Name: Phocaeicola dorei 175
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1612

Type strain:

Species: Phocaeicola dorei

Strain Designation: 175

Culture col. no.: DSM 17855, JCM 13471, CCUG 53892

Strain history: M. Sakamoto <-- M. Matsumoto 175.

NCBI tax ID(s): 483217 (strain), 357276 (species)

SI-ID 297141

DSM 17855, JCM 13471, CCUG 53892

Other strains from Phocaeicola dorei

P. dorei Cla-CZ-110, DSM 108974
P. dorei HM-27, 9/1/42 FAA, DSM 24903

Section

Phocaeicola dorei 175 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human feces.

Gram-negative
rod-shaped
anaerobe
human pathogen
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 dorei**
	Full Scientific Name (LPSN)	Phocaeicola dorei (Bakir et al. 2006) García-López et al. 2020

Synonym

Bacteroides dorei

Information on morphological and physiological properties Morphology

[Ref.: #31780]	Gram stain	negative

[Ref.: #31780]	Cell length	1.6-4.2 µm

[Ref.: #31780]	Cell width	0.8-1.2 µm

[Ref.: #31780]	Cell shape	rod-shaped

[Ref.: #31780]	Motility	no

[Ref.: #7141]	Incubation period	1-2 days

[Ref.: #60061]	Incubation period	2 days

[Ref.: #31780]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7141]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #7141]

Culture medium growth

[Ref.: #7141]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7141]

Culture medium composition

expand / minimize

[Ref.: #7141]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #7141]

Culture medium growth

[Ref.: #7141]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7141]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7141]	growth	37 °C
[Ref.: #31780]	growth	37 °C
[Ref.: #31780]	optimum	37 °C
[Ref.: #60061]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7141]	Temperature range	mesophilic
[Ref.: #31780]	Temperature range	mesophilic
[Ref.: #60061]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31780]			optimum	7
[Ref.: #31780]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7141]	Oxygen tolerance	anaerobe
[Ref.: #31780]	Oxygen tolerance	anaerobe
[Ref.: #60061]	Oxygen tolerance	anaerobe

[Ref.: #31780]

Ability of spore formation

[Ref.: #31780]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31780]	arabinose ChEBI	+	carbon source
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[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.: #68367]	esculin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]	gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	L-rhamnose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	lactose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	maltose ChEBI	+	builds acid from	* from API 20A
[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.: #31780]	rhamnose ChEBI	+	carbon source
[Ref.: #68367]	salicin ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sorbitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #31780]	sucrose ChEBI	+	carbon source
[Ref.: #68367]	sucrose ChEBI	+	builds acid from	* from API 20A
[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
[Ref.: #31780]	xylose ChEBI	+	carbon source
	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.: #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.: #68367]	beta-glucosidase	-	3.2.1.21	* from API 20A
[Ref.: #68367]	gelatinase	-		* from API 20A
[Ref.: #68380]	glycin arylamidase	+		* 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]	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, 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.: #7141]	2024	-	-	+	-	+	+	+	-	+	+	-	-	-	-	+	-	+	-	+	-	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.: #7141]	12914	-	-	+	+	-	+	-	+	+/-	+	-	-	-	+	-	-	+	-	-	+	+	+	-	+	+	+	-	+/-	-
[Ref.: #7141]	12216	-	-	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	+	-	+	-	+/-	-	+/-	+	+	-	+	-
[Ref.: #7141]	12215	-	-	+	+	+/-	+	-	+	-	+	+/-	+/-	-	+	-	-	+	+/-	-	+	+/-	+	-	+/-	+	+	+/-	+	-
[Ref.: #7141]	12214	-	-	+	+	-	+	+	+	not determinedn.d.	+	+	+	+	+	-	-	+	+	-	+	+/-	+	-	+/-	+	+	+/-	+/-	not determinedn.d.

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

[Ref.: #7141]	Sample type/isolated from	human feces
[Ref.: #7141]	Country	Japan
[Ref.: #7141]	Country ISO 3 Code	JPN
[Ref.: #7141]	Continent	Asia

[Ref.: #60061]	Sample type/isolated from	Human feces
[Ref.: #60061]	Country	Japan
[Ref.: #60061]	Country ISO 3 Code	JPN
[Ref.: #60061]	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 AB242142 (>99% sequence identity) for Phocaeicola dorei subclade from Microbeatlas

Aquatic Samples	4422
Soil Samples	671
Animal Samples	124015
Plant Samples	277
Total Samples	129385

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

[Ref.: #7141]	Pathogenicity (human)	yes, in single cases
[Ref.: #7141]	Biosafety level	1	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.: #7141]	Glomerella tucumanensis genes for 18S rRNA, ITS1, 5.8S rRNA, ITS2, 28S rRNA, partial and complete sequence, strain: Cf-03	AB242412	585	ENA	129314 tax ID
[Ref.: #31780]	Bacteroides dorei gene for 16S rRNA, partial sequence, strain:JCM 13471	AB242142	1493	GenBank	483217 tax ID
[Ref.: #20218]	Bacteroides dorei strain DSM 17855 16S ribosomal RNA gene, partial sequence	HQ012025	932	ENA	357276 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phocaeicola dorei DSM 17855	GCA_000156075	scaffold	GenBank	483217 tax ID
[Ref.: #66792]	Phocaeicola dorei DSM 17855	GCA_013009555	complete	GenBank	357276 tax ID	*
[Ref.: #66792]	Bacteroides dorei DSM 17855	483217.6	wgs	PATRIC	483217 tax ID	*
[Ref.: #66792]	Bacteroides dorei strain DSM 17855	357276.1035	complete	PATRIC	357276 tax ID	*
[Ref.: #66792]	Phocaeicola dorei DSM 17855	642979370	draft	JGI IMG/M	483217 tax ID	*
[Ref.: #66792]	Phocaeicola dorei DSM 17855	GCA_025146415	complete	GenBank	357276 tax ID	*

[Ref.: #7141]	GC-content	43 mol%
[Ref.: #7141]	GC-content	42.0 mol%	sequence analysis
[Ref.: #67770]	GC-content	43 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 Diaspora project based on: Phocaeicola dorei DSM 17855 NCBI: GCA_013009555.1
[Ref.: #69480]	motile	no	93.133	yes
[Ref.: #69480]	flagellated	no	97.224	yes
[Ref.: #69480]	gram-positive	no	96.531	yes
[Ref.: #69480]	anaerobic	yes	98.301	yes
[Ref.: #69480]	aerobic	no	96.93	no
[Ref.: #69480]	halophile	no	90.76	no
[Ref.: #69480]	spore-forming	no	94.441	yes
[Ref.: #69480]	glucose-util	yes	90.712	no
[Ref.: #69480]	thermophile	no	98.896	no
[Ref.: #69480]	glucose-ferment	yes	74.912	no

Availability in culture collections External links

[Ref.: #7141]

Culture collection no.

DSM 17855, JCM 13471, CCUG 53892

[Ref.: #71257]

SI-ID 297141

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets.	Jones DR, Thomas D, Alger N, Ghavidel A, Inglis GD, Abbott DW	Biotechnol Biofuels	10.1186/s13068-018-1027-x	2018	*
Phylogeny	Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.	Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.024026-0	2010	*
Phylogeny	Bacteroides dorei sp. nov., isolated from human faeces.	Bakir MA, Sakamoto M, Kitahara M, Matsumoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64257-0	2006	*

References

#7141

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17855

#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 )

#31780

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 #28052 (see below)

#60061 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53892

#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) .

#71257

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-ID297141.1 )

#28052

IJSEM 1639 2006 ( DOI 10.1099/ijs.0.64257-0 , PubMed 16825642 )

* These data were automatically processed and therefore are not curated

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Phocaeicola dorei DSM 17855

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