Name: Phocaeicola coprophilus CCUG 55424
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1622

Type strain:

Species: Phocaeicola coprophilus

Culture col. no.: CCUG 55424, CB 42, DSM 18228, JCM 13818

Strain history: H. Hayashi CB42.

NCBI tax ID(s): 387090 (species)

SI-ID 309435

DSM 18228, JCM 13818, CCUG 55424

Special Collections

Other strains from Phocaeicola coprophilus

Section

Phocaeicola coprophilus CCUG 55424 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from human faeces.

Gram-negative
rod-shaped
anaerobe
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 coprophilus**
	Full Scientific Name (LPSN)	Phocaeicola coprophilus (Hayashi et al. 2007) García-López et al. 2020

Synonym

Bacteroides coprophilus

Information on morphological and physiological properties Morphology

[Ref.: #32112]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.068

[Ref.: #32112]	Cell length	2.5-4.1 µm

[Ref.: #32112]	Cell width	0.7-0.8 µm

[Ref.: #32112]	Cell shape	rod-shaped

[Ref.: #32112]	Motility	no

[Ref.: #7443]

Incubation period

2-3 days

[Ref.: #32112]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7443]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #7443]

Culture medium growth

[Ref.: #7443]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7443]

Culture medium composition

expand / minimize

[Ref.: #7443]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #7443]

Culture medium growth

[Ref.: #7443]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7443]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7443]	growth	37 °C
[Ref.: #60584]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7443]	Oxygen tolerance	anaerobe
[Ref.: #32112]	Oxygen tolerance	aerobe
[Ref.: #60584]	Oxygen tolerance	anaerobe

[Ref.: #32112]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %93.096

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #32112]	cellobiose ChEBI	+	carbon source
[Ref.: #32112]	glutamate ChEBI	+	carbon source
[Ref.: #32112]	glycine ChEBI	+	carbon source
[Ref.: #32112]	histidine ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #32112]	leucine ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #32112]	phenylalanine ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #32112]	serine 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]	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.: #7443]	12245	-	-	+	+	-	+	+	-	-	+	+	+	-	+	-	-	+	+	-	+	+	+	-	+/-	+	-	+	not determinedn.d.	not determinedn.d.
[Ref.: #7443]	12244	-	-	+	+	-	+	+	-	-	+	+/-	+	-	+	-	-	+	+	-	+	+	+	-	+	+	-	+	-	-

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

[Ref.: #7443]	Sample type/isolated from	human faeces
[Ref.: #7443]	Country	Japan
[Ref.: #7443]	Country ISO 3 Code	JPN
[Ref.: #7443]	Continent	Asia

[Ref.: #60584]	Sample type/isolated from	Human feces
[Ref.: #60584]	Country	Japan
[Ref.: #60584]	Country ISO 3 Code	JPN
[Ref.: #60584]	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 AB260026 (>99% sequence identity) for Phocaeicola coprophilus subclade from Microbeatlas

Aquatic Samples	4526
Soil Samples	1337
Animal Samples	68517
Plant Samples	419
Total Samples	74799

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

[Ref.: #7443]

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.: #7443]	Bacteroides coprophilus gene for 16S ribosomal RNA, partial sequence, strain: CB42 (= JCM 13818, = DSM 18228)	AB260026	1492	GenBank ENA	547042 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phocaeicola coprophilus DSM 18228 = JCM 13818	GCA_000157915	scaffold	GenBank ENA	547042 tax ID
[Ref.: #67770]	Phocaeicola coprophilus DSM 18228 = JCM 13818	GCA_001315785	contig	GenBank ENA	547042 tax ID
[Ref.: #66792]	Bacteroides coprophilus DSM 18228 = JCM 13818	547042.10	wgs	PATRIC	547042 tax ID	*
[Ref.: #66792]	Bacteroides coprophilus DSM 18228, JCM 13818	2731957552	draft	JGI IMG/M	547042 tax ID	*
[Ref.: #66792]	Bacteroides coprophilus DSM 18228, JCM 13818	643886197	draft	JGI IMG/M	547042 tax ID	*

[Ref.: #7443]	GC-content	44.7 mol%
[Ref.: #7443]	GC-content	45.7 mol%	sequence analysis
[Ref.: #67770]	GC-content	44.7 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: Bacteroides coprophilus DSM 18228 = JCM 13818 PATRIC: 547042.10
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.068	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	87.807	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.096	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	89.4	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	93.499	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	87.595	yes

Availability in culture collections External links

[Ref.: #7443]

Culture collection no.

CCUG 55424, CB 42, DSM 18228, JCM 13818

[Ref.: #71268]

SI-ID 309435

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bacteroides coprophilus sp. nov., isolated from human faeces.	Hayashi H, Shibata K, Bakir MA, Sakamoto M, Tomita S, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64979-0	2007	*

References

#7443

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18228

#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 )

#32112

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 #28357 (see below)

#60584 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55424

#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) .

#71268

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-ID309435.1 )

#28357

IJSEM 1323 2007 ( DOI 10.1099/ijs.0.64979-0 , PubMed 17551051 )

* These data were automatically processed and therefore are not curated

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Bacteroides coprophilus DSM 18228 = JCM 13818

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