Alistipes putredinis (DSM 17216, CCUG 45780, CIP 104286)

Name: Alistipes putredinis (DSM 17216, CCUG 45780, CIP 104286)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14029

Type strain

Strain Designation Carlier 10203, strain 1 Ando, 10203, 1 And

Culture col. no. DSM 17216 CCUG 45780 CIP 104286 ATCC 29800 Carlier 10203 5 more

NCBI tax ID(s) 445970 28117

Special Collections DSMZ CCUG JCM CIP

History <- CCUG; CCUG 45780 <- CIP; CIP 104286 <- J.-P. Carlier; Carlier 10203 <- ATCC; ATCC 29800 <- E. P. Cato; VPI 3293 <- S. Suzuki; strain 1 Ando CCUG 45780 <-- CIP 104286 <-- J. P. Carlier 10203 <-- ATCC 29800 <-- E. P. Cato VPI 3293 <-- S. Suzuki strain 1 Ando. CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10203 <- ATCC <- E.P. Cato: strain VPI 3293 <- S. Suzuki: strain 1 And

Links

Alistipes putredinis Carlier 10203 is an anaerobe, mesophilic human pathogen that was isolated from Human, feces.

anaerobe mesophilic human pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 92936

ATCC 29800,CIP 104286,CCUG 45780,DSM 17216,JCM 16772

@ref 20215

Last LPSN update 2026-02-09 11:21:18

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes putredinis

Full scientific name Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003

Synonyms (2)

Bacteroides putredinis
"Bacillus putredinis"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7
125438	negative	93.975

Colony morphology

6820

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6820	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
35647	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
6820	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
122073	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6820	positive	growth	37	mesophilic
35647	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6820	anaerobe
125439	obligate anaerobe	93.5

Spore formation

@ref	Spore formation	Confidence
125439		99.9
125438		93.099

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	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	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	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	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	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
6820	-	-	-	-	-	+/-	-	-	-	-	-	-	+	-	-	+	+	-	+/-	+	+/-	-	-	+/-	+	+/-	-	+	-
6820	-	-	-	-	-	+/-	-	-	-	-	-	-	+	-	-	+	+	-	+/-	+	+/-	-	-	+/-	+	-	-	+	-
6820	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type
6820	Human, feces
67770	Human specimens
122073	Human, Feces

Taxonmaps

69479

Global distribution of 16S sequence AB554232 (>99% sequence identity) for Alistipes from Microbeatlas

Aquatic Samples	12321
Soil Samples	2823
Animal Samples	235653
Plant Samples	821
Total Samples	251618

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
6820			2	Risk group (German classification) According to TRBA 466
122073			1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM15446v1 assembly for Alistipes putredinis DSM 17216	scaffold	GCA_000154465	445970.5	641736205	445970	74.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6820	Bacteroides putredinis ATCC 29800 16S ribosomal RNA gene, complete sequence	L16497	1468		28117
67770	Alistipes putredinis gene for 16S ribosomal RNA, partial sequence, strain: JCM 16772	AB554232	1488		28117

GC content

@ref	GC-content (mol%)	Method
6820	55
6820	53.3	sequence analysis
67770	55	high performance liquid chromatography (HPLC)
67770	53.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alistipes putredinis DSM 17216
NCBI: GCA_000154465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.90	no
125439	motility	BacteriaNetⓘ	yes	67.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	93.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes putredinis DSM 17216
PATRIC: 445970.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.98	no
125438	anaerobic	anaerobicⓘ	yes	84.09	yes
125438	spore-forming	spore-formingⓘ	no	93.10	no
125438	aerobic	aerobicⓘ	no	92.46	yes
125438	thermophilic	thermophileⓘ	no	94.49	no
125438	flagellated	motile2+ⓘ	no	88.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome.	Liu P, Hu S, He Z, Feng C, Dong G, An S, Liu R, Xu F, Chen Y, Ying X.	Front Microbiol	10.3389/fmicb.2022.828254	2022
	Lipid complexation reduces rice starch digestibility and boosts short-chain fatty acid production via gut microbiota.	Shen Y, An Z, Huyan Z, Shu X, Wu D, Zhang N, Pellegrini N, Rubert J.	NPJ Sci Food	10.1038/s41538-023-00230-1	2023
	Complete Genome Sequence of Bacteroidales Strain CF from a Chloroform-Dechlorinating Enrichment Culture.	Tang S, Edwards EA.	Genome Announc	10.1128/genomea.01066-13	2013
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
	Gut-Thyroid axis: How gut microbial dysbiosis associated with euthyroid thyroid cancer.	Ishaq HM, Mohammad IS, Hussain R, Parveen R, Shirazi JH, Fan Y, Shahzad M, Hayat K, Li H, Ihsan A, Muhammad KS, Usman M, Zhang S, Yuan L, Ullah S, Paiva-Santos AC, Xu J.	J Cancer	10.7150/jca.66816	2022
Metabolism	Depletion of microbiome-derived molecules in the host using Clostridium genetics.	Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH, Fischbach MA.	Science	10.1126/science.aav1282	2019
Phylogeny	Evolutionary divergence of chloroplast FAD synthetase proteins.	Yruela I, Arilla-Luna S, Medina M, Contreras-Moreira B.	BMC Evol Biol	10.1186/1471-2148-10-311	2010
	Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes.	Lin HH, Liao YC.	Sci Rep	10.1038/srep24175	2016
Transcriptome	Biochemical analysis of pistol self-cleaving ribozymes.	Harris KA, Lunse CE, Li S, Brewer KI, Breaker RR.	RNA	10.1261/rna.052514.115	2015
	Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients.	Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P, Xu J.	Int J Biol Sci	10.7150/ijbs.24151	2018
	RELMbeta sets the threshold for microbiome-dependent oral tolerance.	Stephen-Victor E, Kuziel GA, Martinez-Blanco M, Jugder BE, Benamar M, Wang Z, Chen Q, Lozano GL, Abdel-Gadir A, Cui Y, Fong J, Saint-Denis E, Chang I, Nadeau KC, Phipatanakul W, Zhang A, Farraj FA, Holder-Niles F, Zeve D, Breault DT, Schmitz-Abe K, Rachid R, Crestani E, Rakoff-Nahoum S, Chatila TA.	Nature	10.1038/s41586-024-08440-7	2025
	Novel systems modeling methodology in comparative microbial metabolomics: identifying key enzymes and metabolites implicated in autism spectrum disorders.	Heberling C, Dhurjati P.	Int J Mol Sci	10.3390/ijms16048949	2015
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
	The prevalence of species and strains in the human microbiome: a resource for experimental efforts.	Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M.	PLoS One	10.1371/journal.pone.0097279	2014
	Metagenomic analysis of the medicinal leech gut microbiota.	Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J.	Front Microbiol	10.3389/fmicb.2014.00151	2014
Enzymology	Degradation of the low-calorie sugar substitute 5-ketofructose by different bacteria.	Schiessl J, Kosciow K, Garschagen LS, Hoffmann JJ, Heymuth J, Franke T, Deppenmeier U.	Appl Microbiol Biotechnol	10.1007/s00253-021-11168-3	2021
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Genetics	In vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota.	Kim BS, Kim JN, Cerniglia CE.	J Biomed Biotechnol	10.1155/2011/838040	2011
Genetics	Inter-individual differences in the gene content of human gut bacterial species.	Zhu A, Sunagawa S, Mende DR, Bork P.	Genome Biol	10.1186/s13059-015-0646-9	2015
Pathogenicity	Vesiculation from Pseudomonas aeruginosa under SOS.	Maredia R, Devineni N, Lentz P, Dallo SF, Yu J, Guentzel N, Chambers J, Arulanandam B, Haskins WE, Weitao T.	ScientificWorldJournal	10.1100/2012/402919	2012
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
Phylogeny	Comparative fecal metagenomics unveils unique functional capacity of the swine gut.	Lamendella R, Domingo JW, Ghosh S, Martinson J, Oerther DB.	BMC Microbiol	10.1186/1471-2180-11-103	2011
	Bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.	Silverio AL, Saier MH.	J Membr Biol	10.1007/s00232-011-9364-8	2011
Genetics	Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics.	Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori PL, Hirt RP.	BMC Genomics	10.1186/1471-2164-11-99	2010
	Alistipes putredinis CCUG 45780^T exacerbates DSS-induced colitis in mice via modulation of gut microbiota and succinate metabolism.	Niu M, He QY, Chen YX, Liu SM, Pan YQ, Zhu XR, Miao YL, Du Y.	BMC Microbiol	10.1186/s12866-025-04445-y	2025
	Western diet contributes to the pathogenesis of non-alcoholic steatohepatitis in male mice via remodeling gut microbiota and increasing production of 2-oleoylglycerol.	Yang M, Qi X, Li N, Kaifi JT, Chen S, Wheeler AA, Kimchi ET, Ericsson AC, Rector RS, Staveley-O'Carroll KF, Li G.	Nat Commun	10.1038/s41467-023-35861-1	2023
Genetics	The Primary Research on the Gut Microbes in KKAy Mice.	Li Y, Han L, Xu M, Guo J, Feng M, Wang X.	Indian J Microbiol	10.1007/s12088-013-0410-3	2014
	Identification of Prevotella Oralis as a possible target antigen in children with Enthesitis related arthritis.	Stoll ML, Duck LW, Chang MH, Colbert RA, Nigrovic PA, Thompson SD, Elson CO.	Clin Immunol	10.1016/j.clim.2020.108463	2020
	Gut Microbiota Alterations from Three-Strain Yogurt Formulation Treatments in Slow-Transit Constipation.	Li XR, Liu CJ, Tang XD, Zhang HM, Luo YY, Zhang L, Yang E.	Can J Infect Dis Med Microbiol	10.1155/2020/4583973	2020
	Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima.	Pope PB, Vivekanand V, Eijsink VG, Horn SJ.	3 Biotech	10.1007/s13205-012-0097-x	2013
	Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.	Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K.	Sci Rep	10.1038/s41598-024-54769-4	2024
	A Soybean Resistant Protein-Containing Diet Increased the Production of Reg3gamma Through the Regulation of the Gut Microbiota and Enhanced the Intestinal Barrier Function in Mice.	Ogita T, Namai F, Mikami A, Ishiguro T, Umezawa K, Uyeno Y, Shimosato T.	Front Nutr	10.3389/fnut.2021.701466	2021
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
	Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.	Hagihara M, Yamashita M, Ariyoshi T, Minemura A, Yoshida C, Higashi S, Oka K, Takahashi M, Ota A, Maenaka A, Iwasaki K, Hirai J, Shibata Y, Umemura T, Mori T, Kato H, Asai N, Mikamo H.	iScience	10.1016/j.isci.2025.113502	2025
Metabolism	Gut microbial carbohydrate metabolism contributes to insulin resistance.	Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.	Nature	10.1038/s41586-023-06466-x	2023
Genetics	Non contiguous-finished genome sequence and description of Alistipes obesi sp. nov.	Hugon P, Ramasamy D, Lagier JC, Rivet R, Couderc C, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.3336746	2013

References

#6820	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17216
#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 )
#35647	; Curators of the CIP;
#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 .
#122073	Collection of Institut Pasteur ; Curators of the CIP; CIP 104286
#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 putredinis (DSM 17216, CCUG 45780, CIP 104286)

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

Metabolite production

Metabolite tests

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_000154465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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