Strain identifier

BacDive ID: 12539

Type strain: Yes

Species: Hoylesella shahii

Strain Designation: EHS11

Strain history: M. Sakamoto EHS11.

NCBI tax ID(s): 1122991 (strain), 228603 (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: 5929

BacDive-ID: 12539

DSM-Number: 15611

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

description: Hoylesella shahii EHS11 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human oral cavity, saliva of a peridontally healthy subject.

NCBI tax id

NCBI tax idMatching level
228603species
1122991strain

strain history

@refhistory
5929<- M. Sakamoto; EHS-11
67770M. Sakamoto EHS11.

doi: 10.13145/bacdive12539.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Hoylesella
  • species: Hoylesella shahii
  • full scientific name: Hoylesella shahii (Sakamoto et al. 2004) Hitch et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Prevotella shahii

@ref: 5929

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella shahii

full scientific name: Prevotella shahii Sakamoto et al. 2004

strain designation: EHS11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30045negative9.15 µm0.65 µmrod-shapedno
69480no95.799
69480negative99.998

pigmentation

  • @ref: 30045
  • production: no

Culture and growth conditions

culture medium

  • @ref: 5929
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: 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
5929positivegrowth37mesophilic
59371positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5929anaerobe
30045anaerobe
59371anaerobe
69480anaerobe99.69

spore formation

@refspore formationconfidence
30045no
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
300455291gelatin+carbon source
3004517234glucose+carbon source
3004517716lactose+carbon source
3004517306maltose+carbon source
3004537684mannose+carbon source
30045506227N-acetylglucosamine+carbon source
3004516634raffinose+carbon source
3004517992sucrose+carbon source

enzymes

@refvalueactivityec
30045acid phosphatase+3.1.3.2
30045alkaline phosphatase+3.1.3.1
30045alpha-galactosidase+3.2.1.22
30045gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5929human oral cavity, saliva of a peridontally healthy subjectJapanJPNAsia
59371Human saliva,periodontally healthy subject
67770Human oral cavity

isolation source categories

Cat1Cat2
#Host#Human
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_4478.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_198;96_687;97_798;98_3366;99_4478&stattab=map
  • Last taxonomy: Prevotella shahii subclade
  • 16S sequence: AB108825
  • Sequence Identity:
  • Total samples: 20678
  • soil counts: 217
  • aquatic counts: 149
  • animal counts: 20236
  • plant counts: 76

Safety information

risk assessment

  • @ref: 5929
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5929
  • description: Prevotella shahii gene for 16S rRNA, complete sequence
  • accession: AB108825
  • length: 1490
  • database: ena
  • NCBI tax ID: 228603

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella shahii DSM 15611 = JCM 120831122991.5wgspatric1122991
66792Prevotella shahii JCM 120831235817.5wgspatric1122991
66792Prevotella shahii DSM 156112585427597draftimg1122991
66792Prevotella shahii JCM 120832585427909draftimg1122991
67770Hoylesella shahii DSM 15611 = JCM 12083GCA_000613445contigncbi1122991
67770Hoylesella shahii DSM 15611 = JCM 12083GCA_003201715scaffoldncbi1122991

GC content

@refGC-contentmethod
592944.3
6777044.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.523yes
flagellatedno97.105yes
gram-positiveno97.778no
anaerobicyes98.395yes
aerobicno98.328yes
halophileno85.61no
spore-formingno95.112no
thermophileno98.837yes
glucose-utilyes86.492yes
glucose-fermentyes60.779no

External links

@ref: 5929

culture collection no.: DSM 15611, JCM 12083, CCUG 51933, KCTC 15078

straininfo link

  • @ref: 81756
  • straininfo: 127938

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143039Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity.Sakamoto M, Suzuki M, Huang Y, Umeda M, Ishikawa I, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.02876-02004DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humans, Molecular Sequence Data, Mouth/*microbiology, Phenotype, Phylogeny, Prevotella/*classification/genetics/*isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityPathogenicity
Phylogeny31214821Prevotella koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion.Park SN, Lim YK, Shin JH, Jo E, Chang YH, Shin Y, Paek J, Ji S, Kim H, Kook JKCurr Microbiol10.1007/s00284-019-01720-w2019Bacterial Typing Techniques, Base Composition, Dental Plaque/*microbiology, Fatty Acids/chemistry/metabolism, Female, Genome, Bacterial, Humans, Middle Aged, Periodontitis/*microbiology, Phylogeny, Prevotella/classification/genetics/*isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5929Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15611)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15611
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
30045Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2640628776041
59371Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51933)https://www.ccug.se/strain?id=51933
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/
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
81756Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127938.1StrainInfo: A central database for resolving microbial strain identifiers