Phocaeicola abscessus (DSM 21584, CCUG 55929, CSUR P22)

Name: Phocaeicola abscessus (DSM 21584, CCUG 55929, CSUR P22)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18135

Type strain

Strain Designation 7401987

Culture col. no. DSM 21584 CCUG 55929 CSUR P22 7401987 JCM 16570

NCBI tax ID(s) 1204719 555313

Special Collections DSMZ CCUG JCM Literature strains

Links

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

Gram-negative motile coccus-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398071

JCM 16570,DSM 21584,CCUG 55929

@ref 20215

Last LPSN update 2025-12-16 09:51:16

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Phocaeicola

Species Phocaeicola abscessus

Full scientific name Phocaeicola abscessus Al Masalma et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29169	negative	0.4-0.9 µm	0.3-0.6 µm	coccus-shaped
125438	negative				92.867
125439	negative				99.8

Colony morphology

60799

Incubation period3 days

Pigmentation

29169

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15823	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15823	positive	growth	37	mesophilic
29169	positive	optimum	37	mesophilic
60799	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
15823	anaerobe
29169	anaerobe
60799	anaerobe

Spore formation

@ref	Spore formation	Confidence
29169
125438		92.363
125439		99.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
29169	23652 ChEBI	dextrin	+	carbon source
29169	33984 ChEBI	fucose	+	carbon source
29169	17234 ChEBI	glucose	+	carbon source
29169	29987 ChEBI	glutamate	+	carbon source
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
29169	25115 ChEBI	malate	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
29169	15361 ChEBI	pyruvate	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
29169	30031 ChEBI	succinate	+	carbon source
29169	27082 ChEBI	trehalose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
29169	acid phosphatase	+	3.1.3.2
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
29169	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
29169	alpha-galactosidase	+	3.2.1.22
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	+		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
15823	-	-	+	+	+	-	-	+	-	+	-	-	-	+	-	-	+	+/-	-	+	-	+/-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Organ	#Brain
#Host Body-Site	#Other	#Abscess
#Infection	#Patient	-

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
15823	human brain abscess		Marseille	France	FRA	Europe
60799	Human brain abscess	2007-07-01	Marseille,Timone hospital	France	FRA	Europe
67770	Human brain abscess sample

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15823	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM31244v1 assembly for Phocaeicola abscessus CCUG 55929	scaffold	GCA_000312445	1204719.3	2556793004	1204719	64.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15823	Phocaeicola abscessus strain CCUG 55929 16S ribosomal RNA gene, partial sequence	EU694176	1497		1204719
67770	Phocaeicola abscessus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16570	AB595138	1492		1204719

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phocaeicola abscessus CCUG 55929
NCBI: GCA_000312445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	87.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	motility	BacteriaNetⓘ	no	68.50	no
125439	spore_formation	BacteriaNetⓘ	no	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phocaeicola abscessus CCUG 55929
PATRIC: 1204719.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.87	no
125438	anaerobic	anaerobicⓘ	yes	81.55	yes
125438	spore-forming	spore-formingⓘ	no	92.36	yes
125438	aerobic	aerobicⓘ	no	90.58	yes
125438	thermophilic	thermophileⓘ	no	92.87	no
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus.	Buenestado-Serrano S, Martinez-Lirola M, Herranz-Martin M, Esteban J, Broncano-Lavado A, Molero-Salinas A, Sanz-Perez A, Blazquez J, Ruedas-Lopez A, Toro C, Lopez-Roa P, Domingo D, Zamarron E, Ruiz Serrano MJ, Munoz P, Perez-Lago L, Garcia de Viedma D.	Nat Commun	10.1038/s41467-024-46552-w	2024
	Novel role of FTO in regulation of gut-brain communication via Desulfovibrio fairfieldensis-produced hydrogen sulfide under arsenic exposure.	Chen R, Chai X, Zhang Y, Zhou T, Xia Y, Jiang X, Lv B, Zhang J, Zhou L, Tian X, Wang R, Mao L, Zhao F, Zhang H, Hu J, Qiu J, Zou Z, Chen C.	Gut Microbes	10.1080/19490976.2024.2438471	2025
	Proposal of a Method for Harmonized Broth Microdilution Antimicrobial Susceptibility Testing of Avibacterium gallinarum.	Gutgemann F, Muller A, Churin Y, Jung A, Kumm F, Heuvelink A, Yue M, Kehrenberg C.	J Clin Microbiol	10.1128/jcm.00419-22	2022
	Presence of pathogenic bacteria in faeces from dogs fed raw meat-based diets or dry kibble.	Runesvard E, Wikstrom C, Fernstrom LL, Hansson I.	Vet Rec	10.1136/vr.105644	2020
	The structures of oligosaccharides isolated from the lipopolysaccharide of Moraxella catarrhalis serotype B, strain CCUG 3292.	Edebrink P, Jansson PE, Widmalm G, Holme T, Rahman M.	Carbohydr Res	10.1016/s0008-6215(96)90132-9	1996
Pathogenicity	The nickel resistance determinant cloned from the enterobacterium Klebsiella oxytoca: conjugational transfer, expression, regulation and DNA homologies to various nickel-resistant bacteria.	Stoppel RD, Meyer M, Schlegel HG.	Biometals	10.1007/bf00156161	1995
	The Immunopathogenic Potential of Arcobacter butzleri - Lessons from a Meta-Analysis of Murine Infection Studies.	Golz G, Alter T, Bereswill S, Heimesaat MM.	PLoS One	10.1371/journal.pone.0159685	2016
	Arcobacter butzleri Induce Colonic, Extra-Intestinal and Systemic Inflammatory Responses in Gnotobiotic IL-10 Deficient Mice in a Strain-Dependent Manner.	Golz G, Karadas G, Alutis ME, Fischer A, Kuhl AA, Breithaupt A, Gobel UB, Alter T, Bereswill S, Heimesaat MM.	PLoS One	10.1371/journal.pone.0139402	2015
	Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics.	Salva-Serra F, Jaen-Luchoro D, Marathe NP, Adlerberth I, Moore ERB, Karlsson R.	Front Microbiol	10.3389/fmicb.2022.1089140	2022
Enzymology	Posaconazole in human serum: a greater pharmacodynamic effect than predicted by the non-protein-bound serum concentration.	Lignell A, Lowdin E, Cars O, Chryssanthou E, Sjolin J.	Antimicrob Agents Chemother	10.1128/aac.01671-10	2011
Phylogeny	Discrimination of Mycobacterium abscessus subsp. massiliense from Mycobacterium abscessus subsp. abscessus in clinical isolates by multiplex PCR.	Nakanaga K, Sekizuka T, Fukano H, Sakakibara Y, Takeuchi F, Wada S, Ishii N, Makino M, Kuroda M, Hoshino Y.	J Clin Microbiol	10.1128/jcm.01327-13	2014
Phylogeny	Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences.	Pombert JF, Sistek V, Boissinot M, Frenette M.	BMC Microbiol	10.1186/1471-2180-9-232	2009
	In vitro and in vivo interactions of Haemophilus ducreyi with host phagocytes.	Ahmed HJ, Johansson C, Svensson LA, Ahlman K, Verdrengh M, Lagergard T.	Infect Immun	10.1128/iai.70.2.899-908.2002	2002
Enzymology	Identification of some charcoal-black-pigmented CDC fermentative coryneform group 4 isolates as Rothia dentocariosa and some as Corynebacterium aurimucosum: proposal of Rothia dentocariosa emend. Georg and Brown 1967, Corynebacterium aurimucosum emend. Yassin et al. 2002, and Corynebacterium nigricans Shukla et al. 2003 pro synon. Corynebacterium aurimucosum.	Daneshvar MI, Hollis DG, Weyant RS, Jordan JG, MacGregor JP, Morey RE, Whitney AM, Brenner DJ, Steigerwalt AG, Helsel LO, Raney PM, Patel JB, Levett PN, Brown JM.	J Clin Microbiol	10.1128/jcm.42.9.4189-4198.2004	2004
Phylogeny	Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients.	Hoshino T, Fujiwara T, Kilian M.	J Clin Microbiol	10.1128/jcm.43.12.6073-6085.2005	2005
Phylogeny	Low-temperature isolation of disease-suppressive bacteria and characterization of a distinctive group of pseudomonads.	Johansson PM, Wright SA.	Appl Environ Microbiol	10.1128/aem.69.11.6464-6474.2003	2003
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
	Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma.	Chen JW, Shih CJ, Wu LW, Wu YC, Chiang WF, Chen YL, Wu JH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005703	2023
Phylogeny	Catabacter hongkongensis gen. nov., sp. nov., isolated from blood cultures of patients from Hong Kong and Canada.	Lau SK, McNabb A, Woo GK, Hoang L, Fung AM, Chung LM, Woo PC, Yuen KY.	J Clin Microbiol	10.1128/jcm.01831-06	2007
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
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 )
#25593	IJSEM 2232 2009 ( DOI 10.1099/ijs.0.007823-0 , PubMed 19620382 )
#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
#60799	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55929
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Phocaeicola abscessus (DSM 21584, CCUG 55929, CSUR P22)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000312445

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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