Peptoniphilus timonensis (DSM 25367, CSUR P165, KCTC 15412)

Name: Peptoniphilus timonensis (DSM 25367, CSUR P165, KCTC 15412)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24765

Type strain

Strain Designation JC401

Culture col. no. DSM 25367 CSUR P165 KCTC 15412 JC401

NCBI tax ID(s) 1268254

Special Collections DSMZ KCTC

History DSMZ <- J.-C. Lagier, Timone Hospital, Marseille, France; JC401 <- J.-C. Lagier, URMITE, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France KCTC <- DSM <- JC Lagier, Timone Hospital, Marseille, France, JC401 <- JC Lagier, URMITE, 27 bd Jean Moulin, 13385 Marseille Cedex 05, France

Links

Peptoniphilus timonensis JC401 is an anaerobe, coccus-shaped bacterium that was isolated from human feces from a healthy 16-year-old male volunteer patient.

coccus-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397380

KCTC 15412,DSM 25367

@ref 20215

Last LPSN update 2026-05-29 08:30:41

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Tissierellales

Family Peptoniphilaceae

Genus Peptoniphilus

Species Peptoniphilus timonensis

Full scientific name Peptoniphilus timonensis Mishra et al. 2015

Morphology

Cell morphology

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

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20728	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)
20728	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
20728	anaerobe
67771	anaerobe
125438	anaerobe	94.358

Spore formation

@ref	Spore formation	Confidence
67771
125439		91.618

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	16199 ChEBI	urea	-	hydrolysis	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	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
20728	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	+	+	-	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Host	#Human	#Male
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
20728	human feces from a healthy 16-year-old male volunteer patient	Homo sapiens	Guinean-Sudanian zone, Dielmo	Senegal	SEN	Africa
67771	From human feces from a healthy 16-year-old male volunteer patient	Homo sapiens	Guinean-Sudanian zone, Dielmo	Senegal	SEN	Africa

Taxonmaps

69479

Global distribution of 16S sequence JN657222 (>99% sequence identity) for Peptoniphilus timonensis from Microbeatlas

Aquatic Samples	1251
Soil Samples	1347
Animal Samples	33105
Plant Samples	317
Total Samples	36020

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20728	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM31202v1 assembly for Peptoniphilus timonensis JC401	scaffold	GCA_000312025	1095770.3	2619619100	1095770	44.22

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20728	Peptoniphilus timonensis JC401 16S ribosomal RNA gene, partial sequence	JN657222	1286		1095770

GC content

@ref	GC-content (mol%)	Method
20728	30.7	sequence analysis
67771	30.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM31202v1 assembly for Peptoniphilus timonensis JC401
NCBI: GCA_000312025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	89.72	no
125439	motility	BacteriaNetⓘ	no	76.57	no
125439	gram_stain	BacteriaNetⓘ	positive	63.79	no
125439	spore_formation	BacteriaNetⓘ	no	91.62	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Peptoniphilus timonensis JC401 JC401
NCBI: GCA_000312025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	82.49	yes
125438	anaerobic	anaerobicⓘ	yes	94.36	no
125438	aerobic	aerobicⓘ	no	97.28	no
125438	spore-forming	spore-formingⓘ	no	73.01	no
125438	thermophilic	thermophileⓘ	no	93.49	no
125438	flagellated	motile2+ⓘ	no	86.68	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov.	Mishra AK, Lagier JC, Robert C, Raoult D, Fournier PE	Stand Genomic Sci	10.4056/sigs.2956294	2012

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 )
#20728	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25367
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Peptoniphilus timonensis (DSM 25367, CSUR P165, KCTC 15412)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000312025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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