Alistipes ihumii (DSM 26107, CSUR P204, DSM 109016)

Name: Alistipes ihumii (DSM 26107, CSUR P204, DSM 109016)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131498

Type strain

Strain Designation AP11

Culture col. no. DSM 26107 CSUR P204 DSM 109016 JCM 32776 AP11

NCBI tax ID(s) 1470347

Special Collections DSMZ JCM Cadoret human gut

History <- JCM; JCM 32776 <- S. Gronow, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH; DSM 26107 <- J.-C. Lagier, Timone Hospital, Marseille, France; CSUR P204 <- A. Pfleiderer; AP11 DSM 26107 <-- J.-C. Lagier; Timone Hosp., France; AP11 <-- A. Pfleiderer.

Links

Alistipes ihumii AP11 is a bacterium that was isolated from human feces of a French Caucasian female.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398550

DSM 109016

@ref 20215

Last LPSN update 2026-02-09 11:31:28

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes ihumii

Full scientific name Alistipes ihumii Pfleiderer et al. 2017

Synonyms (1)

"Candidatus Alistipes ihumii"

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	100
125438	negative	97.738

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64789	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
64789	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)
64789	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	95.4

Spore formation

@ref	Spore formation	Confidence
125439		99.9
125438		93.494

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	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	tryptophan deaminase	-	4.1.99.1	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
64789	-	-	-	-	-	+/-	-	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
64789	human feces of a French Caucasian female	France	FRA	Europe
67770	Fecal flora of a 21-year-old French Caucasian female

Taxonmaps

69479

Global distribution of 16S sequence JX101692 (>99% sequence identity) for Alistipes ihumii subclade from Microbeatlas

Aquatic Samples	584
Soil Samples	90
Animal Samples	26797
Plant Samples	12
Total Samples	27483

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64789	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	ASM2514466v1 assembly for Alistipes ihumii AP11	complete	GCA_025144665	1211813.138	8049278100	1211813	96.53
67770	ASM32120v1 assembly for Alistipes ihumii AP11	contig	GCA_000321205	1211813.3	2551306355	1211813	64.53

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Alistipes ihumii AP11 16S ribosomal RNA gene, partial sequence	JX101692	1494		1211813

GC content

@ref	GC-content (mol%)	Method
64789	57.9	sequence analysis
67770	57.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alistipes ihumii AP11
PATRIC: 1211813.138

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	95.40	no
125439	gram_stain	BacteriaNetⓘ	negative	100.00	no
125439	motility	BacteriaNetⓘ	yes	51.60	no
125439	spore_formation	BacteriaNetⓘ	no	99.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes ihumii AP11 AP11
NCBI: GCA_025144665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.74	no
125438	anaerobic	anaerobicⓘ	yes	78.92	no
125438	aerobic	aerobicⓘ	no	85.30	no
125438	spore-forming	spore-formingⓘ	no	93.49	no
125438	thermophilic	thermophileⓘ	no	95.41	yes
125438	flagellated	motile2+ⓘ	no	89.68	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
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
Genetics	Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov.	Pfleiderer A, Mishra AK, Lagier JC, Robert C, Caputo A, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.4698398	2014

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 )
#64789	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 109016
#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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Alistipes ihumii (DSM 26107, CSUR P204, DSM 109016)

Name and taxonomic classification

Morphology

Cell 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_025144665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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