Phocaeicola vulgatus (DSM 107446, WCA-389-WT-3C)

Name: Phocaeicola vulgatus (DSM 107446, WCA-389-WT-3C)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158887

Type strain

Strain Designation WCA-389-WT-3C

Culture col. no. DSM 107446 WCA-389-WT-3C

NCBI tax ID(s) 821

Special Collections DSMZ Pig DZIF

History DSMZ <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; WCA-389-WT-3C

Links

Phocaeicola vulgatus WCA-389-WT-3C is a bacterium that was isolated from feces; pig, 8 weeks old, wild type.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407287

DSM 107446

@ref 20215

Last LPSN update 2026-05-29 08:44:04

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, ...
130883	P. vulgatus 39a-cc-B-5824-ARE, DSM 28735
157626	P. vulgatus H4_2, DSM 108222
157627	P. vulgatus H5_1, DSM 108228
157628	P. vulgatus H6_5, DSM 108234
174363	P. vulgatus HUN383, NLAE-zl-G202, DSM 116443

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	92.462
125439	negative	94.296

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65709	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
65709	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

Culture temp

@ref	Growth	Type	Temperature (°C)
65709	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	anaerobe	93.657
125439	obligate anaerobe	98.496

Spore formation

@ref	Spore formation	Confidence
125438		90.416
125439		99.907

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
65709	feces; pig, 8 weeks old, wild type	Kranzberg (Bavaria)	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence MN537534 (>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
65709	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
66792	ASM969654v1 assembly for Phocaeicola vulgatus WCA-389-WT-3C	contig	GCA_009696545	821.3500	821	54.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65709	Phocaeicola vulgatus strain DSM 107446 16S ribosomal RNA gene, partial sequence	MN537534	1470		821

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM969654v1 assembly for Phocaeicola vulgatus WCA-389-WT-3C
NCBI: GCA_009696545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.50	no
125439	gram_stain	BacteriaNetⓘ	negative	94.30	no
125439	motility	BacteriaNetⓘ	no	88.15	no
125439	spore_formation	BacteriaNetⓘ	no	99.91	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides vulgatus strain WCA-389-WT-3C
PATRIC: 821.3500

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.46	no
125438	anaerobic	anaerobicⓘ	yes	93.66	no
125438	aerobic	aerobicⓘ	no	95.02	no
125438	spore-forming	spore-formingⓘ	no	90.42	no
125438	thermophilic	thermophileⓘ	no	95.33	yes
125438	flagellated	motile2+ⓘ	no	88.60	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 )
#65709	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107446
#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) .
#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 .
#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 )

Content

About us