Strain identifier

BacDive ID: 1628

Type strain: Yes

Species: Bacteroides clarus

Strain Designation: A 20

Strain history: Y. Watanabe A20 (=YIT 12056).

NCBI tax ID(s): 762984 (strain), 626929 (species)

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General

@ref: 16376

BacDive-ID: 1628

DSM-Number: 22519

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

description: Bacteroides clarus A 20 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces .

NCBI tax id

NCBI tax idMatching level
626929species
762984strain

strain history

@refhistory
16376<- Y. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan <- F. Nagai and M. Morotomi
67770Y. Watanabe A20 (=YIT 12056).

doi: 10.13145/bacdive1628.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides clarus
  • full scientific name: Bacteroides clarus Watanabe et al. 2010

@ref: 16376

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides clarus

full scientific name: Bacteroides clarus Watanabe et al. 2010

strain designation: A 20

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29531negative0.7-2.9 µm0.5-1 µmrod-shapedno
69480no95.092
69480negative99.997

pigmentation

  • @ref: 29531
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16376CHOPPED 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
16376PYG 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
16376positivegrowth37mesophilic
29531positivegrowth37mesophilic
29531positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29531positivegrowth7
29531positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16376anaerobe
29531anaerobe
69480anaerobe99.618

spore formation

@refspore formationconfidence
29531no
69481no100
69480no99.983

observation

@refobservation
29531aggregates in chains
67770quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2953117754glycerol+carbon source
2953129864mannitol+carbon source
2953126546rhamnose+carbon source
2953117814salicin+carbon source
2953130911sorbitol+carbon source
2953127082trehalose+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
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
29531alpha-galactosidase+3.2.1.22
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
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
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
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16376+-+-+++-+--+-++-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16376-+/-++-++--++++--++--+---+++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16376human faeces (healthy Japanese adult male)TokyoJapanJPNAsia
62494Human feces,healthy adult manJapanJPNAsia2009
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4450.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_994;97_2694;98_3344;99_4450&stattab=map
  • Last taxonomy: Bacteroides clarus subclade
  • 16S sequence: AB547638
  • Sequence Identity:
  • Total samples: 24128
  • soil counts: 122
  • aquatic counts: 805
  • animal counts: 23186
  • plant counts: 15

Safety information

risk assessment

  • @ref: 16376
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides clarus gene for 16S ribosomal RNA, partial sequence, strain: JCM 16067AB5476381488ena762984
16376Bacteroides clarus gene for 16S rRNA, partial sequence, strain: YIT 12056AB4908011479ena762984

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides clarus YIT 12056GCA_900129655contigncbi762984
66792Bacteroides clarus YIT 12056762984.3wgspatric762984
66792Bacteroides clarus YIT 12056762984.10wgspatric762984
66792Bacteroides clarus DSM 225192695420967draftimg762984
66792Bacteroides clarus YIT 12056651324010draftimg762984
67770Bacteroides clarus YIT 12056GCA_000195615scaffoldncbi762984

GC content

@refGC-contentmethod
1637645.3high performance liquid chromatography (HPLC)
2953145.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.75no
flagellatedno96.152yes
gram-positiveno97.61no
anaerobicyes98.691yes
halophileno92.431no
spore-formingno94.42yes
glucose-utilyes88.638no
aerobicno98.107yes
thermophileno98.885yes
glucose-fermentyes73.926no

External links

@ref: 16376

culture collection no.: DSM 22519, JCM 16067, CCUG 60911, YIT 12056, KCTC 15128

straininfo link

  • @ref: 71274
  • straininfo: 403364

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19767355Bacteroides clarus sp. nov., Bacteroides fluxus sp. nov. and Bacteroides oleiciplenus sp. nov., isolated from human faeces.Watanabe Y, Nagai F, Morotomi M, Sakon H, Tanaka RInt J Syst Evol Microbiol10.1099/ijs.0.015107-02009Bacteroides/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsPathogenicity
Phylogeny35635547Bacteroides propionicigenes sp. nov., isolated from human faeces.Sun XW, Abdugheni R, Huang HJ, Wang YJ, Jiang MZ, Liu C, Zhou N, Jiang H, Liu SJInt J Syst Evol Microbiol10.1099/ijsem.0.0053972022Adult, Bacterial Typing Techniques, *Bacteroides, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Feces/microbiology, Humans, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16376Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22519)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22519
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
29531Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125928
62494Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60911)https://www.ccug.se/strain?id=60911
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71274Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403364.1StrainInfo: A central database for resolving microbial strain identifiers