Name: Phocaeicola abscessus 7401987
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 18135

Type strain:

Species: Phocaeicola abscessus

Strain Designation: 7401987

Culture col. no.: DSM 21584, CCUG 55929, CSUR P22, JCM 16570

Strain history: CCUG 55929 <-- V. Roux 7401987.

NCBI tax ID(s): 1204719 (strain), 555313 (species)

SI-ID 398071

DSM 21584, CCUG 55929

Section

Phocaeicola abscessus 7401987 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human brain abscess.

coccus-shaped
Gram-negative
motile
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 abscessus**
	Full Scientific Name (LPSN)	Phocaeicola abscessus Al Masalma et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29169]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #29169]	Cell length	0.4-0.9 µm

[Ref.: #29169]	Cell width	0.3-0.6 µm

[Ref.: #29169]	Cell shape	coccus-shaped

[Ref.: #29169]	Motility	yes

[Ref.: #60799]

Incubation period

3 days

[Ref.: #29169]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15823]

Culture medium

CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)

[Ref.: #15823]

Culture medium growth

[Ref.: #15823]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15823]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15823]	growth	37 °C
[Ref.: #29169]	optimum	37 °C
[Ref.: #60799]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #15823]	Temperature range	mesophilic
[Ref.: #29169]	Temperature range	mesophilic
[Ref.: #60799]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #15823]	Oxygen tolerance	anaerobe
[Ref.: #29169]	Oxygen tolerance	anaerobe
[Ref.: #60799]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #29169]	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

	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.: #29169]	dextrin ChEBI	+	carbon source
[Ref.: #29169]	fucose ChEBI	+	carbon source
[Ref.: #29169]	glucose ChEBI	+	carbon source
[Ref.: #29169]	glutamate ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #29169]	malate ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #29169]	pyruvate ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #29169]	succinate ChEBI	+	carbon source
[Ref.: #29169]	trehalose 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.: #29169]	acid phosphatase	+	3.1.3.2
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #29169]	alkaline phosphatase	+	3.1.3.1
[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.: #29169]	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
[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]	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
	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.: #15823]	12390	-	-	+	+	+	-	-	+	-	+	-	-	-	+	-	-	+	+/-	-	+	-	+/-	-	-	+	-	-	-	-

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

[Ref.: #15823]	Sample type/isolated from	human brain abscess
[Ref.: #15823]	Geographic location (country and/or sea, region)	Marseille
[Ref.: #15823]	Country	France
[Ref.: #15823]	Country ISO 3 Code	FRA
[Ref.: #15823]	Continent	Europe

[Ref.: #60799]	Sample type/isolated from	Human brain abscess
[Ref.: #60799]	Sampling date	2007-07-01
[Ref.: #60799]	Geographic location (country and/or sea, region)	Marseille,Timone hospital
[Ref.: #60799]	Country	France
[Ref.: #60799]	Country ISO 3 Code	FRA
[Ref.: #60799]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Human brain abscess sample
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Organ	#Brain
#Host Body-Site	#Other	#Abscess
#Infection	#Patient	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB595138 (>99% sequence identity) for Phocaeicola abscessus subclade from Microbeatlas

Aquatic Samples	298
Soil Samples	181
Animal Samples	14336
Plant Samples	74
Total Samples	14889

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

[Ref.: #15823]

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.: #15823]	Phocaeicola abscessus strain CCUG 55929 16S ribosomal RNA gene, partial sequence	EU694176	1497	ENA	1204719 tax ID
[Ref.: #67770]	Phocaeicola abscessus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16570	AB595138	1492	ENA	1204719 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phocaeicola abscessus CCUG 55929	GCA_000312445	scaffold	GenBank	1204719 tax ID
[Ref.: #66792]	Phocaeicola abscessus CCUG 55929	1204719.3	wgs	PATRIC	1204719 tax ID	*
[Ref.: #66792]	Phocaeicola abscessus CCUG 55929	2556793004	draft	JGI IMG/M	1204719 tax ID	*

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 abscessus CCUG 55929 CCUG 55929 NCBI: GCA_000312445.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phocaeicola abscessus CCUG 55929 PATRIC: 1204719.3
[Ref.: #69480]	motile	no	87.551	yes
[Ref.: #69480]	gram-positive	no	96.411	no
[Ref.: #69480]	anaerobic	yes	98.81	yes
[Ref.: #69480]	aerobic	no	98.24	no
[Ref.: #69480]	halophile	no	82.778	no
[Ref.: #69480]	spore-forming	no	96.65	yes
[Ref.: #69480]	thermophile	no	96.488	no
[Ref.: #69480]	glucose-util	yes	87.891	yes
[Ref.: #69480]	flagellated	no	97.62	no
[Ref.: #69480]	glucose-ferment	yes	54.946	no

Availability in culture collections External links

[Ref.: #15823]

Culture collection no.

DSM 21584, CCUG 55929, CSUR P22, JCM 16570

[Ref.: #87122]

SI-ID 398071

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca.	Kralova S, Davidova-Gerzova L, Valcek A, Bezdicek M, Rychlik I, Rezacova V, Cizek A	Microbiol Spectr	10.1128/spectrum.01954-21	2022	*
Genetics	Non-contiguous finished genome sequence of Phocaeicola abscessus type strain 7401987(T.).	Roux V, Robert C, Raoult D	Stand Genomic Sci	10.4056/sigs.4428244	2013	*
Phylogeny	Phocaeicola abscessus gen. nov., sp. nov., an anaerobic bacterium isolated from a human brain abscess sample.	Al Masalma M, Raoult D, Roux V	Int J Syst Evol Microbiol	10.1099/ijs.0.007823-0	2009	*

References

#15823

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21584

#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 )

#29169

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 #25593 (see below)

#60799 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55929

#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 )

#87122

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-ID398071.1 )

#25593

IJSEM 2232 2009 ( DOI 10.1099/ijs.0.007823-0 , PubMed 19620382 )

* These data were automatically processed and therefore are not curated

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