Phocaeicola massiliensis (DSM 17679, CCUG 48901, CIP 107942)

Name: Phocaeicola massiliensis (DSM 17679, CCUG 48901, CIP 107942)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1611

Type strain

Strain Designation B84634, 84634

Culture col. no. DSM 17679 CCUG 48901 CIP 107942 B84634 JCM 13223 1 more

NCBI tax ID(s) 204516

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- V. Roux; B84634 <- Timone Hospital 2003, P. Berger, Timone Hosp., Marseille, France: strain 84634 D. Raoult B84634. CIP <- 2003, P. Berger, Timone Hosp., Marseille, France: strain 84634

Links

Phocaeicola massiliensis B84634 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from blood culture of a newborn.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 138972

CCUG 48901,CIP 107942,JCM 13223,DSM 17679

@ref 20215

Last LPSN update 2026-02-09 11:18:08

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Phocaeicola

Species Phocaeicola massiliensis

Full scientific name Phocaeicola massiliensis (Fenner et al. 2005) García-López et al. 2020

Synonyms (3)

"Candidatus Bacteroides massiliensis"
"Candidatus Bacteroides massiliae"
Bacteroides massiliensis

BacDive ID	Other strains from **Phocaeicola massiliensis** (1)	Type strain
161297	P. massiliensis JCM 12982

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31339	negative	3 µm	1.1 µm	rod-shaped
120849	negative			rod-shaped
125438	negative				91.652
125439	negative				96.2

Colony morphology

@ref	Incubation period
7121	1-2 days
120849

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7121	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
38242	MEDIUM 45 - for Columbia agar with sheep blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
120849	CIP Medium 45	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7121	positive	growth	37
31339	positive	growth	25-42
31339	positive	optimum	37
38242	positive	growth	37
58392	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7121	anaerobe
31339	anaerobe
58392	anaerobe
120849	anaerobe
125438	anaerobe	92.371
125439	anaerobe	99.3

Spore formation

@ref	Spore formation	Confidence
31339
125438		94.46
125439		99.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
120849	17057 ChEBI	cellobiose	-	degradation
120849	17108 ChEBI	D-arabinose	-	degradation
120849	15824 ChEBI	D-fructose	+	degradation
120849	17634 ChEBI	D-glucose	+	degradation
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
120849	65327 ChEBI	D-xylose	-	degradation
31339	4853 ChEBI	esculin	+	hydrolysis
120849	4853 ChEBI	esculin	+	hydrolysis
31339	28757 ChEBI	fructose	+	carbon source
31339	28260 ChEBI	galactose	+	carbon source
31339	17234 ChEBI	glucose	+	carbon source
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
31339	17716 ChEBI	lactose	+	carbon source
120849	17716 ChEBI	lactose	+	degradation
31339	17306 ChEBI	maltose	+	carbon source
120849	17306 ChEBI	maltose	+	degradation
31339	37684 ChEBI	mannose	+	carbon source
31339	28053 ChEBI	melibiose	+	carbon source
31339	506227 ChEBI	N-acetylglucosamine	+	carbon source
120849	17632 ChEBI	nitrate	-	reduction
120849	17632 ChEBI	nitrate	+	respiration
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
120849	16301 ChEBI	nitrite	-	reduction
31339	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
120849	17814 ChEBI	salicin	-	degradation
31339	30911 ChEBI	sorbitol	+	carbon source
31339	17992 ChEBI	sucrose	+	carbon source
120849	17992 ChEBI	sucrose	+	degradation
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
120849	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
31339	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
31339	alpha-galactosidase	+	3.2.1.22
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
120849	amylase	+
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	+	3.2.1.23	from API zym
120849	beta-galactosidase	-	3.2.1.23
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
120849	caseinase	+	3.4.21.50
120849	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120849	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
120849	gelatinase	-
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
120849	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
120849	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
120849	oxidase	-
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
120849	protease	-
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
120849	tween esterase	-
120849	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120849	-	+	+	-	-	-	-	-	-	-	+	-	-	+	-	-	-	+	-	-

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
7121	-	-	+	+	-	+	-	-	-	+	+	+	+	+	-	-	+	+	-	+	+	+	-	+	+	-	-	+	-
7121	-	-	+	+	-	+	-	-	-	+	+	+	+	+	-	-	+	+	-	+	-	+	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Infection	#Patient	#Blood culture

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7121	blood culture of a newborn		Marseille	France	FRA	Europe
58392	Human blood,newborn	2002-05-21	Marseille	France	FRA	Europe
67770	Blood culture of a newborn
120849	Human, Blood		Marseille	France	FRA	Europe	2002

Taxonmaps

69479

Global distribution of 16S sequence AB510703 (>99% sequence identity) for Phocaeicola massiliensis subclade from Microbeatlas

Aquatic Samples	6340
Soil Samples	946
Animal Samples	152755
Plant Samples	364
Total Samples	160405

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
7121	yes, in single cases	1	Risk group (German classification) According to TRBA 466
120849		2	Risk group (French 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	Bact_mass_DSM_17679_V1 assembly for Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223	scaffold	GCA_000382445	1121098.3	2531839249	1121098	67.26
67770	ASM37308v1 assembly for Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223	scaffold	GCA_000373085	1121098.4	2515154074	1121098	58.45
124043	ASM3100165v1 assembly for Phocaeicola massiliensis DSM 17679	contig	GCA_031001655	204516.483		204516	54.43
67770	ASM61354v1 assembly for Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223	contig	GCA_000613545	1121098.7	2585427948	1121098	8.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7121	Bacteroides massiliensis strain B84634 16S ribosomal RNA gene, partial sequence	AY126616	1493		1121098
67770	Bacteroides massiliensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13223	AB510703	1478		1121098

GC content

@ref	GC-content (mol%)	Method
7121	49
7121	42.7	sequence analysis
67770	49	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 DSM 17679
NCBI: GCA_000382445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.30	no
125439	gram_stain	BacteriaNetⓘ	negative	96.20	no
125439	motility	BacteriaNetⓘ	no	69.30	no
125439	spore_formation	BacteriaNetⓘ	no	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223
PATRIC: 1121098.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	91.65	no
125438	anaerobic	anaerobicⓘ	yes	92.37	yes
125438	spore-forming	spore-formingⓘ	no	94.46	yes
125438	aerobic	aerobicⓘ	no	90.91	yes
125438	thermophilic	thermophileⓘ	no	95.07	yes
125438	flagellated	motile2+ⓘ	no	88.60	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Microbially-produced folate forms support the growth of Roseburia intestinalis but not its competitive fitness in fecal batch fermentations.	Kundra P, Geirnaert A, Pugin B, Pluss S, Kariluoto S, Lacroix C, Greppi A.	BMC Microbiol	10.1186/s12866-024-03528-6	2024
	Xylo-oligosaccharide-based prebiotics upregulate the proteins of the Sus-like system in caecal Bacteroidetes of the chicken: evidence of stimbiotic mechanism.	Amir SE, Naeem M, Boocock D, Coveney C, O'Neill HM, Bedford MR, Burton EJ.	Poult Sci	10.1016/j.psj.2023.103113	2023
	GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance.	Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, Krzystek A, de Wouters T, Braegger C, Lacroix C, Pugin B.	Front Microbiol	10.3389/fmicb.2021.656895	2021
Metabolism	Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion.	Okumura S, Konishi Y, Narukawa M, Sugiura Y, Yoshimoto S, Arai Y, Sato S, Yoshida Y, Tsuji S, Uemura K, Wakita M, Matsudaira T, Matsumoto T, Kawamoto S, Takahashi A, Itatani Y, Miki H, Takamatsu M, Obama K, Takeuchi K, Suematsu M, Ohtani N, Fukunaga Y, Ueno M, Sakai Y, Nagayama S, Hara E.	Nat Commun	10.1038/s41467-021-25965-x	2021
	Response of cell volume in Mytilus gill to acute salinity change.	Neufeld DS, Wright SH.	J Exp Biol	10.1242/jeb.199.2.473	1996
Metabolism	Selective targeting of BCL6 induces oncogene addiction switching to BCL2 in B-cell lymphoma.	Dupont T, Yang SN, Patel J, Hatzi K, Malik A, Tam W, Martin P, Leonard J, Melnick A, Cerchietti L.	Oncotarget	10.18632/oncotarget.6513	2016
Metabolism	Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans.	Pudlo NA, Urs K, Kumar SS, German JB, Mills DA, Martens EC.	mBio	10.1128/mbio.01282-15	2015
Metabolism	Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals.	Theilmann MC, Goh YJ, Nielsen KF, Klaenhammer TR, Barrangou R, Abou Hachem M.	mBio	10.1128/mbio.01421-17	2017
Metabolism	Chimeric receptor mRNA transfection as a tool to generate antineoplastic lymphocytes.	Rabinovich PM, Komarovskaya ME, Wrzesinski SH, Alderman JL, Budak-Alpdogan T, Karpikov A, Guo H, Flavell RA, Cheung NK, Weissman SM, Bahceci E.	Hum Gene Ther	10.1089/hum.2008.068	2009
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	Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon.	Ngom II, Mailhe M, Ricaboni D, Vitton V, Benezech A, Khelaifia S, Michelle C, Cadoret F, Armstrong N, Levasseur A, Raoult D, Million M.	New Microbes New Infect	10.1016/j.nmni.2017.11.009	2018
	Identification of a New Serine Alkaline Peptidase from the Moderately Halophilic Virgibacillus natechei sp. nov., Strain FarD^T and its Application as Bioadditive for Peptide Synthesis and Laundry Detergent Formulations.	Mechri S, Bouacem K, Amziane M, Dab A, Nateche F, Jaouadi B.	Biomed Res Int	10.1155/2019/6470897	2019
Phylogeny	Phocaeicola faecalis sp. nov., a strictly anaerobic bacterial strain adapted to the human gut ecosystem.	Wang C, Li S, Zhang Z, Yu Z, Yu L, Tian F, Chen W, Zhai Q	Antonie Van Leeuwenhoek	10.1007/s10482-021-01595-7	2021
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
Phylogeny	Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn.	Fenner L, Roux V, Mallet MN, Raoult D	Int J Syst Evol Microbiol	10.1099/ijs.0.63350-0	2005

References

#7121	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17679
#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 )
#27653	IJSEM 1335 2005 ( DOI 10.1099/ijs.0.63350-0 , PubMed 15879278 )
#31339	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 #27653
#38242	; Curators of the CIP;
#58392	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48901
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#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 .
#120849	Collection of Institut Pasteur ; Curators of the CIP; CIP 107942
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 massiliensis (DSM 17679, CCUG 48901, CIP 107942)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000382445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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