Alistipes timonensis (DSM 25383, CSUR P148, JCM 32780)

Name: Alistipes timonensis (DSM 25383, CSUR P148, JCM 32780)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24536

Type strain

Strain Designation JC136

Culture col. no. DSM 25383 CSUR P148 JCM 32780 JC136

NCBI tax ID(s) 1465754

Special Collections DSMZ JCM

History DSMZ <- J.-C. Lagier, Timone Hospital, Marseille, France; JC136 JCM <-- DSM 25383 <-- J.-C. Lagier; Timone Hosp., France; JC136.

Links

Alistipes timonensis JC136 is an anaerobe bacterium that was isolated from human fecal flora of a healthy patient.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402297

JCM 32780,DSM 25383

@ref 20215

Last LPSN update 2026-05-29 08:30:38

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes timonensis

Full scientific name Alistipes timonensis Lagier et al. 2014

BacDive ID	Other strains from **Alistipes timonensis** (1)	Type strain
131513	A. timonensis CC-5826-WT-bac, DSM 27924

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.954
125438		92.188
125438	negative	96.863

Colony morphology

20277

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20277	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
20277	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

Culture temp

@ref	Growth	Type	Temperature (°C)
20277	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
20277	anaerobe
125439	obligate anaerobe	95.979

Spore formation

@ref	Spore formation	Confidence
125438		93.999
125439		99.994

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	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-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	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	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
20277	-	-	+	+	-	-	+	-	+/-	+/-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-
20277	-	-	-	+	-	-	+	-	-	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
20277	human fecal flora of a healthy patient	Homo sapiens	Senegal	SEN	Africa
67770	Fecal flora of a healthy patient in Senegal	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence JF824799 (>99% sequence identity) for Alistipes timonensis from Microbeatlas

Aquatic Samples	72
Soil Samples	68
Animal Samples	14087
Plant Samples	92
Total Samples	14319

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20277	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2693429854 annotated assembly for Alistipes timonensis JC136 DSM 25383	scaffold	GCA_900107675	1033731.11	2693429854	1033731	72.89
67770	ASM28545v1 assembly for Alistipes timonensis JC136 P148	contig	GCA_000285455	1033731.3	2547132133	1033731	69.95

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20277	Alistipes timonensis JC136 16S ribosomal RNA gene, partial sequence	JF824799	1423		1033731

GC content

@ref	GC-content (mol%)	Method
20277	58.82	sequence analysis
67770	58.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2693429854 annotated assembly for Alistipes timonensis JC136 DSM 25383
NCBI: GCA_900107675

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	99.95	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	95.98	no
125439	motility	BacteriaNetⓘ	yes	75.51	no
125439	spore_formation	BacteriaNetⓘ	no	99.99	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes timonensis JC136 strain DSM 25383
PATRIC: 1033731.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.86	no
125438	anaerobic	anaerobicⓘ	yes	82.61	no
125438	spore-forming	spore-formingⓘ	no	94.00	no
125438	aerobic	aerobicⓘ	no	90.51	yes
125438	thermophilic	thermophileⓘ	no	95.62	yes
125438	flagellated	motile2+ⓘ	no	92.19	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Young rat microbiota extracts strongly inhibit fibrillation of alpha-synuclein and protect neuroblastoma cells and zebrafish against alpha-synuclein toxicity.	Shiraz MG, Nielsen J, Widmann J, Chung KHK, Davis TP, Rasmussen C, Scavenius C, Enghild JJ, Martin-Gallausiaux C, Singh Y, Javed I, Otzen DE.	Mol Cells	10.1016/j.mocell.2024.100161	2025
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
Pathogenicity	Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease.	Older EA, Zhang J, Ferris ZE, Xue D, Zhong Z, Mitchell MK, Madden M, Wang Y, Chen H, Nagarkatti P, Nagarkatti M, Fan D, Ellermann M, Li YX, Li J.	Nat Commun	10.1038/s41467-024-53670-y	2024
Metabolism	Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization.	Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW, Lee KS, Lee KS, Sziranyi B, Vesely C, Decker T, Stocker R, Warth B, von Bergen M, Wagner M, Berry D.	Nat Commun	10.1038/s41467-020-18928-1	2020
	The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health.	Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A.	Front Immunol	10.3389/fimmu.2020.00906	2020
Genetics	Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov.	Lagier JC, Armougom F, Mishra AK, Nguyen TT, Raoult D, Fournier PE	Stand Genomic Sci	10.4056/sigs.2685971	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 )
#20277	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25383
#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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Alistipes timonensis (DSM 25383, CSUR P148, JCM 32780)

Name and taxonomic classification

Morphology

Cell morphology

Colony 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_900107675

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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