Name: Phocaeicola coprocola M16
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1608

Type strain:

Species: Phocaeicola coprocola

Strain Designation: M16

Culture col. no.: DSM 17136, JCM 12979, CCUG 54635

Strain history: M. Kitahara M16.

NCBI tax ID(s): 470145 (strain), 310298 (species)

SI-ID 231853

JCM 12979, DSM 17136, CCUG 54635

Other strains from Phocaeicola coprocola

P. coprocola JCM 12980
P. coprocola JCM 12981

Section

Phocaeicola coprocola M16 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human feces.

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	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Bacteroidaceae*
	Genus	*Phocaeicola*
	Species	**Phocaeicola coprocola**
	Full Scientific Name (LPSN)	Phocaeicola coprocola (Kitahara et al. 2005) García-López et al. 2020

Synonym

Bacteroides coprocola

Information on morphological and physiological properties Morphology

[Ref.: #31548]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #31548]	Cell length	2.5 µm

[Ref.: #31548]	Cell width	0.8 µm

[Ref.: #31548]	Cell shape	rod-shaped

[Ref.: #31548]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.009

[Ref.: #6783]

Incubation period

2-3 days

[Ref.: #31548]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6783]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #6783]	growth	37 °C
[Ref.: #31548]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #6783]	Temperature range	mesophilic
[Ref.: #31548]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6783]	Oxygen tolerance	anaerobe
[Ref.: #31548]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %98.82

[Ref.: #31548]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

[Ref.: #31548]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-10, MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #31548]	cellobiose ChEBI	+	carbon source
[Ref.: #68367]	cellobiose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-glucose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-mannitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-mannose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-xylose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31548]	esculin ChEBI	+	hydrolysis
[Ref.: #68367]	esculin ChEBI	+	hydrolysis	* from API 20A
[Ref.: #68367]	gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #31548]	glucose ChEBI	+	carbon source
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #31548]	lactose ChEBI	+	carbon source
[Ref.: #68367]	lactose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31548]	maltose ChEBI	+	carbon source
[Ref.: #68367]	maltose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31548]	mannose ChEBI	+	carbon source
[Ref.: #68367]	melezitose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68367]	raffinose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31548]	rhamnose ChEBI	+	carbon source
[Ref.: #31548]	salicin ChEBI	+	carbon source
[Ref.: #68367]	salicin ChEBI	+	builds acid from	* from API 20A
[Ref.: #31548]	sorbitol ChEBI	+	carbon source
[Ref.: #68367]	sorbitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sucrose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31548]	trehalose ChEBI	+	carbon source
[Ref.: #68367]	trehalose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	tryptophan ChEBI	-	energy source	* from API 20A, API rID32A
[Ref.: #68367]	urea ChEBI	-	hydrolysis	* from API 20A, API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68367]		indole ChEBI	no	* from API 20A, API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A, API 20A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #31548]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68380]	alkaline phosphatase	+	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	+	3.2.1.51	* from API rID32A
[Ref.: #31548]	alpha-galactosidase	+	3.2.1.22
[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, API 20A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #6783]	catalase	-	1.11.1.6
[Ref.: #68367]	catalase	-	1.11.1.6	* from API 20A
[Ref.: #6783]	cytochrome-c oxidase	-	1.9.3.1
[Ref.: #68367]	gelatinase	-		* from API 20A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* 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, API 20A
	Only first 10 entries are displayed. Click here to see all.

API® 20A:

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

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #6783]	2020	-	-	+	-	+	+	+	+	+	-	-	+	-	+	+	-	+	-	+/-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.
[Ref.: #6783]	2019	-	-	+	-	+	+	+	+	+	-	-	+	-	+	+	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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.: #6783]	12200	-	-	+	+	-	+	+	+/-	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+	-
[Ref.: #6783]	12199	-	-	+	+	-	+	+	-	-	+	-	-	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+/-	-
[Ref.: #6783]	12198	-	-	+	+	-	+	+	-	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	+/-	-

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

[Ref.: #6783]	Sample type/isolated from	human feces
[Ref.: #6783]	Country	Japan
[Ref.: #6783]	Country ISO 3 Code	JPN
[Ref.: #6783]	Continent	Asia

[Ref.: #60272]	Sample type/isolated from	Human feces
[Ref.: #60272]	Country	Japan
[Ref.: #60272]	Country ISO 3 Code	JPN
[Ref.: #60272]	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 AB200224 (>99% sequence identity) for Phocaeicola coprocola subclade from Microbeatlas

Aquatic Samples	11373
Soil Samples	2696
Animal Samples	155260
Plant Samples	888
Total Samples	170217

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

[Ref.: #6783]

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.: #6783]	Bacteroides coprocola gene for 16S rRNA, partial sequence, strain: M16	AB200224	1490	ENA	470145 tax ID
[Ref.: #20218]	UNVERIFIED: Bacteroides coprocola 16S ribosomal RNA and tRNA-Ile-like gene, partial sequence	EU136688	1853	ENA	310298 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phocaeicola coprocola DSM 17136	GCA_000154845	scaffold	GenBank	470145 tax ID
[Ref.: #66792]	Phocaeicola coprocola DSM 17136 FDAARGOS_1577	GCA_020731235	contig	GenBank	470145 tax ID	*
[Ref.: #66792]	Bacteroides coprocola DSM 17136	470145.6	wgs	PATRIC	470145 tax ID	*
[Ref.: #66792]	Phocaeicola coprocola DSM 17136	642791613	draft	JGI IMG/M	470145 tax ID	*

[Ref.: #6783]	GC-content	42.4 mol%
[Ref.: #67770]	GC-content	42.4 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: Phocaeicola coprocola DSM 17136 DSM 17136 NCBI: GCA_000154845.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bacteroides coprocola DSM 17136 PATRIC: 470145.6
[Ref.: #69480]	gram-positive	no	97.362	yes
[Ref.: #69480]	anaerobic	yes	98.774	yes
[Ref.: #69480]	halophile	no	86.36	no
[Ref.: #69480]	spore-forming	no	95.732	yes
[Ref.: #69480]	glucose-util	yes	89.328	yes
[Ref.: #69480]	aerobic	no	98.396	no
[Ref.: #69480]	flagellated	no	96.481	yes
[Ref.: #69480]	thermophile	no	97.692	no
[Ref.: #69480]	motile	no	92.004	no
[Ref.: #69480]	glucose-ferment	yes	70.409	no

Availability in culture collections External links

[Ref.: #6783]

Culture collection no.

DSM 17136, JCM 12979, CCUG 54635

[Ref.: #71253]

SI-ID 231853

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.	Mendez-Salazar EO, Vazquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, Cubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martinez-Flores K, Fernandez-Torres J, Lozada-Perez C, Pineda C, Sanchez-Gonzalez A, Silveira LH, Burguete-Garcia AI, Orbe-Orihuela C, Lagunas-Martinez A, Vazquez-Gomez A, Lopez-Reyes A, Palacios-Gonzalez B, Martinez-Nava GA	Mol Med	10.1186/s10020-021-00311-5	2021	*
Phylogeny	Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.	Lan PTN, Sakamoto M, Sakata S, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64517-0	2006	*
Phylogeny	Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces.	Kitahara M, Sakamoto M, Ike M, Sakata S, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.63788-0	2005	*

References

#6783

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17136

#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 )

#31548

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 #27839 (see below)

#60272 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54635

#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;

#68367

Automatically annotated from API 20A .

#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) .

#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 )

#71253

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-ID231853.1 )

#27839

IJSEM 2143 2005 ( DOI 10.1099/ijs.0.63788-0 , PubMed 16166722 )

* These data were automatically processed and therefore are not curated

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Phocaeicola coprocola DSM 17136 DSM 17136

Bacteroides coprocola DSM 17136

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