Strain identifier

BacDive ID: 1607

Type strain: Yes

Species: Phocaeicola plebeius

Strain Designation: M12

Strain history: M. Kitahara M12.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6782

BacDive-ID: 1607

DSM-Number: 17135

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

description: Phocaeicola plebeius M12 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
484018strain
310297species

strain history

@refhistory
6782<- Maki Kitahara, M12
67770M. Kitahara M12.

doi: 10.13145/bacdive1607.20230509.8.1

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 plebeius
  • full scientific name: Phocaeicola plebeius (Kitahara et al. 2005) García-López et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Bacteroides plebeius

@ref: 6782

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Phocaeicola

species: Phocaeicola plebeius

full scientific name: Phocaeicola plebeius (Kitahara et al. 2005) García-López et al. 2020

strain designation: M12

type strain: yes

Morphology

cell morphology

  • @ref: 31548
  • gram stain: negative
  • cell length: 3 µm
  • cell width: 0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation period
67823-7 days
602712 days

pigmentation

  • @ref: 31548
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6782COLUMBIA 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
6782CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) Yeast extract 5.0 g/l K2HPO4 5.0 g/l Pectin 0.5 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
6782positivegrowth37mesophilic
31548positiveoptimum37mesophilic
60271positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6782anaerobe
31548anaerobe
60271anaerobe

spore formation

  • @ref: 31548
  • spore formation: no

observation

@refobservation
31548aggregates in clumps
67770quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3154822599arabinose+carbon source
3154817057cellobiose+carbon source
3154817234glucose+carbon source
3154817716lactose+carbon source
3154817306maltose+carbon source
3154837684mannose+carbon source
3154816634raffinose+carbon source
3154826546rhamnose+carbon source
3154817992sucrose+carbon source
3154818222xylose+carbon source
315484853esculin+hydrolysis
6838016199urea-hydrolysis
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
31548alkaline phosphatase+3.1.3.1
31548alpha-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-
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
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380urease-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
60271-+--------++++---+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
60271--++--++-+------++-+-+--++---
6782-+/-++-+/-+/-+/--+------++-+-+--+++/-+-
6782--++-+/--+/--++/-+/-----++-+++-+++++-
6782-+/-++-+++-++/-+-+--+++++-+/-++++-
6782--++-----+------+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6782human fecesJapanJPNAsia
60271Human faecesJapanJPNAsia
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_12193.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_258;96_4788;97_5805;98_7283;99_12193&stattab=map
  • Last taxonomy: Phocaeicola plebeius subclade
  • 16S sequence: AB200217
  • Sequence Identity:
  • Total samples: 37805
  • soil counts: 244
  • aquatic counts: 1112
  • animal counts: 36355
  • plant counts: 94

Safety information

risk assessment

  • @ref: 6782
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6782
  • description: Bacteroides plebeius gene for 16S rRNA, partial sequence, strain: M12
  • accession: AB200217
  • length: 1490
  • database: ena
  • NCBI tax ID: 484018

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides plebeius DSM 17135484018.6wgspatric484018
66792Bacteroides plebeius M12, DSM 17135642979351draftimg484018
67770Phocaeicola plebeius DSM 17135GCA_000187895scaffoldncbi484018

GC content

@refGC-contentmethod
678243.9
6777043.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.027yes
anaerobicyes99.04yes
halophileno84.007no
spore-formingno96.153yes
glucose-utilyes89.06yes
aerobicno98.083yes
thermophileno96.88yes
motileno93.011yes
flagellatedno97.406yes
glucose-fermentyes69.439no

External links

@ref: 6782

culture collection no.: CCUG 54634, DSM 17135, JCM 12973

straininfo link

  • @ref: 71252
  • straininfo: 231847

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166722Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces.Kitahara M, Sakamoto M, Ike M, Sakata S, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.63788-02005Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification/physiology, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Feces/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityPathogenicity
Phylogeny17158987Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.Lan PTN, Sakamoto M, Sakata S, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64517-02006Animals, Bacterial Typing Techniques, Bacteroides/chemistry/*classification/genetics/isolation & purification, Cecum/*microbiology, Chickens/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Enzymology30110640Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.Kearney SM, Gibbons SM, Erdman SE, Alm EJCell Rep10.1016/j.celrep.2018.07.0322018Animals, Bacterial Load, Bacteroides/isolation & purification/*physiology, Diet/*methods, Eating/physiology, Feces/microbiology, Female, Gastrointestinal Microbiome/*physiology, Mice, Mice, Inbred C57BL, Seaweed/*chemistry, Symbiosis/*physiology, Verrucomicrobia/isolation & purification/physiologyPhylogeny
Pathogenicity36058421Altered gut microbiota correlates with behavioral problems but not gastrointestinal symptoms in individuals with autism.Chen YC, Lin HY, Chien Y, Tung YH, Ni YH, Gau SSBrain Behav Immun10.1016/j.bbi.2022.08.0152022*Autism Spectrum Disorder/metabolism, *Autistic Disorder, Biomarkers, *Gastrointestinal Diseases/complications, *Gastrointestinal Microbiome/genetics, Humans, *Problem BehaviorMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6782Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17135)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17135
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
31548Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2783928776041
60271Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54634)https://www.ccug.se/strain?id=54634
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
71252Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID231847.1StrainInfo: A central database for resolving microbial strain identifiers