Phocaeicola vulgatus (DSM 28735, 39a-cc-B-5824-ARE)

Name: Phocaeicola vulgatus (DSM 28735, 39a-cc-B-5824-ARE)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130883

Type strain

Strain Designation 39a-cc-B-5824-ARE

Culture col. no. DSM 28735 39a-cc-B-5824-ARE

NCBI tax ID(s) 821

Special Collections DSMZ Mouse DZIF

History DSMZ <- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; 39a-cc-B-5824-ARE

Links

Phocaeicola vulgatus 39a-cc-B-5824-ARE is an anaerobe bacterium that was isolated from caecal content; TNF^deltaARE/+ C57BL/6 mouse.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 405579

DSM 28735

@ref 20215

Last LPSN update 2026-05-29 08:37:29

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Phocaeicola

Species Phocaeicola vulgatus

Full scientific name Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020

Synonyms (1)

Bacteroides vulgatus

BacDive ID	Other strains from **Phocaeicola vulgatus** (8)	Type strain
1601	P. vulgatus LRA 049 07 85, DSM 1447, ATCC 8482, CCUG ... (type strain)
1588	P. vulgatus mprl 1840, MPRL 1840/MH4, DSM 9670
1602	P. vulgatus CCUG 12546, KCTC 2639, DSM 3289, ATCC 29327, ...
157626	P. vulgatus H4_2, DSM 108222
157627	P. vulgatus H5_1, DSM 108228
157628	P. vulgatus H6_5, DSM 108234
158887	P. vulgatus WCA-389-WT-3C, DSM 107446
174363	P. vulgatus HUN383, NLAE-zl-G202, DSM 116443

Morphology

Cell morphology

@ref	Confidence	Gram stain
125438	90.5
125438	92.823	negative
125439	93.764	negative

Colony morphology

22192

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22192	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
22192	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22192	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
22192	anaerobe
125438	anaerobe	92.3
125439	obligate anaerobe	99.593

Spore formation

@ref	Spore formation	Confidence
125439		99.696

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
22192	-	-	+	+	+	+	-	+	+	+	+	+	+	+	-	-	+	-	-	+	-	-	+	-	+	+	-	+	-
22192	-	-	+	+	+	+	-	+	+	+	+	+	+	+	-	-	+	-	-	+	-	-	+	-	+	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22192	caecal content; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364743 (>99% sequence identity) for Phocaeicola vulgatus subclade from Microbeatlas

Aquatic Samples	2761
Soil Samples	881
Animal Samples	148487
Plant Samples	380
Total Samples	152509

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
22192	yes, in single cases	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
124043	ASM1676693v1 assembly for Phocaeicola vulgatus FDAARGOS_1099	chromosome	GCA_016766935	821.4032	821	89.14
66792	ASM2462203v1 assembly for Phocaeicola vulgatus DSM 28735	contig	GCA_024622035	821.4951	821	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22192	Phocaeicola vulgatus strain 39a-cc-B-5824-ARE 16S ribosomal RNA gene, partial sequence	KR364743	1416		821

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1676693v1 assembly for Phocaeicola vulgatus FDAARGOS_1099
NCBI: GCA_016766935

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.59	no
125439	gram_stain	BacteriaNetⓘ	negative	93.76	no
125439	motility	BacteriaNetⓘ	no	78.44	no
125439	spore_formation	BacteriaNetⓘ	no	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phocaeicola vulgatus strain FDAARGOS_1099 strain Not applicable
PATRIC: 821.4032

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.82	no
125438	anaerobic	anaerobicⓘ	yes	92.30	yes
125438	aerobic	aerobicⓘ	no	94.42	yes
125438	spore-forming	spore-formingⓘ	no	89.90	no
125438	thermophilic	thermophileⓘ	no	96.17	yes
125438	flagellated	motile2+ⓘ	no	90.50	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 )
#22192	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28735
#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 .
#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 .
#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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