Alistipes communis (DSM 108979, JCM 32850, 5CBH24)

Name: Alistipes communis (DSM 108979, JCM 32850, 5CBH24)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159608

Type strain

Strain Designation 5CBH24

Culture col. no. DSM 108979 JCM 32850 5CBH24

NCBI tax ID(s) 2585118

Special Collections DSMZ JCM Literature strains

History <- M. Sakamoto, JCM, RIKEN Bioresource Research Center, Tsukuba, Japan; JCM 32850 M. Sakamoto; RIKEN BRC-JCM, Japan; 5CBH24.

Links

Alistipes communis 5CBH24 is an anaerobe, mesophilic, rod-shaped prokaryote that forms circular colonies and was isolated from Feces of woman.

rod-shaped colony-forming anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404981

JCM 32850,DSM 108979

@ref 20215

Last LPSN update 2026-02-09 11:38:41

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes communis

Full scientific name Alistipes communis Sakamoto et al. 2020

Synonyms (1)

"Alistipes obesi"

BacDive ID	Other strains from **Alistipes communis** (2)	Type strain
164356	A. communis JCM 32778, CSUR P186, DSM 25724
164389	A. communis JCM 32851

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Gram stain	Confidence
125439				negative	99.9
125438					90.375
125438				negative	96.188
69544	1.7 µm	0.8 µm	rod-shaped
69544			coccus-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
69544	0.1-0.2 mm	grey	circular	4 days	EG agar
69544	0.1-1 mm	gray	circular	4 days	EG agar

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66434	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
69544	EG agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
66434	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
69544	positive	growth	25-37	mesophilic
69544	positive	optimum	37	mesophilic

Culture pH

@ref	Ability	Type	PH
69544	positive	optimum	7
69544	positive	growth	6.3-7.8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
69544	anaerobe
125438	anaerobe	93.311
125439	obligate anaerobe	95.1

Spore formation

@ref	Spore formation	Confidence
125439		99.8
125438		94.494
69544

Observation

@ref	Observation
69544	Growth occurs on medium containing 20 % (w/v) bile. Aesculin is hydrolysed. Gelatin is not digested. Indole is not produced, pigmented variable.
69544	The major end-products in peptone-yeast extract-glucose broth (1 %, w/v, of each) are succinate, acetate and propionate.

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69544	17057 ChEBI	cellobiose	+	builds acid from
69544	16899 ChEBI	D-mannitol	+	builds acid from
69544	16024 ChEBI	D-mannose	+	builds acid from
69544	17924 ChEBI	D-sorbitol	+	builds acid from
69544	65327 ChEBI	D-xylose	-	builds acid from
69544	65327 ChEBI	D-xylose	+/-	builds acid from
69544	4853 ChEBI	esculin	-	hydrolysis
69544	4853 ChEBI	esculin	+	hydrolysis
69544	5291 ChEBI	gelatin	-	assimilation
69544	5291 ChEBI	gelatin	+	assimilation
69544	17234 ChEBI	glucose	+	builds acid from
69544	17754 ChEBI	glycerol	+	builds acid from
69544	35581 ChEBI	indole	-	assimilation
69544	35581 ChEBI	indole	+	assimilation
69544	30849 ChEBI	L-arabinose	-	builds acid from
69544	30849 ChEBI	L-arabinose	+/-	builds acid from
69544	62345 ChEBI	L-rhamnose	+	builds acid from
69544	17716 ChEBI	lactose	+	builds acid from
69544	17306 ChEBI	maltose	+	builds acid from
69544	6731 ChEBI	melezitose	+	builds acid from
69544	16634 ChEBI	raffinose	+	builds acid from
69544	17814 ChEBI	salicin	-	builds acid from
69544	17814 ChEBI	salicin	+/-	builds acid from
69544	17992 ChEBI	sucrose	+	builds acid from
69544	27082 ChEBI	trehalose	+	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite
69544	2676	amoxicillin
69544	17698	chloramphenicol
69544	100241	ciprofloxacin
69544	48923	erythromycin
69544	27701	oxytetracycline
69544	17334	penicillin

Enzymes

@ref	Value	Activity	Ec
69544	catalase	-	1.11.1.6
69544	catalase	+/-	1.11.1.6
69544	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
66434	Feces of woman	Tsukuba	Japan	JPN	Asia
67770	Feces of a woman in the forties		Japan	JPN	Asia
69544	the faecal samples of healthy Japanese humans.	Tsukuba	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC468799 (>99% sequence identity) for Alistipes communis subclade from Microbeatlas

Aquatic Samples	1636
Soil Samples	518
Animal Samples	76517
Plant Samples	101
Total Samples	78772

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Acom_1.0 assembly for Alistipes communis 5CBH24	complete	GCA_006542665	2585118.3	8067829347	2585118	97.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66434	Alistipes communis 5CBH24 gene for 16S ribosomal RNA, partial sequence	LC468799	1484		2585118

GC content

@ref	GC-content (mol%)	Method
67770	58.5	genome sequence analysis
69544	61.3	genome sequence analysis
69544	58	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alistipes communis 5CBH24
NCBI: GCA_006542665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.80	no
125439	motility	BacteriaNetⓘ	yes	76.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	95.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes communis 5CBH24
NCBI: GCA_006542665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.19	no
125438	anaerobic	anaerobicⓘ	yes	93.31	yes
125438	aerobic	aerobicⓘ	no	94.74	no
125438	spore-forming	spore-formingⓘ	no	94.49	no
125438	thermophilic	thermophileⓘ	no	95.99	yes
125438	flagellated	motile2+ⓘ	no	90.38	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
Phylogeny	Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.	Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003778	2020

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 )
#66434	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108979
#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;
#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 .
#69544	Mitsuo Sakamoto, Nao Ikeyama, Yusuke Ogata, Wataru Suda, Takao Iino, Masahira Hattori, Moriya Ohkuma.: Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.. IJSEM 70: 2020 ( DOI 10.1099/ijsem.0.003778 )
#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 communis (DSM 108979, JCM 32850, 5CBH24)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Antibiotic resistance

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_006542665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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