Name: Collinsella intestinalis RCA56-68
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3047

Type strain:

Species: Collinsella intestinalis

Strain Designation: RCA56-68

Culture col. no.: CCUG 45296, CIP 106914, DSM 13280, JCM 10643, RCA 56-68

Strain history: CIP <- 2001, JCM <- Y. Benno: strain RCA56-68

NCBI tax ID(s): 521003 (strain), 147207 (species)

SI-ID 49453

DSM 13280, JCM 10643, CCUG 45296, CIP 106914

Other strains from Collinsella intestinalis

C. intestinalis 3WC8.2, DSM 13632
C. intestinalis 3WC5, DSM 13635
C. intestinalis JCM 10644

Section

Collinsella intestinalis RCA56-68 is an anaerobe, mesophilic bacterium that was isolated from human feces.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Coriobacteriia*
	Order	*Coriobacteriales*
	Family	*Coriobacteriaceae*
	Genus	*Collinsella*
	Species	**Collinsella intestinalis**
	Full Scientific Name (LPSN)	Collinsella intestinalis Kageyama and Benno 2000

Information on morphological and physiological properties Morphology

[Ref.: #120256]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #120256]	Cell shape	rod-shaped

[Ref.: #120256]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.743

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4990]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #4990]

Culture medium growth

[Ref.: #4990]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4990]

Culture medium composition

expand / minimize

[Ref.: #40616]

Culture medium

MEDIUM 137 - for Ruminococcus hansenii and Rarobacter incanus

[Ref.: #40616]

Culture medium growth

[Ref.: #40616]

Culture medium composition

expand / minimize

[Ref.: #120256]

Culture medium

CIP Medium 137

[Ref.: #120256]

Culture medium growth

[Ref.: #120256]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #4990]	growth	37 °C
[Ref.: #40616]	growth	37 °C
[Ref.: #56722]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #120256]	growth	37 °C

[Ref.: #4990]	Temperature range	mesophilic
[Ref.: #40616]	Temperature range	mesophilic
[Ref.: #56722]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #120256]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4990]	Oxygen tolerance	anaerobe
[Ref.: #56722]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.567

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

[Ref.: #4990]	Murein short key	A11.33
[Ref.: #4990]	Murein types	A4alpha L-Lys-D-Glu

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	+	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[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.: #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.: #4990]	12595	-	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	+	-	-	-	+	-	-	-	+	+	-	-

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

[Ref.: #4990]	Sample type/isolated from	human feces
[Ref.: #4990]	Country	Japan
[Ref.: #4990]	Country ISO 3 Code	JPN
[Ref.: #4990]	Continent	Asia

[Ref.: #56722]	Sample type/isolated from	Human feces
[Ref.: #56722]	Country	Japan
[Ref.: #56722]	Country ISO 3 Code	JPN
[Ref.: #56722]	Continent	Asia

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

[Ref.: #120256]	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?

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

[Ref.: #4990]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120256]	Biosafety level	1	Risk group (French classification)

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]	Collinsella sp. RCA56-68 gene for 16S rRNA	AB031063	1459	ENA	521003 tax ID
[Ref.: #4990]	Hepatitis C virus gene for core protein, partial cds, clone:N5	AB030163	300	ENA	11103 tax ID
[Ref.: #20218]	Collinsella intestinalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 10643	AB558489	1466	ENA	147207 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Collinsella intestinalis DSM 13280	GCA_000156175	scaffold	GenBank	521003 tax ID
[Ref.: #66792]	Collinsella intestinalis DSM 13280	521003.7	wgs	PATRIC	521003 tax ID	*
[Ref.: #66792]	Collinsella intestinalis DSM 13280	2562617146	draft	JGI IMG/M	521003 tax ID	*

[Ref.: #4990]

GC-content

64.4 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Collinsella intestinalis DSM 13280 DSM 13280 NCBI: GCA_000156175.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Collinsella intestinalis DSM 13280 PATRIC: 521003.7
[Ref.: #69480]	gram-positive	yes	91.812	no
[Ref.: #69480]	anaerobic	yes	98.532	yes
[Ref.: #69480]	halophile	no	69.531	no
[Ref.: #69480]	spore-forming	no	95.628	no
[Ref.: #69480]	glucose-util	yes	86.129	no
[Ref.: #69480]	aerobic	no	99.286	no
[Ref.: #69480]	thermophile	no	96.399	yes
[Ref.: #69480]	motile	no	95.881	no
[Ref.: #69480]	flagellated	no	98.201	no
[Ref.: #69480]	glucose-ferment	yes	75.444	no

Availability in culture collections External links

[Ref.: #4990]

Culture collection no.

CCUG 45296, CIP 106914, DSM 13280, JCM 10643, RCA 56-68

[Ref.: #72567]

SI-ID 49453

References

#4990

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13280

#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 )

#40616 ; Curators of the CIP;
#56722 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45296

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72567

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-ID49453.1 )

#120256 Collection of Institut Pasteur ; Curators of the CIP; CIP 106914
* These data were automatically processed and therefore are not curated

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Collinsella intestinalis DSM 13280 DSM 13280

Collinsella intestinalis DSM 13280

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