Collinsella stercoris (DSM 13279, JCM 10641, CCUG 45295)

Name: Collinsella stercoris (DSM 13279, JCM 10641, CCUG 45295)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3046

Type strain

Strain Designation RCA55-54

Culture col. no. DSM 13279 JCM 10641 CCUG 45295 CIP 106913 RCA 55-54 1 more

NCBI tax ID(s) 445975 147206

Special Collections DSMZ CCUG JCM CIP

Links

Collinsella stercoris RCA55-54 is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from human feces.

Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49452

DSM 13279,JCM 10641,CCUG 45295,CIP 106913

@ref 20215

Last LPSN update 2025-12-16 09:47:27

Domain Bacillati

Phylum Actinomycetota

Class Coriobacteriia

Order Coriobacteriales

Family Coriobacteriaceae

Genus Collinsella

Species Collinsella stercoris

Full scientific name Collinsella stercoris Kageyama and Benno 2000

BacDive ID	Other strains from **Collinsella stercoris** (4)	Type strain
161011	C. stercoris JCM 10642
161024	C. stercoris JCM 10709
161025	C. stercoris JCM 10710
161026	C. stercoris JCM 10711

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
123314	positive	rod-shaped
125439	negative			97.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4989	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
123314	CIP Medium 137		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4989	positive	growth	37	mesophilic
56721	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4989	anaerobe
56721	anaerobe
125439	anaerobe	94.6

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Murein

@ref	Murein short key	Type
4989	A21.04	A4ß L-Orn-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
4989	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+/-	+	-	-	-	+/-	-	-	-	+/-	+/-	-	-
4989	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	+	-	-	-	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4989	human feces	Japan	JPN	Asia
56721	Human feces	Japan	JPN	Asia
67770	Human feces
123314	Human, Feces	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4989	1	Risk group (German classification) According to TRBA 466
123314	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Collinsella stercoris DSM 13279 strain FDAARGOS_1572	complete		445975.14		445975	98.82
66792	ASM2073546v1 assembly for Collinsella stercoris DSM 13279 FDAARGOS_1572	complete	GCA_020735465	445975.13	8111085423	445975	96.33
66792	ASM2514962v1 assembly for Collinsella stercoris DSM 13279	complete	GCA_025149625	147206.16		147206	95.81
67770	ASM15621v1 assembly for Collinsella stercoris DSM 13279	scaffold	GCA_000156215	445975.6	642979321	445975	40.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Collinsella stercoris gene for 16S ribosomal RNA, partial sequence, strain: JCM 10641	AB558488	1466		147206
67770	Collinsella sp. RCA55-54 gene for 16S rRNA	AB031061	1458		445975

GC content

@ref	GC-content (mol%)	Method
4989	61.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Collinsella stercoris DSM 13279 FDAARGOS_1572
NCBI: GCA_020735465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	85.20	no
125439	gram_stain	BacteriaNetⓘ	negative	97.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	94.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Collinsella stercoris DSM 13279 FDAARGOS_1572
NCBI: GCA_020735465.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	77.59	no
125438	anaerobic	anaerobicⓘ	yes	89.62	yes
125438	aerobic	aerobicⓘ	no	96.84	no
125438	spore-forming	spore-formingⓘ	no	79.97	no
125438	thermophilic	thermophileⓘ	no	91.06	no
125438	flagellated	motile2+ⓘ	no	85.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Transcriptome	Gut metatranscriptomics based de novo assembly reveals microbial signatures predicting immunotherapy outcomes in non-small cell lung cancer.	Dora D, Kiraly P, Somodi C, Ligeti B, Dulka E, Galffy G, Lohinai Z.	J Transl Med	10.1186/s12967-024-05835-y	2024
	Mapping the T cell repertoire to a complex gut bacterial community.	Nagashima K, Zhao A, Atabakhsh K, Bae M, Blum JE, Weakley A, Jain S, Meng X, Cheng AG, Wang M, Higginbottom S, Dimas A, Murugkar P, Sattely ES, Moon JJ, Balskus EP, Fischbach MA.	Nature	10.1038/s41586-023-06431-8	2023
	Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host.	D'Angelo F, Fernandez-Fueyo E, Garcia PS, Shomar H, Pelosse M, Manuel RR, Buke F, Liu S, van den Broek N, Duraffourg N, de Ram C, Pabst M, Bouveret E, Gribaldo S, Py B, Ollagnier de Choudens S, Barras F, Bokinsky G.	Elife	10.7554/elife.70936	2022
	The changing metabolic landscape of bile acids - keys to metabolism and immune regulation.	Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC.	Nat Rev Gastroenterol Hepatol	10.1038/s41575-024-00914-3	2024
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Genetics	Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides.	Ravcheev DA, Thiele I.	Front Genet	10.3389/fgene.2017.00111	2017
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
Genetics	Stemming epigenetics in marine stramenopiles.	Maumus F, Rabinowicz P, Bowler C, Rivarola M.	Curr Genomics	10.2174/138920211796429727	2011
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
Genetics	Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov.	Padmanabhan R, Dubourg G, Jean-Christophe lagier, Nguyen TT, Couderc C, Rossi-Tamisier M, Caputo A, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.5399696	2014
	'Collinsella provencensis' sp. nov., 'Parabacteroides bouchesdurhonensis' sp. nov. and 'Sutterella seckii,' sp. nov., three new bacterial species identified from human gut microbiota.	Dione N, Ngom II, Valles C, Cadoret F, Fournier PE, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2018.02.003	2018

References

#4989	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13279
#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 )
#56721	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 45295
#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 .
#123314	Collection of Institut Pasteur ; Curators of the CIP; CIP 106913
#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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Collinsella stercoris (DSM 13279, JCM 10641, CCUG 45295)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_020735465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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