Name: Collinsella tanakaei DSM 22478
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3050

Type strain:

Species: Collinsella tanakaei

Culture col. no.: DSM 22478, JCM 16071, YIT 12063, KCTC 15132

Strain history: Y. Watanabe A40 (=YIT 12063).

NCBI tax ID(s): 742742 (strain), 626935 (species)

SI-ID 398191

DSM 22478

Special Collections

Other strains from Collinsella tanakaei

Section

Collinsella tanakaei DSM 22478 is an obligate anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faeces .

Gram-positive
rod-shaped
mesophilic
obligate anaerobe
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	*Actinomycetota*
	Class	*Coriobacteriia*
	Order	*Coriobacteriales*
	Family	*Coriobacteriaceae*
	Genus	*Collinsella*
	Species	**Collinsella tanakaei**
	Full Scientific Name (LPSN)	Collinsella tanakaei Nagai et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29633]	Gram stain	positive

[Ref.: #29633]	Cell length	1-3.3 µm

[Ref.: #29633]	Cell width	0.5-1 µm

[Ref.: #29633]	Cell shape	rod-shaped

[Ref.: #29633]	Motility	no

[Ref.: #29633]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16260]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #16260]

Culture medium growth

[Ref.: #16260]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16260]

Culture medium composition

expand / minimize

[Ref.: #16260]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #16260]

Culture medium growth

[Ref.: #16260]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16260]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16260]	growth	37 °C
[Ref.: #29633]	growth	37 °C
[Ref.: #29633]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #29633]			optimum	7
[Ref.: #29633]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #16260]	Oxygen tolerance	obligate anaerobe
[Ref.: #29633]	Oxygen tolerance	anaerobe

[Ref.: #29633]

Ability of spore formation

[Ref.: #29633]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	+	hydrolysis	* from API rID32A
[Ref.: #29633]	cellobiose ChEBI	+	carbon source
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #29633]	esculin ChEBI	+	hydrolysis
[Ref.: #29633]	glucose ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #29633]	lactose ChEBI	+	carbon source
[Ref.: #29633]	maltose ChEBI	+	carbon source
[Ref.: #29633]	mannose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #29633]	salicin ChEBI	+	carbon source
[Ref.: #29633]	sucrose ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[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]	arginine dihydrolase	+	3.5.3.6	* 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.: #16260]	14112	-	+	-	-	-	+	+	-	-	-	+	+/-	-	-	-	-	+	+	+	-	-	+	-	-	-	+	+	-	-

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

[Ref.: #16260]	Sample type/isolated from	human faeces (healthy Japanese adult)
[Ref.: #16260]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #16260]	Country	Japan
[Ref.: #16260]	Country ISO 3 Code	JPN
[Ref.: #16260]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Human feces
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB601001 (>99% sequence identity) for Collinsella tanakaei subclade from Microbeatlas

Aquatic Samples	106
Soil Samples	49
Animal Samples	4896
Plant Samples	1
Total Samples	5052

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

[Ref.: #16260]

Biosafety level

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.: #16260]	Collinsella tanakaei gene for 16S rRNA, partial sequence, strain: YIT 12063	AB490807	1491	GenBank ENA	742742 tax ID
[Ref.: #20218]	Collinsella tanakaei gene for 16S ribosomal RNA, partial sequence	AB601001	1469	GenBank ENA	742742 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Collinsella tanakaei YIT 12063	GCA_000225705	scaffold	GenBank ENA	742742 tax ID
[Ref.: #66792]	Collinsella tanakaei YIT 12063	742742.3	wgs	PATRIC	742742 tax ID	*
[Ref.: #66792]	Collinsella tanakaei YIT 12063	2513237344	draft	JGI IMG/M	742742 tax ID	*

[Ref.: #16260]	GC-content	60.8-61 mol%
[Ref.: #67770]	GC-content	60.8 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Collinsella tanakaei YIT 12063 PATRIC: 742742.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	80.948	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	84.84	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	81.29	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	92.178	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.292	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	83.625	yes

Availability in culture collections External links

[Ref.: #16260]

Culture collection no.

DSM 22478, JCM 16071, YIT 12063, KCTC 15132

[Ref.: #72570]

SI-ID 398191

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Completion of the gut microbial epi-bile acid pathway.	Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM	Gut Microbes	10.1080/19490976.2021.1907271	2021	*
Phylogeny	Collinsella vaginalis sp. nov. strain Marseille-P2666(T), a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis.	Diop A, Diop K, Tomei E, Armstrong N, Bretelle F, Raoult D, Fenollar F, Fournier PE	Int J Syst Evol Microbiol	10.1099/ijsem.0.003221	2019	*
Phylogeny	Slackia piriformis sp. nov. and Collinsella tanakaei sp. nov., new members of the family Coriobacteriaceae, isolated from human faeces.	Nagai F, Watanabe Y, Morotomi M	Int J Syst Evol Microbiol	10.1099/ijs.0.017533-0	2009	*

References

#16260

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22478

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29633

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 #26023 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#72570

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-ID398191.1 )

#26023

IJSEM 2639 2010 ( DOI 10.1099/ijs.0.017533-0 , PubMed 20023061 )

* These data were automatically processed and therefore are not curated

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Collinsella tanakaei YIT 12063

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