Gordonibacter pamelaeae (DSM 110924, 3C)

Name: Gordonibacter pamelaeae (DSM 110924, 3C)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159554

Type strain

Strain Designation 3C

Culture col. no. DSM 110924 3C

NCBI tax ID(s) 471189

Special Collections DSMZ DZIF

Links

Gordonibacter pamelaeae 3C is a mesophilic prokaryote that was isolated from feces, human.

mesophilic genome sequence

Name and taxonomic classification

SI-ID 397471

DSM 110924

@ref 20215

Last LPSN update 2025-12-16 10:08:17

Domain Bacillati

Phylum Actinomycetota

Class Coriobacteriia

Order Eggerthellales

Family Eggerthellaceae

Genus Gordonibacter

Species Gordonibacter pamelaeae

Full scientific name Gordonibacter pamelaeae Würdemann et al. 2009

BacDive ID	Other strains from **Gordonibacter pamelaeae** (1)	Type strain
3075	G. pamelaeae 7-10-1-b, DSM 19378, CCUG 55131, KCTC 15161, ... (type strain)

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66380	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Brain heart infusion 37.0 g/l Arginine 10.0 g/l Distilled water
66380	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66380	positive	growth	37	mesophilic

Physiology and metabolism

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

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
66380	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
66380	feces, human	Cambridge, Massachusetts	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
66380	yes, in single cases	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM334038v1 assembly for Gordonibacter pamelaeae 3C	scaffold	GCA_003340385	471189.9	8074174689	471189	70.87

Genome browser: GCA_003340385

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gordonibacter pamelaeae 3C
NCBI: GCA_003340385.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.55	no
125438	anaerobic	anaerobicⓘ	yes	87.74	no
125438	aerobic	aerobicⓘ	no	93.11	no
125438	spore-forming	spore-formingⓘ	no	73.18	no
125438	thermophilic	thermophileⓘ	no	91.50	yes
125438	flagellated	motile2+ⓘ	no	79.50	no

Literature

Title	Authors	Journal	DOI	Year
Enzymatic carbon-fluorine bond cleavage by human gut microbes.	Probst SI, Felder FD, Poltorak V, Mewalal R, Blaby IK, Robinson SL.	Proc Natl Acad Sci U S A	10.1073/pnas.2504122122	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 )
#66380	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 110924
#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) .
#68380	Automatically annotated from API rID32A .
#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 )
#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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Gordonibacter pamelaeae (DSM 110924, 3C)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003340385

Genome-based predictions

Predictions

Literature

Literature

References

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