Alistipes onderdonkii subsp. vulgaris (DSM 108977, JCM 32839, 3BBH6)

Name: Alistipes onderdonkii subsp. vulgaris (DSM 108977, JCM 32839, 3BBH6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159606

Type strain

Strain Designation 3BBH6

Culture col. no. DSM 108977 JCM 32839 3BBH6

NCBI tax ID(s) 2585117

Special Collections DSMZ JCM Literature strains

History DSMZ <- M. Sakamoto, JCM, RIKEN Bioresource Research Center, Tsukuba; 3BBH6 JCM <-- M. Sakamoto; RIKEN BRC-JCM, Japan; 3BBH6.

Links

Alistipes onderdonkii subsp. vulgaris 3BBH6 is a bacterium that was isolated from Feces of woman.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402377

JCM 32839,DSM 108977

@ref 20215

Last LPSN update 2026-05-29 08:44:14

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Rikenellaceae

Genus Alistipes

Species Alistipes onderdonkii subsp. vulgaris

Full scientific name Alistipes onderdonkii subsp. vulgaris Sakamoto et al. 2020

BacDive ID	Other strains from **Alistipes onderdonkii subsp. vulgaris** (9)	Type strain
164380	A. onderdonkii subsp. vulgaris JCM 32840
164381	A. onderdonkii subsp. vulgaris JCM 32841
164382	A. onderdonkii subsp. vulgaris JCM 32842
164383	A. onderdonkii subsp. vulgaris JCM 32843
164384	A. onderdonkii subsp. vulgaris JCM 32844
164385	A. onderdonkii subsp. vulgaris JCM 32845
164386	A. onderdonkii subsp. vulgaris JCM 32846
164387	A. onderdonkii subsp. vulgaris JCM 32847
164388	A. onderdonkii subsp. vulgaris JCM 32849

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.715
125439	negative	99.856

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66432	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

Culture temp

@ref	Growth	Type	Temperature (°C)
66432	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate anaerobe	98.271

Spore formation

@ref	Spore formation	Confidence
125438		94.476
125439		99.984

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	Host species	Geographic location	Country	Country ISO 3 Code	Continent
66432	Feces of woman	Homo sapiens	Tsukuba	Japan	JPN	Asia
67770	Feces of a woman in the forties	Homo sapiens		Japan	JPN	Asia
69544	the faecal samples of healthy Japanese humans	Homo sapiens	Tsukuba	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC468789 (>99% sequence identity) for Alistipes onderdonkii subclade from Microbeatlas

Aquatic Samples	5936
Soil Samples	1356
Animal Samples	169152
Plant Samples	565
Total Samples	177009

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Aond_1.0 assembly for Alistipes onderdonkii subsp. vulgaris 3BBH6	complete	GCA_006542645	2585117.3	2884622180	2585117	98.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66432	Alistipes onderdonkii subsp. vulgaris 3BBH6 gene for 16S ribosomal RNA, partial sequence	LC468789	1456		2585117

GC content

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

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aond_1.0 assembly for Alistipes onderdonkii subsp. vulgaris 3BBH6
BV-BRC: 2585117.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	99.86	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	98.27	no
125439	motility	BacteriaNetⓘ	yes	49.29	no
125439	spore_formation	BacteriaNetⓘ	no	99.98	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes onderdonkii subsp. vulgaris 3BBH6
NCBI: GCA_006542645.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.72	no
125438	anaerobic	anaerobicⓘ	yes	81.71	no
125438	aerobic	aerobicⓘ	no	88.00	no
125438	spore-forming	spore-formingⓘ	no	94.48	no
125438	thermophilic	thermophileⓘ	no	98.74	no
125438	flagellated	motile2+ⓘ	no	89.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.	Kwan SY, Gonzales KA, Jamal MA, Stevenson HL, Tan L, Lorenzi PL, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Jenq RR, Beretta L.	Gut Microbes	10.1080/19490976.2024.2399260	2024
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 )
#66432	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 108977
#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 onderdonkii subsp. vulgaris (DSM 108977, JCM 32839, 3BBH6)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_006542645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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