Peptoniphilus gorbachii (JCM 15634, KCTC 5947, DSM 21461)

Name: Peptoniphilus gorbachii (JCM 15634, KCTC 5947, DSM 21461)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18004

Type strain

Culture col. no. JCM 15634 KCTC 5947 DSM 21461 ATCC BAA-1383 CCUG 53341 1 more

NCBI tax ID(s) 411567

Special Collections DSMZ CCUG JCM KCTC

History DSMZ <- CCUG; CCUG 53341 <- Y. Song, VA Medical Center West Los Angeles, USA; JCM <-- CCUG 53341 <-- Y. Song WAL 10418. KCTC <- CCUG <- Y Song, VAMC, Los Angeles, USA

Links

Peptoniphilus gorbachii JCM 15634 is an anaerobe, coccus-shaped bacterium that was isolated from human abscess, groin.

coccus-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400460

ATCC BAA-1383,KCTC 5947,JCM 15634,DSM 21461,CCUG 53341

@ref 20215

Last LPSN update 2026-05-29 08:29:09

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Tissierellales

Family Peptoniphilaceae

Genus Peptoniphilus

Species Peptoniphilus gorbachii

Full scientific name Peptoniphilus gorbachii Song et al. 2010

Morphology

Cell morphology

@ref	Cell shape	Gram stain
67771	coccus-shaped
67771		positive

Colony morphology

59871

Incubation period2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15720	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
15720	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)
15720	positive	growth	37
59871	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
15720	anaerobe
59871	anaerobe
67771	anaerobe
125438	anaerobe	95.28

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	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	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	glutamyl-glutamate arylamidase	+		from API rID32A
68380	histidine arylamidase	+		from API rID32A
68380	L-arginine arylamidase	+		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	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	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
15720	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+/-	+	-	-	+	+	-	+	-	+	+	+	+
15720	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	+/-	-	+	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
15720	human abscess, groin	Homo sapiens		Los Angeles, California	USA	USA	North America
59871	Human abscess,groin	Homo sapiens	1992-11-01	California,Los Angeles	USA	USA	North America
67770	Human clinical specimens	Homo sapiens
67771	From human abscess, groin	Homo sapiens		California, Los Angeles	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15720	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	ASM1690811v1 assembly for Peptoniphilus gorbachii DSM 21461	contig	GCA_016908115	411567.4	2901072628	411567	74.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15720	Peptoniphilus sp. WAL 10418 16S ribosomal RNA gene, partial sequence	DQ911241	1404		411567

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1690811v1 assembly for Peptoniphilus gorbachii DSM 21461
NCBI: GCA_016908115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	69.91	no
125439	motility	BacteriaNetⓘ	no	65.12	no
125439	gram_stain	BacteriaNetⓘ	positive	50.18	no
125439	spore_formation	BacteriaNetⓘ	no	68.42	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Peptoniphilus gorbachii strain DSM 21461
PATRIC: 411567.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.30	no
125438	anaerobic	anaerobicⓘ	yes	95.28	yes
125438	spore-forming	spore-formingⓘ	no	69.29	no
125438	aerobic	aerobicⓘ	no	97.82	yes
125438	thermophilic	thermophileⓘ	no	92.10	yes
125438	flagellated	motile2+ⓘ	no	87.78	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Peptoniphilus gorbachii alleviates collagen-induced arthritis in mice by improving intestinal homeostasis and immune regulation.	Kim S, Chun SH, Cheon YH, Kim M, Kim HO, Lee H, Hong ST, Park SJ, Park MS, Suh YS, Lee SI.	Front Immunol	10.3389/fimmu.2023.1286387	2023
Phylogeny	Variations in Gut Microbiome are Associated with Prognosis of Hypertriglyceridemia-Associated Acute Pancreatitis.	Hu X, Gong L, Zhou R, Han Z, Ji L, Zhang Y, Zhang S, Wu D.	Biomolecules	10.3390/biom11050695	2021
	Clinical Presentation and Incidence of Anaerobic Bacteria in Surgically Treated Biliary Tract Infections and Cholecystitis.	Strohaker J, Wiegand L, Beltzer C, Konigsrainer A, Ladurner R, Meier A.	Antibiotics (Basel)	10.3390/antibiotics10010071	2021
	Evaluation of Antibiotic Susceptibility of Gram-Positive Anaerobic Cocci Isolated from Cancer Patients of the N. N. Blokhin Russian Cancer Research Center.	Shilnikova II, Dmitrieva NV.	J Pathog	10.1155/2015/648134	2015
	HiBC: a publicly available collection of bacterial strains isolated from the human gut.	Hitch TCA, Masson JM, Pauvert C, Bosch J, Nuchtern S, Treichel NS, Baloh M, Razavi S, Afrizal A, Kousetzi N, Aguirre AM, Wylensek D, Coates AC, Jennings SAV, Panyot A, Viehof A, Schmitz MA, Stuhrmann M, Deis EC, Bisdorf K, Chiotelli MD, Lissin A, Schober I, Witte J, Cramer T, Riedel T, Wende M, Winter KA, Amend L, Riva A, Trinh S, Mitchell L, Hartman J, Berry D, Seitz J, Bossert LC, Grognot M, Allers T, Strowig T, Pester M, Abt B, Reimer LC, Overmann J, Clavel T.	Nat Commun	10.1038/s41467-025-59229-9	2025
Pathogenicity	Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection.	Tamarelle J, Ma B, Gajer P, Humphrys MS, Terplan M, Mark KS, Thiebaut ACM, Forney LJ, Brotman RM, Delarocque-Astagneau E, Bavoil PM, Ravel J.	J Infect Dis	10.1093/infdis/jiz499	2020
	Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.	Gomez Exposito R, de Bruijn I, Postma J, Raaijmakers JM.	Front Microbiol	10.3389/fmicb.2017.02529	2017
Enzymology	Specific microbial attachment to root knot nematodes in suppressive soil.	Adam M, Westphal A, Hallmann J, Heuer H.	Appl Environ Microbiol	10.1128/aem.03905-13	2014
	Vaginal Microbiota and Mucosal Pharmacokinetics of Tenofovir in Healthy Women Using a 90-Day Tenofovir/Levonorgestrel Vaginal Ring.	Thurman AR, Ravel J, Gajer P, Marzinke MA, Ouattara LA, Jacot T, Peet MM, Clark MR, Doncel GF.	Front Cell Infect Microbiol	10.3389/fcimb.2022.799501	2022
Pathogenicity	Insight into the intestinal microbiome of farrowing sows following the administration of garlic (Allium sativum) extract and probiotic bacteria cultures under farming conditions.	Satora M, Magdziarz M, Rzasa A, Rypula K, Ploneczka-Janeczko K.	BMC Vet Res	10.1186/s12917-020-02659-y	2020
Phylogeny	Development of a flow chart for identification of gram-positive anaerobic cocci in the clinical laboratory.	Song Y, Liu C, Finegold SM.	J Clin Microbiol	10.1128/jcm.01872-06	2007
Phylogeny	A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.	Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernandez SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischoder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Sproer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T.	Nat Commun	10.1038/s41467-020-19929-w	2020
Genetics	Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.	Mishra AK, Hugon P, Lagier JC, Nguyen TT, Robert C, Couderc C, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.3276687	2013
Phylogeny	Peptoniphilus faecalis sp. nov., isolated from swine faeces.	Ryu SW, Kim JS, Oh BS, Yu SY, Lee JS, Park SH, Kang SW, Lee J, Lee MK, Rhee MS, Jung H, Hur TY, Kim HB, Kim JK, Lee JH, Lee JH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004836	2021
Phylogeny	Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin.	Song Y, Liu C, Finegold SM	J Clin Microbiol	10.1128/JCM.00213-07	2007

References

#15720	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21461
#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 )
#59871	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53341
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Peptoniphilus gorbachii (JCM 15634, KCTC 5947, DSM 21461)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016908115

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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