Name: Gordonibacter pamelaeae 7-10-1-b
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3075

Type strain:

Species: Gordonibacter pamelaeae

Strain Designation: 7-10-1-b

Culture col. no.: DSM 19378, CCUG 55131, KCTC 15161, JCM 16334

Strain history: <- DSM <- C Strompl, HZI, Braunschweig, Germany; 7-10-1-b

NCBI tax ID(s): 471189 (species)

SI-ID 397643

DSM 19378, CCUG 55131

Special Collections

Other strains from Gordonibacter pamelaeae

Section

Gordonibacter pamelaeae 7-10-1-b is an anaerobe, Gram-positive, motile human pathogen that was isolated from patient with active Crohn’s disease, colon, sigmoid region.

Gram-positive
motile
ovoid-shaped
anaerobe
human pathogen
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 pamelaeae**
	Full Scientific Name (LPSN)	Gordonibacter pamelaeae Würdemann et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29087]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #68367]	Gram stain	positive * from API 20A

[Ref.: #29087]	Cell length	1 µm

[Ref.: #29087]	Cell width	0.55 µm

[Ref.: #29087]	Cell shape	ovoid-shaped

[Ref.: #29087]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #60472]

Incubation period

2 days

[Ref.: #29087]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8081]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #8081]

Culture medium growth

[Ref.: #8081]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8081]

Culture medium composition

expand / minimize

[Ref.: #8081]

Culture medium

WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)

[Ref.: #8081]

Culture medium growth

[Ref.: #8081]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8081]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8081]	growth	37 °C
[Ref.: #29087]	optimum	37 °C
[Ref.: #60472]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8081]	Oxygen tolerance	anaerobe
[Ref.: #29087]	Oxygen tolerance	anaerobe
[Ref.: #60472]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #29087]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no
[Ref.: #68367]	Ability of spore formation	no * from API 20A

[Ref.: #67771]

Observation

quinones: MK-6, MMK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29087]	arginine ChEBI	+	carbon source
[Ref.: #68380]	arginine ChEBI	+	hydrolysis	* from API rID32A
[Ref.: #68367]	cellobiose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-glucose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-mannitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-mannose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68367]	D-xylose ChEBI	-	builds acid from	* from API 20A
[Ref.: #29087]	dextrin ChEBI	+	carbon source
[Ref.: #68367]	gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68367]	L-rhamnose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	lactose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	maltose ChEBI	-	builds acid from	* from API 20A
[Ref.: #29087]	mannose ChEBI	+	carbon source
[Ref.: #68367]	melezitose ChEBI	-	builds acid from	* from API 20A
[Ref.: #29087]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #29087]	phenylalanine ChEBI	+	carbon source
[Ref.: #29087]	pyruvate ChEBI	+	carbon source
[Ref.: #68367]	raffinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68367]	salicin ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sorbitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sucrose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	trehalose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	tryptophan ChEBI	-	energy source	* from API 20A, API rID32A
[Ref.: #68367]	urea ChEBI	-	hydrolysis	* from API 20A, API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68367]		indole ChEBI	no	* from API 20A, API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A, API 20A

	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.: #29087]	catalase	+	1.11.1.6
[Ref.: #68367]	gelatinase	-		* from API 20A
[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, API 20A
	Only first 10 entries are displayed. Click here to see all.

API® 20A:

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

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #8081]	2123	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.	-	+	not determinedn.d.

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.: #8081]	12678	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #8081]	12677	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #8081]	Sample type/isolated from	patient with active Crohn’s disease, colon, sigmoid region
[Ref.: #8081]	Geographic location (country and/or sea, region)	Kiel, Univ.-Hospital Schleswig-Holstein, Clinic for General Internal Medicine
[Ref.: #8081]	Country	Germany
[Ref.: #8081]	Country ISO 3 Code	DEU
[Ref.: #8081]	Continent	Europe

[Ref.: #60472]	Sample type/isolated from	Human intestinal biopsy,inflammatory bowel disease
[Ref.: #60472]	Sampling date	2007-02-01
[Ref.: #60472]	Geographic location (country and/or sea, region)	Kiel
[Ref.: #60472]	Country	Germany
[Ref.: #60472]	Country ISO 3 Code	DEU
[Ref.: #60472]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Sigmoid region of the colon of a patient suffering from active Crohn's disease

[Ref.: #67771]	Sample type/isolated from	From patient with active Crohnâ€™s disease, colon
[Ref.: #67771]	Geographic location (country and/or sea, region)	sigmoid region, Clinic for General Internal Medicine, Kiel, Univ.-Hospital Schleswig-Holstein
[Ref.: #67771]	Country	Germany
[Ref.: #67771]	Country ISO 3 Code	DEU
[Ref.: #67771]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Infection	#Inflammation	-
#Infection	#Patient	-
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM886059 (>99% sequence identity) for Gordonibacter pamelaeae subclade from Microbeatlas

Aquatic Samples	726
Soil Samples	33
Animal Samples	13755
Plant Samples	10
Total Samples	14524

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

[Ref.: #8081]	Pathogenicity (human)	yes, in single cases
[Ref.: #8081]	Biosafety level	1	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.: #8081]	Gordonibacter pamelaeae partial 16S ribosomal RNA gene, type strain 7-10-1-bT	AM886059	1431	GenBank ENA	657308 tax ID
[Ref.: #67770]	Gordonibacter pamelaeae gene for 16S ribosomal RNA, partial sequence	AB566419	1470	GenBank ENA	471189 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Gordonibacter pamelaeae 7-10-1-b 7-10-1-bT	GCA_000210055	chromosome	GenBank ENA	657308 tax ID
[Ref.: #66792]	Gordonibacter pamelaeae 7-10-1-b	657308.3	complete	PATRIC	657308 tax ID	*
[Ref.: #66792]	Gordonibacter pamelaeae 7-10-1-bT, DSM 19378	650377943	complete	JGI IMG/M	657308 tax ID	*

[Ref.: #8081]	GC-content	66.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29087]	GC-content	66.4 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Gordonibacter pamelaeae 7-10-1-b PATRIC: 657308.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	56	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gordonibacter pamelaeae 7-10-1-b PATRIC: 657308.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	82.193	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	88.001	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	78.26	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	93.8	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	88.596	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	81.5	no

Availability in culture collections External links

[Ref.: #8081]

Culture collection no.

DSM 19378, CCUG 55131, KCTC 15161, JCM 16334

[Ref.: #72594]

SI-ID 397643

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rubneribacter badeniensis gen. nov., sp. nov. and Enteroscipio rubneri gen. nov., sp. nov., new members of the Eggerthellaceae isolated from human faeces.	Danylec N, Gobl A, Stoll DA, Hetzer B, Kulling SE, Huch M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002705	2018	*
Phylogeny	Gordonibacter faecihominis sp. nov., isolated from human faeces.	Jin JS, Lee KC, Park IS, Kim KK, Ahn JS, Benno Y, Hattori M, Lee JS	Antonie Van Leeuwenhoek	10.1007/s10482-014-0212-6	2014	*
Metabolism	Description of urolithin production capacity from ellagic acid of two human intestinal Gordonibacter species.	Selma MV, Beltran D, Garcia-Villalba R, Espin JC, Tomas-Barberan FA	Food Funct	10.1039/c4fo00092g	2014	*
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	*
Phylogeny	Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov.	Wurdemann D, Tindall BJ, Pukall R, Lunsdorf H, Strompl C, Namuth T, Nahrstedt H, Wos-Oxley M, Ott S, Schreiber S, Timmis KN, Oxley AP	Int J Syst Evol Microbiol	10.1099/ijs.0.005900-0	2009	*

References

#8081

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19378

#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 )

#29087

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 #25516 (see below)

#60472 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55131

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68367

Automatically annotated from API 20A .

#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) .

#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 )

#72594

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-ID397643.1 )

#25516

IJSEM 1405 2009 ( DOI 10.1099/ijs.0.005900-0 , PubMed 19502325 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Gordonibacter pamelaeae in external resources:
SILVA
BRENDA
PANGAEA
GBIF