Strain identifier

BacDive ID: 1612

Type strain: Yes

Species: Phocaeicola dorei

Strain Designation: 175

Strain history: M. Sakamoto <-- M. Matsumoto 175.

NCBI tax ID(s): 483217 (strain), 357276 (species)

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General

@ref: 7141

BacDive-ID: 1612

DSM-Number: 17855

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

description: Phocaeicola dorei 175 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
357276species
483217strain

strain history

@refhistory
7141<- M. Sakamoto; 175 <- M. Matsumoto
67770M. Sakamoto <-- M. Matsumoto 175.

doi: 10.13145/bacdive1612.20230509.8.1

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 dorei
  • full scientific name: Phocaeicola dorei (Bakir et al. 2006) García-López et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides dorei

@ref: 7141

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Phocaeicola

species: Phocaeicola dorei

full scientific name: Phocaeicola dorei (Bakir et al. 2006) García-López et al. 2020

strain designation: 175

type strain: yes

Morphology

cell morphology

  • @ref: 31780
  • gram stain: negative
  • cell length: 1.6-4.2 µm
  • cell width: 0.8-1.2 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation period
71411-2 days
600612 days

pigmentation

  • @ref: 31780
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7141COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
7141PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
7141positivegrowth37mesophilic
31780positivegrowth37mesophilic
31780positiveoptimum37mesophilic
60061positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
31780positivegrowth7
31780positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7141anaerobe
31780anaerobe
60061anaerobe

spore formation

  • @ref: 31780
  • spore formation: no

observation

  • @ref: 31780
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3178022599arabinose+carbon source
3178026546rhamnose+carbon source
3178017992sucrose+carbon source
3178018222xylose+carbon source
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase+3.2.1.51
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380alpha-arabinosidase+3.2.1.55
68380alpha-glucosidase+3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
7141--+-+++-++----+-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7141--++-+-++/-+---+--+--+++-+++-+/--
7141--++-+-+-+++-+--++-+-+/--+/-++-+-
7141--+++/-+-+-++/-+/--+--++/--++/-+-+/-+++/-+-
7141--++-++++++++--++-++/-+-+/-+++/-+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7141human fecesJapanJPNAsia
60061Human fecesJapanJPNAsia
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_829.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_500;97_572;98_658;99_829&stattab=map
  • Last taxonomy: Phocaeicola dorei subclade
  • 16S sequence: AB242142
  • Sequence Identity:
  • Total samples: 129385
  • soil counts: 671
  • aquatic counts: 4422
  • animal counts: 124015
  • plant counts: 277

Safety information

risk assessment

  • @ref: 7141
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides dorei strain DSM 17855 16S ribosomal RNA gene, partial sequenceHQ012025932ena357276
31780Bacteroides dorei gene for 16S rRNA, partial sequence, strain:JCM 13471AB2421421493nuccore483217
7141Glomerella tucumanensis genes for 18S rRNA, ITS1, 5.8S rRNA, ITS2, 28S rRNA, partial and complete sequence, strain: Cf-03AB242412585ena129314

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phocaeicola dorei DSM 17855GCA_013009555completencbi357276
66792Bacteroides dorei DSM 17855483217.6wgspatric483217
66792Bacteroides dorei strain DSM 17855357276.1035completepatric357276
66792Phocaeicola dorei DSM 17855642979370draftimg483217
67770Phocaeicola dorei DSM 17855GCA_000156075scaffoldncbi483217
66792Phocaeicola dorei DSM 17855GCA_025146415completencbi357276
66792Phocaeicola dorei strain DSM 17855357276.1436completepatric357276

GC content

@refGC-contentmethod
714143
714142.0sequence analysis
6777043high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.133yes
flagellatedno97.224yes
gram-positiveno96.531yes
anaerobicyes98.301yes
aerobicno96.93no
halophileno90.76no
spore-formingno94.441yes
glucose-utilyes90.712no
thermophileno98.896no
glucose-fermentyes74.912no

External links

@ref: 7141

culture collection no.: DSM 17855, JCM 13471, CCUG 53892

straininfo link

  • @ref: 71257
  • straininfo: 297141

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Enzymology29441125SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets.Jones DR, Thomas D, Alger N, Ghavidel A, Inglis GD, Abbott DWBiotechnol Biofuels10.1186/s13068-018-1027-x2018

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7141Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17855)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17855
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31780Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128052
60061Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53892)https://www.ccug.se/strain?id=53892
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/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
71257Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297141.1StrainInfo: A central database for resolving microbial strain identifiers