Strain identifier

BacDive ID: 1611

Type strain: Yes

Species: Phocaeicola massiliensis

Strain Designation: B84634, 84634

Strain history: CIP <- 2003, P. Berger, Timone Hosp., Marseille, France: strain 84634

NCBI tax ID(s): 204516 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7121

BacDive-ID: 1611

DSM-Number: 17679

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped, human pathogen

description: Phocaeicola massiliensis B84634 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from blood culture of a newborn.

NCBI tax id

  • NCBI tax id: 204516
  • Matching level: species

strain history

@refhistory
7121<- V. Roux; B84634 <- Timone Hospital
382422003, P. Berger, Timone Hosp., Marseille, France: strain 84634
67770D. Raoult B84634.
120849CIP <- 2003, P. Berger, Timone Hosp., Marseille, France: strain 84634

doi: 10.13145/bacdive1611.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • 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

    @refsynonym
    20215Bacteroides massiliensis
    20215Bacteroides massiliae

@ref: 7121

domain: Bacteria

phylum: Bacteroidetes

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

strain designation: B84634, 84634

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31339negative3 µm1.1 µmrod-shapedno
120849negativerod-shapedno

colony morphology

@refincubation period
71211-2 days
120849

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7121CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: 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
38242MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
120849CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
7121positivegrowth37mesophilic
31339positivegrowth25-42
31339positiveoptimum37mesophilic
38242positivegrowth37mesophilic
58392positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7121anaerobe
31339anaerobe
58392anaerobe
120849anaerobe

spore formation

  • @ref: 31339
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3133928757fructose+carbon source
3133928260galactose+carbon source
3133917234glucose+carbon source
3133917716lactose+carbon source
3133917306maltose+carbon source
3133937684mannose+carbon source
3133928053melibiose+carbon source
31339506227N-acetylglucosamine+carbon source
3133916634raffinose+carbon source
3133930911sorbitol+carbon source
3133917992sucrose+carbon source
313394853esculin+hydrolysis
12084917108D-arabinose-degradation
12084915824D-fructose+degradation
12084917634D-glucose+degradation
12084965327D-xylose-degradation
12084917057cellobiose-degradation
12084917716lactose+degradation
12084917306maltose+degradation
12084917814salicin-degradation
12084917992sucrose+degradation
1208494853esculin+hydrolysis
12084917632nitrate-reduction
12084916301nitrite-reduction
12084917632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12084935581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120849-++-------+--+---+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7121--++-+---+++++--++-+++-++--+-
7121--++-+---+++++--++-+-+--+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7121blood culture of a newbornMarseilleFranceFRAEurope
58392Human blood,newbornMarseilleFranceFRAEurope2002-05-21
67770Blood culture of a newborn
120849Human, BloodMarseilleFranceFRAEurope2002

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Infection#Patient#Blood culture

taxonmaps

  • @ref: 69479
  • File name: preview.99_5163.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_2511;97_3065;98_3847;99_5163&stattab=map
  • Last taxonomy: Phocaeicola massiliensis subclade
  • 16S sequence: AB510703
  • Sequence Identity:
  • Total samples: 160405
  • soil counts: 946
  • aquatic counts: 6340
  • animal counts: 152755
  • plant counts: 364

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
7121yes, in single cases1Risk group (German classification)
1208492Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7121Bacteroides massiliensis strain B84634 16S ribosomal RNA gene, partial sequenceAY1266161493ena1121098
67770Bacteroides massiliensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13223AB5107031478ena1121098

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 132231121098.7wgspatric1121098
66792Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 [PRJNA199226]1121098.4wgspatric1121098
66792Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 [PRJNA201686]1121098.3wgspatric1121098
66792Bacteroides massiliensis Timone 84634, DSM 176792585427948draftimg1121098
66792Bacteroides massiliensis Timone 84634, DSM 176792515154074draftimg1121098
66792Bacteroides massiliensis Timone 84634, DSM 176792531839249draftimg1121098
67770Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223 DSM 17679GCA_000382445scaffoldncbi1121098
67770Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223GCA_000373085scaffoldncbi1121098
67770Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223GCA_000613545contigncbi1121098

GC content

@refGC-contentmethod
712149
712142.7sequence analysis
6777049high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.376yes
flagellatedno97.372no
gram-positiveno97.018no
anaerobicyes98.276yes
aerobicno98.309yes
halophileno89.474no
spore-formingno95.235no
thermophileno99.127yes
glucose-utilyes87.683yes
glucose-fermentyes69.081no

External links

@ref: 7121

culture collection no.: DSM 17679, CCUG 48901, CIP 107942, JCM 13223

straininfo link

  • @ref: 71256
  • straininfo: 138972

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879278Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn.Fenner L, Roux V, Mallet MN, Raoult DInt J Syst Evol Microbiol10.1099/ijs.0.63350-02005Anaerobiosis, Bacterial Typing Techniques, Bacteroides/*classification/*isolation & purification, Bacteroides Infections/*microbiology, Base Composition, Blood/*microbiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, Bacterial, Genes, rRNA, Gentian Violet, Humans, Infant, Newborn, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny16825642Bacteroides dorei sp. nov., isolated from human faeces.Bakir MA, Sakamoto M, Kitahara M, Matsumoto M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64257-02006Anaerobiosis, Bacterial Typing Techniques, Bacteroides/*classification/cytology/*isolation & purification/physiology, Bacteroides Infections/*microbiology, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Feces/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, BacterialPathogenicity
Phylogeny20495039Bacteroides 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 MInt J Syst Evol Microbiol10.1099/ijs.0.024026-02010Anaerobiosis, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, Chinchilla/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny34129122Phocaeicola 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 QAntonie Van Leeuwenhoek10.1007/s10482-021-01595-72021Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Ecosystem, *Fatty Acids, Female, Humans, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7121Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17679)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17679
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31339Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2765328776041
38242Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5509
58392Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48901)https://www.ccug.se/strain?id=48901
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71256Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138972.1StrainInfo: A central database for resolving microbial strain identifiers
120849Curators of the CIPCollection of Institut Pasteur (CIP 107942)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107942