Name: Alistipes onderdonkii subsp. onderdonkii KCTC 15237
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14031

Type strain:

Species: Alistipes onderdonkii subsp. onderdonkii

Culture col. no.: KCTC 15237, DSM 19147, ATCC BAA-1178, CCUG 48946, WAL 8169, JCM 16771

Strain history: <- CCUG <- Y Song, WAL 8169

NCBI tax ID(s): 328813 (species), 2706586 (subspecies)

SI-ID 297119

ATCC BAA-1178, CCUG 48946, DSM 19147, JCM 16771

Special Collections

Other strains from Alistipes onderdonkii subsp. onderdonkii

Section

When using BacDive for research please cite our paper

Alistipes onderdonkii subsp. onderdonkii KCTC 15237 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human abdominal abscess.

Gram-negative
rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Rikenellaceae*
	Genus	*Alistipes*
	Species	**Alistipes onderdonkii subsp. onderdonkii**
	Full Scientific Name (LPSN)	Alistipes onderdonkii subsp. onderdonkii (Song et al. 2006) Sakamoto et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #31803]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %94.818
[Ref.: #125439]	Gram stain	negative Confidence in %99.7

[Ref.: #31803]	Cell length	0.5-3 µm

[Ref.: #31803]	Cell width	0.2-0.5 µm

[Ref.: #31803]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31803]	Motility	no

[Ref.: #58400]

Incubation period

1 day

[Ref.: #31803]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7936]

Culture medium

COLUMBIA BLOOD AGAR (DSMZ Medium 429)

[Ref.: #7936]

Culture medium growth

[Ref.: #7936]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7936]

Culture medium composition

expand / minimize

[Ref.: #7936]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #7936]

Culture medium growth

[Ref.: #7936]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7936]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7936]	growth	37 °C
[Ref.: #31803]	growth	37 °C
[Ref.: #31803]	optimum	37 °C
[Ref.: #58400]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #31803]			optimum	7
[Ref.: #31803]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7936]	Oxygen tolerance	anaerobe
[Ref.: #31803]	Oxygen tolerance	anaerobe
[Ref.: #58400]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate anaerobe Confidence in %99

[Ref.: #31803]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %94.476
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.8

[Ref.: #31803]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #31803]	esculin ChEBI	+	hydrolysis
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #31803]	mannose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #31803]	raffinose ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	+	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #31803]		indole ChEBI	yes
[Ref.: #68380]		indole ChEBI	yes	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #31803]		indole ChEBI	+
[Ref.: #68380]		indole ChEBI	+	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	+	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	+		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	+	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #7936]	13618	-	+/-	+	+	-	+	-	-	-	+	+	+	-	-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7936]	Sample type/isolated from	human abdominal abscess
[Ref.: #7936]	Country	USA
[Ref.: #7936]	Country ISO 3 Code	USA
[Ref.: #7936]	Continent	North America

[Ref.: #58400]	Sample type/isolated from	Human abdominal abscess
[Ref.: #58400]	Sampling date	1989
[Ref.: #58400]	Geographic location (country and/or sea, region)	Los Angeles
[Ref.: #58400]	Country	USA
[Ref.: #58400]	Country ISO 3 Code	USA
[Ref.: #58400]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Human specimens

[Ref.: #67771]	Sample type/isolated from	From human abdominal abscess
[Ref.: #67771]	Country	USA
[Ref.: #67771]	Country ISO 3 Code	USA
[Ref.: #67771]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Other	#Abdomen
#Host Body-Site	#Other	#Abscess
#Infection	#Patient	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY974071 (>99% sequence identity) for Alistipes onderdonkii subclade from Microbeatlas

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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7936]	Pathogenicity (human)	yes, in single cases
[Ref.: #7936]	Biosafety level	1	Risk group (German classification) According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Alistipes onderdonkii gene for 16S ribosomal RNA, partial sequence, strain: JCM 16771	AB554231	1489	GenBank ENA	328813 tax ID
[Ref.: #7936]	Alistipes onderdonkii strain WAL 8169 16S ribosomal RNA gene, partial sequence	AY974071	1440	GenBank ENA	328813 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Alistipes onderdonkii WAL 8169 = DSM 19147	GCA_000374505	scaffold	GenBank ENA	1203611 tax ID
[Ref.: #66792]	Alistipes onderdonkii DSM 19147	1120974.3	wgs	PATRIC	1203611 tax ID	*
[Ref.: #66792]	Alistipes onderdonkii WAL 8169, DSM 19147	2517572213	draft	JGI IMG/M	1203611 tax ID	*
[Ref.: #66792]	Alistipes onderdonkii DSM 19147	GCA_025145285	complete	GenBank ENA	328813 tax ID	*
[Ref.: #66792]	Alistipes onderdonkii strain DSM 19147	328813.144	complete	PATRIC	328813 tax ID	*

[Ref.: #7936]	GC-content	58 mol%
[Ref.: #67770]	GC-content	58 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	57.8 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	58.0 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alistipes onderdonkii DSM 19147 NCBI: GCA_025145285.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	94.818	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	85.136	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	87.929	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	94.476	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.74	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89.595	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alistipes onderdonkii strain DSM 19147 PATRIC: 328813.144
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate anaerobe	99
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	55.7
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.8

Availability in culture collections External links

[Ref.: #7936]

Culture collection no.

KCTC 15237, DSM 19147, ATCC BAA-1178, CCUG 48946, WAL 8169, JCM 16771

[Ref.: #83198]

SI-ID 297119

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
Phylogeny	Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin.	Song Y, Kononen E, Rautio M, Liu C, Bryk A, Eerola E, Finegold SM	Int J Syst Evol Microbiol	10.1099/ijs.0.64318-0	2006	*

References

#7936

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19147

#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 )

#31803

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28072 (see below)

#58400 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48946

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#83198

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297119.1 )

#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 .

#28072

IJSEM 1985 2006 ( DOI 10.1099/ijs.0.64318-0 , PubMed 16902041 )

* These data were automatically processed and therefore are not curated

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Alistipes onderdonkii DSM 19147

Alistipes onderdonkii strain DSM 19147

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