Anaerococcus degeneri (DSM 29674, CCUG 69679, UMCG-104)

Name: Anaerococcus degeneri (DSM 29674, CCUG 69679, UMCG-104)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132505

Type strain

Strain Designation UMCG-104, gpac104, UMCG-gpac104

Culture col. no. DSM 29674 CCUG 69679 UMCG-104 gpac104 UMCG-gpac104

NCBI tax ID(s) 361500

Special Collections DSMZ CCUG

Links

Anaerococcus degeneri UMCG-104 is a mesophilic prokaryote that was isolated from abdominal abscess.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398642

DSM 29674,CCUG 69679

@ref 20215

Last LPSN update 2025-12-16 10:01:32

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Tissierellales

Family Peptoniphilaceae

Genus Anaerococcus

Species Anaerococcus degeneri

Full scientific name Anaerococcus degeneri corrig. Veloo et al. 2017

Synonyms (1)

Anaerococcus degenerii

BacDive ID	Other strains from **Anaerococcus degeneri** (1)	Type strain
152335	A. degeneri CCUG 46465

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24294	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24294	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	93.5

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	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	L-arginine arylamidase	+		from API rID32A
68380	leucine arylamidase	+	3.4.11.1	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	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
24294	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	+	-	+/-	-	+	-	-	+/-	+/-	+/-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Other	#Abdomen
#Host Body-Site	#Other	#Abscess

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24294	abdominal abscess	University Medical Center Groningen	Netherlands	NLD	Europe
63646	Abdominal abscess,human	Groningen	Netherlands	NLD	Europe

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
24294	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
124043	ASM2021568v1 assembly for Anaerococcus degeneri FDAARGOS_1538	scaffold	GCA_020215685	361500.4	8067238955	361500	74.76
66792	ASM1787447v1 assembly for Anaerococcus degeneri DSM 29674	contig	GCA_017874475	361500.3	2913522466	361500	69.16

Genome browser: GCA_020215685

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24294	Anaerococcus degenerii partial 16S rRNA gene, type strain gpac104T	AM176528	1445		361500

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Anaerococcus degeneri DSM 29674
NCBI: GCA_017874475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.90	no
125439	motility	BacteriaNetⓘ	no	70.70	no
125439	gram_stain	BacteriaNetⓘ	positive	67.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	93.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Anaerococcus degeneri strain DSM 29674
PATRIC: 361500.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	83.04	no
125438	anaerobic	anaerobicⓘ	yes	87.15	no
125438	spore-forming	spore-formingⓘ	no	71.12	no
125438	aerobic	aerobicⓘ	no	95.16	no
125438	thermophilic	thermophileⓘ	no	93.90	no
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Anaerococcus degenerii sp. nov., isolated from human clinical specimens.	Veloo AC, Elgersma PE, van Winkelhoff AJ	Anaerobe	10.1016/j.anaerobe.2015.02.002	2015

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 )
#24294	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29674
#63646	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 69679
#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 .
#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 )

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Anaerococcus degeneri (DSM 29674, CCUG 69679, UMCG-104)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

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_020215685

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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