Strain identifier

BacDive ID: 12569

Type strain: Yes

Species: Paraprevotella clara

Strain history: M. Morotomi A7 (=YIT 11840).

NCBI tax ID(s): 762968 (strain), 454154 (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: 8270

BacDive-ID: 12569

DSM-Number: 19731

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

description: Paraprevotella clara DSM 19731 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from faecal sample from healthy Japanese male.

NCBI tax id

NCBI tax idMatching level
762968strain
454154species

strain history

@refhistory
8270<- H. Sakon, Yakult Central Inst. Microbiol. Res., Kunitachi-shi, Japan <- F. Nagai and M. Morotomi; YIT 11840
67770M. Morotomi A7 (=YIT 11840).

doi: 10.13145/bacdive12569.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Paraprevotella
  • species: Paraprevotella clara
  • full scientific name: Paraprevotella clara Morotomi et al. 2009

@ref: 8270

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Paraprevotella

species: Paraprevotella clara

full scientific name: Paraprevotella clara Morotomi et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29184negative1.45 µm0.85 µmrod-shapedno
69480no94.194
69480negative99.998

Culture and growth conditions

culture medium

  • @ref: 8270
  • name: CHOPPED MEAT MEDIUM (DSMZ Medium 78)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/78
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
8270positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8270anaerobe
29184anaerobe
69480anaerobe99.599

spore formation

@refspore formationconfidence
29184no
69481no100
69480no99.999

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2918430089acetate+carbon source
2918422599arabinose+carbon source
2918417234glucose+carbon source
2918429987glutamate+carbon source
2918417716lactose+carbon source
2918417306maltose+carbon source
2918437684mannose+carbon source
2918416634raffinose+carbon source
2918430031succinate+carbon source
2918418222xylose+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-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
29184acid phosphatase+3.1.3.2
29184alkaline phosphatase+3.1.3.1
29184alpha-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-
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8270--++---+--------+--+/-----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8270faecal sample from healthy Japanese maleTokyoJapanJPNAsia
67770Human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_92135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_673;96_9744;97_11740;98_14426;99_92135&stattab=map
  • Last taxonomy: Paraprevotella
  • 16S sequence: AB547651
  • Sequence Identity:
  • Total samples: 3548
  • soil counts: 3
  • aquatic counts: 10
  • animal counts: 3533
  • plant counts: 2

Safety information

risk assessment

  • @ref: 8270
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paraprevotella clara gene for 16S ribosomal RNA, partial sequence, strain: JCM 14859AB5476511480ena454154
8270Paraprevotella clara gene for 16S ribosomal RNA, partial sequenceAB3318961483ena762968

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraprevotella clara YIT 11840GCA_000233955scaffoldncbi762968
66792Paraprevotella clara YIT 11840762968.3wgspatric762968
66792Paraprevotella clara YIT 118402513237390draftimg762968

GC content

@refGC-contentmethod
827048.1high performance liquid chromatography (HPLC)
2918448.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.904yes
flagellatedno97.242yes
gram-positiveno97.644yes
anaerobicyes98.924yes
aerobicno98.149yes
halophileno85.941no
spore-formingno94.586yes
thermophileno98.389yes
glucose-utilyes87.21yes
glucose-fermentyes63.416no

External links

@ref: 8270

culture collection no.: DSM 19731, JCM 14859, YIT 11840

straininfo link

  • @ref: 81783
  • straininfo: 401674

literature

  • topic: Phylogeny
  • Pubmed-ID: 19567577
  • title: Paraprevotella clara gen. nov., sp. nov. and Paraprevotella xylaniphila sp. nov., members of the family 'Prevotellaceae' isolated from human faeces.
  • authors: Morotomi M, Nagai F, Sakon H, Tanaka R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.008169-0
  • year: 2009
  • mesh: Acetic Acid/metabolism, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, Prevotella/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Succinic Acid/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
8270Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19731
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
29184Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125608
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
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
81783Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401674.1StrainInfo: A central database for resolving microbial strain identifiers