Name: Phocaeicola barnesiae BL2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1614

Type strain:

Species: Phocaeicola barnesiae

Strain Designation: BL2

Culture col. no.: DSM 18169, JCM 13652, CCUG 54636

Strain history: M. Sakamoto <-- P. T. N. Lan BL2.

NCBI tax ID(s): 376804 (species)

SI-ID 293997

JCM 13652, DSM 18169, CCUG 54636

Other strains from Phocaeicola barnesiae

P. barnesiae JCM 13653
P. barnesiae JCM 13654
P. barnesiae JCM 13655
P. barnesiae JCM 13656

Section

Phocaeicola barnesiae BL2 is an anaerobe, mesophilic bacterium that was isolated from chicken caecum.

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 barnesiae**
	Full Scientific Name (LPSN)	Phocaeicola barnesiae (Lan et al. 2006) García-López et al. 2020

Synonym

Bacteroides barnesiae

Information on morphological and physiological properties Morphology

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

[Ref.: #69480]	Motility	no Confidence in %92.184

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7343]

Culture medium

COLUMBIA BLOOD AGAR (DSMZ Medium 429)

[Ref.: #7343]

Culture medium growth

[Ref.: #7343]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7343]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7343]	growth	37 °C
[Ref.: #60273]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7343]	Temperature range	mesophilic
[Ref.: #60273]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7343]	Oxygen tolerance	anaerobe
[Ref.: #60273]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

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

[Ref.: #67770]

Observation

quinones: MK-10, MK-11

	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-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]	glycin 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]	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.: #7343]	12227	-	-	+	+	-	+	+	+	-	+	+	+	-	+/-	-	-	+	-	-	+	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #7343]	Sample type/isolated from	chicken caecum
[Ref.: #7343]	Country	Japan
[Ref.: #7343]	Country ISO 3 Code	JPN
[Ref.: #7343]	Continent	Asia

[Ref.: #60273]	Sample type/isolated from	Chicken caecum,healthy animal

[Ref.: #67770]	Sample type/isolated from	Chicken cecum
* marker position based on {}

Isolation sources categories

#Host	#Birds	#Chicken
#Host Body-Site	#Gastrointestinal tract	#Large intestine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB253726 (>99% sequence identity) for Phocaeicola barnesiae subclade from Microbeatlas

Aquatic Samples	36
Soil Samples	4
Animal Samples	1318
Plant Samples	2
Total Samples	1360

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

[Ref.: #7343]

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.: #7343]	Bacteroides barnesiae gene for 16S ribosomal RNA, partial seuqnece, strain: JCM 13652	AB253726	1456	ENA	376804 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 barnesiae DSM 18169 = JCM 13652	GCA_000374585	scaffold	GenBank	1121094 tax ID
[Ref.: #67770]	Phocaeicola barnesiae DSM 18169 = JCM 13652	GCA_000613645	contig	GenBank	1121094 tax ID
[Ref.: #66792]	Bacteroides barnesiae DSM 18169	1121094.3	wgs	PATRIC	1121094 tax ID	*
[Ref.: #66792]	Bacteroides barnesiae JCM 13652	1236490.3	wgs	PATRIC	1121094 tax ID	*
[Ref.: #66792]	Bacteroides barnesiae DSM 18169	2517572120	draft	JGI IMG/M	1121094 tax ID	*
[Ref.: #66792]	Bacteroides barnesiae JCM 13652	2585427859	draft	JGI IMG/M	1121094 tax ID	*

[Ref.: #7343]	GC-content	46.8 mol%
[Ref.: #67770]	GC-content	46.8 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 barnesiae DSM 18169 = JCM 13652 DSM 18169 NCBI: GCA_000374585.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bacteroides barnesiae DSM 18169 PATRIC: 1121094.3
[Ref.: #69480]	motile	no	94.048	no
[Ref.: #69480]	flagellated	no	97.034	no
[Ref.: #69480]	gram-positive	no	97.091	no
[Ref.: #69480]	anaerobic	yes	99.341	yes
[Ref.: #69480]	aerobic	no	98.526	no
[Ref.: #69480]	halophile	no	88.319	no
[Ref.: #69480]	spore-forming	no	93.842	no
[Ref.: #69480]	thermophile	no	98.739	yes
[Ref.: #69480]	glucose-util	yes	82.145	no
[Ref.: #69480]	glucose-ferment	yes	62.93	no

Availability in culture collections External links

[Ref.: #7343]

Culture collection no.

DSM 18169, JCM 13652, CCUG 54636

[Ref.: #71259]

SI-ID 293997

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.	Sakamoto M, Lapidus AL, Han J, Trong S, Haynes M, Reddy TB, Mikhailova N, Huntemann M, Pati A, Ivanova NN, Pukall R, Markowitz VM, Woyke T, Klenk HP, Kyrpides NC, Ohkuma M	Stand Genomic Sci	10.1186/s40793-015-0045-6	2015	*
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	*

References

#7343

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18169

#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 )

#60273 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54636

#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) .

#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 )

#71259

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-ID293997.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Phocaeicola barnesiae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Phocaeicola barnesiae DSM 18169 = JCM 13652 DSM 18169

Bacteroides barnesiae DSM 18169

Change proposal

Change proposal