Phocaeicola dorei (DSM 108974, Cla-CZ-110)

Name: Phocaeicola dorei (DSM 108974, Cla-CZ-110)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160609

Type strain

Strain Designation Cla-CZ-110

Culture col. no. DSM 108974 Cla-CZ-110

NCBI tax ID(s) 357276

Special Collections DSMZ Chicken DZIF

History DSMZ <- T. Clavel, RWTH Aachen; Cla-CZ-110 <- C. Zenner, LMU, München;

Links

Phocaeicola dorei Cla-CZ-110 is a bacterium that was isolated from chicken caecal content, 21days old.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400978

DSM 108974

@ref 20215

Last LPSN update 2026-05-29 08:44:29

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Phocaeicola

Species Phocaeicola dorei

Full scientific name Phocaeicola dorei (Bakir et al. 2006) García-López et al. 2020

Synonyms (1)

Bacteroides dorei

BacDive ID	Other strains from **Phocaeicola dorei** (2)	Type strain
1612	P. dorei 175, DSM 17855, JCM 13471, CCUG 53892 (type strain)
169519	P. dorei HM-27, 9/1/42 FAA, DSM 24903

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.974
125438	negative	94.174
125438		90.095

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
67517	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)		Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
67517	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)
67517	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate anaerobe	99.477
125438	anaerobe	90.764

Spore formation

@ref	Spore formation	Confidence
125439		99.923

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	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	tryptophan deaminase	-	4.1.99.1	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
67517	-	-	+	+	-	+	+/-	+	-	+	+	+	+	+	-	-	+	+	-	+	+	+	+/-	+/-	+	+	+	+	+/-
67517	-	-	+	+	+/-	+	+	+	+/-	+	+	+	+	+	-	-	+	+	-	+	+	+	-	+/-	+	+	+	+	+/-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67517	chicken caecal content, 21days old	Munich	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
67517	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1498296v1 assembly for Phocaeicola dorei DSM 108974	contig	GCA_014982965	357276.1074	357276	74.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67517	Phocaeicola dorei strain ClaCZ110 16S ribosomal RNA gene, partial sequence	MN055948.1	1478		357276

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1498296v1 assembly for Phocaeicola dorei DSM 108974
NCBI: GCA_014982965

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.48	no
125439	motility	BacteriaNetⓘ	no	84.95	no
125439	gram_stain	BacteriaNetⓘ	negative	96.97	no
125439	spore_formation	BacteriaNetⓘ	no	99.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phocaeicola dorei strain DSM 108974
PATRIC: 357276.1074

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.17	no
125438	anaerobic	anaerobicⓘ	yes	90.76	no
125438	spore-forming	spore-formingⓘ	no	88.92	no
125438	aerobic	aerobicⓘ	no	94.21	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	90.10	no

Literature

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 )
#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) .
#67517	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108974
#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 )
#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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