbeatlas

Aquatic Samples	472
Soil Samples	84
Animal Samples	23871
Plant Samples	49
Total Samples	24476

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

[Ref.: #21196]

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.: #21196]	Gordonibacter urolithinfaciens partial 16S rRNA gene, type strain CEBAS 1/15PT	HG000667	1477	ENA	1335613 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gordonibacter urolithinfaciens DSM 27213	GCA_003788975	contig	GenBank	1335613 tax ID	*
[Ref.: #66792]	Gordonibacter urolithinfaciens strain 142160_ID174831	1335613.4	complete	PATRIC	1335613 tax ID	*
[Ref.: #66792]	Gordonibacter urolithinfaciens strain DSM 27213	1335613.12	wgs	PATRIC	1335613 tax ID	*

[Ref.: #21196]

GC-content

66.4 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gordonibacter urolithinfaciens strain 142160_ID174831 PATRIC: 1335613.4
[Ref.: #69480]	motile	no	92.791	no
[Ref.: #69480]	gram-positive	yes	88.106	no
[Ref.: #69480]	anaerobic	yes	98.669	no
[Ref.: #69480]	halophile	no	89.913	no
[Ref.: #69480]	spore-forming	no	87.937	yes
[Ref.: #69480]	glucose-util	yes	63.635	no
[Ref.: #69480]	flagellated	no	98.476	no
[Ref.: #69480]	thermophile	no	99.72	yes
[Ref.: #69480]	aerobic	no	96.283	yes
[Ref.: #69480]	glucose-ferment	no	59.257	no

Availability in culture collections External links

[Ref.: #21196]

Culture collection no.

DSM 27213, CCUG 64261, KCTC 15440, CEBAS 1/15P, CEBAS 1/15

[Ref.: #88614]

SI-ID 402943

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gordonibacter urolithinfaciens sp. nov., a urolithin-producing bacterium isolated from the human gut.	Selma MV, Tomas-Barberan FA, Beltran D, Garcia-Villalba R, Espin JC	Int J Syst Evol Microbiol	10.1099/ijs.0.055095-0	2014	*
Metabolism	Metabolism of different dietary phenolic compounds by the urolithin-producing human-gut bacteria Gordonibacter urolithinfaciens and Ellagibacter isourolithinifaciens.	Garcia-Villalba R, Beltran D, Frutos MD, Selma MV, Espin JC, Tomas-Barberan FA	Food Funct	10.1039/d0fo01649g	2020	*
Metabolism	Evaluation of electron-transferring cofactor mediating enzyme systems involved in urolithin dehydroxylation in Gordonibacter urolithinfaciens DSM 27213.	Watanabe H, Kishino S, Kudoh M, Yamamoto H, Ogawa J	J Biosci Bioeng	10.1016/j.jbiosc.2019.11.014	2020	*
Genetics	Complete Genome Sequence of the New Urolithin-Producing Bacterium Gordonibacter urolithinfaciens DSM 27213(T).	Martinez-Blanch JF, Ramon D, Beltran D, Romo-Vaquero M, Garcia-Villalba R, Espin JC, Tomas-Barberan FA, Codoner FM, Selma MV	Genome Announc	10.1128/genomeA.01120-17	2017	*

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 )

#21196

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27213

#63109 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 64261

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#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) .

#88614

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-ID402943.1 )

* These data were automatically processed and therefore are not curated

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Gordonibacter urolithinfaciens strain 142160_ID174831

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