Strain identifier

BacDive ID: 132203

Type strain: Yes

Species: Parabacteroides faecis

Strain Designation: 157

Strain history: Y. Tanaka 157.

NCBI tax ID(s): 1217282 (species)

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General

@ref: 23992

BacDive-ID: 132203

DSM-Number: 102983

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

description: Parabacteroides faecis 157 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 1217282
  • Matching level: species

strain history

@refhistory
23992<- JCM <- M. Sakamoto, RIKEN, Wako, Saitama, Japan; 157
67770Y. Tanaka 157.

doi: 10.13145/bacdive132203.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Tannerellaceae
  • genus: Parabacteroides
  • species: Parabacteroides faecis
  • full scientific name: Parabacteroides faecis Sakamoto et al. 2015

@ref: 23992

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides faecis

full scientific name: Parabacteroides faecis Sakamoto et al. 2015

strain designation: 157

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480negative99.998
6948092.444no

colony morphology

  • @ref: 63357
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
23992CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 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
23992COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
63357positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
63357anaerobe
69480anaerobe99.687

spore formation

@refspore formationconfidence
69481no100
69480no99.824

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
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
68380serine arylamidase-
68380histidine arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
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
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
23992--++-++/-+-+++/-+---++-+-++/--++/-++/--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
23992human faecesJapanJPNAsia
63357Human faecesJapanJPNAsia2010-11-24
67770Human fecesJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_183104.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_902;97_87705;98_119230;99_183104&stattab=map
  • Last taxonomy: Parabacteroides faecis subclade
  • 16S sequence: AB739697
  • Sequence Identity:
  • Total samples: 882
  • soil counts: 2
  • aquatic counts: 3
  • animal counts: 874
  • plant counts: 3

Safety information

risk assessment

  • @ref: 23992
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23992
  • description: Parabacteroides faecis gene for 16S ribosomal RNA, partial sequence
  • accession: AB739697
  • length: 1442
  • database: ena
  • NCBI tax ID: 1217282

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides faecis DSM 102983GCA_014199665contigncbi1217282
66792Parabacteroides faecis JCM 18682GCA_014647375scaffoldncbi1217282
66792Parabacteroides faecis strain DSM 1029831217282.3wgspatric1217282
66792Parabacteroides faecis strain JCM 186821217282.5wgspatric1217282
66792Parabacteroides faecis DSM 1029832828648469draftimg1217282

GC content

@refGC-contentmethod
2399241.8
6777041.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.694no
gram-positiveno97.447no
anaerobicyes97.927yes
aerobicno97.57yes
halophileno90.905no
spore-formingno93.844no
glucose-utilyes90.227no
thermophileno99.558yes
motileno90.224no
glucose-fermentyes63.403no

External links

@ref: 23992

culture collection no.: DSM 102983, CCUG 66681, JCM 18682

straininfo link

  • @ref: 90556
  • straininfo: 405887

literature

  • topic: Phylogeny
  • Pubmed-ID: 25667391
  • title: Parabacteroides faecis sp. nov., isolated from human faeces.
  • authors: Sakamoto M, Tanaka Y, Benno Y, Ohkuma M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000109
  • year: 2015
  • mesh: Bacterial Proteins/genetics, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Bile, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
23992Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102983Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102983)
63357Curators of the CCUGhttps://www.ccug.se/strain?id=66681Culture Collection University of Gothenburg (CCUG) (CCUG 66681)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405887.1