Bacteroides pyogenes (DSM 20611, ATCC 35418, CCUG 15419)

Name: Bacteroides pyogenes (DSM 20611, ATCC 35418, CCUG 15419)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1594

Type strain

Strain Designation P39-88

Culture col. no. DSM 20611 ATCC 35418 CCUG 15419 JCM 6294 P39-88

NCBI tax ID(s) 1121100 310300

Special Collections DSMZ CCUG JCM Pig DSMZ

History <- Y. Benno, Institute for Physical and Chemical Research, Saitama, Japan; P39-88 Y. Benno P39-88.

Links

Bacteroides pyogenes P39-88 is an anaerobe, mesophilic human pathogen that was isolated from pig faeces.

anaerobe mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 41066

ATCC 35418,DSM 20611,CCUG 15419,JCM 6294,CCM 3724

@ref 20215

Last LPSN update 2025-12-16 09:47:08

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides pyogenes

Full scientific name Bacteroides pyogenes Benno et al. 1983

Synonyms (3)

Bacteroides tectum
Bacteroides tectus
Bacteroides suis

BacDive ID	Other strains from **Bacteroides pyogenes** (5)	Type strain
1593	B. pyogenes 160, DSM 19673, ATCC 43331, CCUG 25929, JCM ...
1595	B. pyogenes P 38024, CCUG 15420, CCM 3725, DSM 20612, ...
155252	B. pyogenes CCUG 57080
156615	B. pyogenes CCUG 63581
156810	B. pyogenes CCUG 65536

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	93.879
125439	negative	99.9

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8959	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
8959	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
8959	positive	growth	37	mesophilic
46249	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8959	anaerobe
46249	anaerobe
125438	anaerobe	90.634
125439	anaerobe	95.3

Spore formation

@ref	Spore formation	Confidence
125438		95.96
125439		99.7

Observation

67770

Observationquinones: MK-10, MK-11

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	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

Fatty acid profile

Metadata FA analysis

@ref

46249

Fatty acid	Percentage	ECL
C15:0 ANTEISO	27.6	14.711
C15:0 ISO	16.3	14.621
C17:0 iso 3OH	14.6	18.161
unknown 13.566	6.5	13.566
C17:0 anteiso	6	16.722
C18:2 ω6,9c/C18:0 ANTE	4.8	17.724
C17:0 iso	3.7	16.629
C16:0	3.4	16
C15:0	3.2	15
C18:1 ω9c	3	17.769
C16:0 3OH	2.3	17.52
C17:0 2OH	1.6	18.249
C16:0 iso	1.3	15.626
C17:0 3OH	1.2	18.535
C15:0 3OH	1.1	16.504
C18:0	1	18
Unidentified	0.5	16.123
C16:1 ω7c	0.4	15.819
C13:0 iso	0.4	12.612
C13:0 ANTEISO	0.4	12.701
C17:0	0.4	17
unknown 16.580	0.4	16.58

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
8959	-	-	-	+	-	+	-	-	-	+	+	-	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+/-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type
8959	pig faeces
46249	Pig abscess (formerly listed as:pig feces)
67770	Pig abscess

Taxonmaps

69479

Global distribution of 16S sequence AB542768 (>99% sequence identity) for Bacteroides pyogenes subclade from Microbeatlas

Aquatic Samples	520
Soil Samples	529
Animal Samples	37576
Plant Samples	142
Total Samples	38767

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
8959			2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM42810v1 assembly for Bacteroides pyogenes DSM 20611 = JCM 6294	scaffold	GCA_000428105	1121100.7	2524614554	1121100	63.94
67770	ASM51175v1 assembly for Bacteroides pyogenes DSM 20611 = JCM 6294	contig	GCA_000511755	1235810.3	2574180081	1121100	16.08

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: ATCC 35418	AB542766	1478	310300
20218	Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: DSM 20611	AB542768	1476	310300
8959	Bacteroides pyogenes strain JCM6294 16S ribosomal RNA gene, partial sequence	EU136683	2063	310300
67770	Bacteroides pyogenes gene for 16S rRNA, partial sequence, strain: JCM 6294	AB200229	1461	310300
67770	Bacteroides pyogenes gene for 16S ribosomal RNA, partial sequence, strain: CCUG 15419	AB542767	1477	310300

GC content

@ref	GC-content (mol%)	Method
8959	46.7
67770	46.8	thermal denaturation, midpoint method (Tm)
67770	46.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacteroides pyogenes DSM 20611 = JCM 6294
NCBI: GCA_000428105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	95.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	motility	BacteriaNetⓘ	no	78.20	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: Bacteroides pyogenes DSM 20611 = JCM 6294 DSM 20611
NCBI: GCA_000428105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.88	no
125438	anaerobic	anaerobicⓘ	yes	90.63	no
125438	aerobic	aerobicⓘ	no	95.64	yes
125438	spore-forming	spore-formingⓘ	no	95.96	no
125438	thermophilic	thermophileⓘ	no	96.94	no
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.	Gruninger RJ, McCormack ML, Chomistek NC, Zaheer R, McAllister TA.	Microbiol Spectr	10.1128/spectrum.00423-25	2025
	Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.	Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Harkonen T, Hamalainen AM, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW.	Proc Natl Acad Sci U S A	10.1073/pnas.1706359114	2017
Metabolism	Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly.	Collado MC, Derrien M, Isolauri E, de Vos WM, Salminen S.	Appl Environ Microbiol	10.1128/aem.01477-07	2007
Enzymology	Bacteremia with Bacteroides pyogenes after a cat bite.	Madsen IR, Justesen US.	J Clin Microbiol	10.1128/jcm.00250-11	2011
Metabolism	Microbial short-chain fatty acids modulate CD8⁺ T cell responses and improve adoptive immunotherapy for cancer.	Luu M, Riester Z, Baldrich A, Reichardt N, Yuille S, Busetti A, Klein M, Wempe A, Leister H, Raifer H, Picard F, Muhammad K, Ohl K, Romero R, Fischer F, Bauer CA, Huber M, Gress TM, Lauth M, Danhof S, Bopp T, Nerreter T, Mulder IE, Steinhoff U, Hudecek M, Visekruna A.	Nat Commun	10.1038/s41467-021-24331-1	2021
Phylogeny	Berberine alters gut microbial function through modulation of bile acids.	Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM.	BMC Microbiol	10.1186/s12866-020-02020-1	2021
Metabolism	Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.	Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P.	Sci Rep	10.1038/s41598-017-10369-z	2017
Metabolism	Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.	Johnston CD, Skeete CA, Fomenkov A, Roberts RJ, Rittling SR.	PLoS One	10.1371/journal.pone.0185234	2017
Metabolism	The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.	Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR.	Gut Microbes	10.1080/19490976.2019.1618173	2020
Genetics	Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine.	Sakamoto M, Oshima K, Suda W, Kitamura K, Iida T, Hattori M, Ohkuma M	Genome Announc	10.1128/genomeA.01242-13	2014
Phylogeny	hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes.	Sakamoto M, Suzuki N, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.021154-0	2010

References

#8959	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20611
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#46249	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 15419
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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Bacteroides pyogenes (DSM 20611, ATCC 35418, CCUG 15419)

Name and taxonomic classification