Strain identifier

BacDive ID: 12556

Type strain: Yes

Species: Hoylesella timonensis

Strain Designation: 4401737

Strain history: CIP <- 2004, V. Roux, Timone Hosp., Marseille, France: strain 4401737

NCBI tax ID(s): 1122992 (strain), 386414 (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: 16581

BacDive-ID: 12556

DSM-Number: 22865

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

description: Hoylesella timonensis 4401737 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human breast abscess .

NCBI tax id

NCBI tax idMatching level
386414species
1122992strain

strain history

@refhistory
16581<- CCUG; CCUG 50105 <- V. Roux, Timone Hospital, Marseille, France
400142004, V. Roux, La Timone Hosp., Marseille, France: strain 4401737
67770CCUG 50105 <-- V. Roux 4401737.
123550CIP <- 2004, V. Roux, Timone Hosp., Marseille, France: strain 4401737

doi: 10.13145/bacdive12556.20230509.8.1

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 timonensis
  • full scientific name: Hoylesella timonensis (Glazunova et al. 2007) Hitch et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Prevotella timonensis

@ref: 16581

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella timonensis

full scientific name: Prevotella timonensis Glazunova et al. 2007 emend. Hahnke et al. 2016

strain designation: 4401737

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31893negative1.1 µm0.4 µmrod-shapedno
69480no93.922
69480negative100
123550negativerod-shapedno

colony morphology

@refincubation period
587432-3 days
123550

pigmentation

  • @ref: 31893
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16581CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
40014MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123550CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
123550CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
16581positivegrowth37mesophilic
31893positivegrowth25-37mesophilic
31893positiveoptimum37mesophilic
40014positivegrowth30mesophilic
58743positivegrowth30-37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16581anaerobe
31893anaerobe
58743anaerobe
69480anaerobe99.655
123550anaerobe

spore formation

@refspore formationconfidence
31893no
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31893581435-dehydro-D-gluconate+carbon source
3189329016arginine+carbon source
3189317234glucose+carbon source
3189317716lactose+carbon source
3189317306maltose+carbon source
31893506227N-acetylglucosamine+carbon source
3189333942ribose+carbon source
318934853esculin+hydrolysis
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
12355017632nitrate-reduction
12355016301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
12355035581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
31893alkaline phosphatase+3.1.3.1
31893alpha-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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5
123550oxidase-
123550alcohol dehydrogenase-1.1.1.1
123550catalase-1.11.1.6
123550lysine decarboxylase-4.1.1.18
123550ornithine decarboxylase-4.1.1.17
123550urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase+3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123550-+++------++-+-+-+-+

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
16581--+-+-+-------+------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16581---+-+---+---+--+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
16581human breast abscess (40-year-old woman)MarseilleFranceFRAEurope
58743Human abscess,breast,40-yr-old womanMarseilleFranceFRAEurope2004-06-01
67770Human breast abscess
123550Human, Mammary abscessMarseilleFranceFRAEurope2004

isolation source categories

Cat1Cat2Cat3
#Host#Human#Female
#Host Body-Site
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_1443.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15971;96_831;97_970;98_1141;99_1443&stattab=map
  • Last taxonomy: Prevotella timonensis subclade
  • 16S sequence: AB547706
  • Sequence Identity:
  • Total samples: 103091
  • soil counts: 1601
  • aquatic counts: 2334
  • animal counts: 98467
  • plant counts: 689

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
16581yes, in single cases1Risk group (German classification)
1235502Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Prevotella timonensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 15640AB5477061493ena1122992
16581Prevotella timonensis strain 4401737 16S ribosomal RNA gene, partial sequenceDQ5189191454ena1122992

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hoylesella timonensis 4401737 = DSM 22865 = JCM 15640GCA_000455445scaffoldncbi1122992
66792Hoylesella timonensis 4401737 = DSM 22865 = JCM 15640GCA_000430565scaffoldncbi1122992
66792Hoylesella timonensis 4401737 = DSM 22865 = JCM 15640GCA_000614005contigncbi1122992
66792Prevotella timonensis 4401737 = DSM 22865 = JCM 156401122992.3wgspatric1122992
66792Prevotella timonensis 4401737 = DSM 22865 = JCM 156401122992.4wgspatric1122992
66792Prevotella timonensis 4401737 = DSM 22865 = JCM 156401122992.6wgspatric1122992
66792Prevotella timonensis 4401737, DSM 228652585427924draftimg1122992
66792Prevotella timonensis 4401737, DSM 228652600255039draftimg1122992
66792Prevotella timonensis 4401737, DSM 228652523533627draftimg1122992

GC content

  • @ref: 16581
  • GC-content: 42.4
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.54yes
flagellatedno97.719yes
gram-positiveno97.322yes
anaerobicyes97.563yes
aerobicno97.013yes
halophileno87.721no
spore-formingno97.577yes
thermophileno98.669no
glucose-utilyes85.251yes
glucose-fermentyes52.721no

External links

@ref: 16581

culture collection no.: JCM 50105, DSM 22865, CCUG 50105, CIP 108522, JCM 15640, KCTC 15080

straininfo link

  • @ref: 81770
  • straininfo: 302772

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392225Prevotella timonensis sp. nov., isolated from a human breast abscess.Glazunova OO, Launay T, Raoult D, Roux VInt J Syst Evol Microbiol10.1099/ijs.0.64609-02007Abscess/*microbiology, Adult, Bacteroidaceae Infections/*microbiology, Breast/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Female, Humans, Molecular Sequence Data, Phylogeny, Prevotella/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/geneticsPathogenicity
Genetics25197502Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737(T.).Roux V, Robert C, Raoult DStand Genomic Sci10.4056/sigs.50989482014

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22865)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22865
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
31893Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128152
40014Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6154
58743Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50105)https://www.ccug.se/strain?id=50105
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
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
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
81770Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302772.1StrainInfo: A central database for resolving microbial strain identifiers
123550Curators of the CIPCollection of Institut Pasteur (CIP 108522)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108522