Strain identifier

BacDive ID: 12560

Type strain: Yes

Species: Prevotella histicola

Strain Designation: T05-04

Strain history: CCUG 55407 <-- J. Downes T05-04 <-- S. J. Hooper.

NCBI tax ID(s): 1236504 (strain), 470565 (species)

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General

@ref: 8356

BacDive-ID: 12560

DSM-Number: 19854

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

description: Prevotella histicola T05-04 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human oral squamous cell carcinoma tissue.

NCBI tax id

NCBI tax idMatching level
1236504strain
470565species

strain history

@refhistory
8356<- J. Downes; T05-04 {2008} <- S. J. Hooper
67770CCUG 55407 <-- J. Downes T05-04 <-- S. J. Hooper.

doi: 10.13145/bacdive12560.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella histicola
  • full scientific name: Prevotella histicola Downes et al. 2008

@ref: 8356

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella histicola

full scientific name: Prevotella histicola Downes et al. 2008 emend. Hahnke et al. 2016

strain designation: T05-04

type strain: yes

Morphology

cell morphology

  • @ref: 32539
  • gram stain: negative
  • cell length: 0.8-3 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation period
83562-3 days
605732 days

pigmentation

  • @ref: 32539
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8356COLUMBIA 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
8356PYG 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
8356positivegrowth37mesophilic
32539positivegrowth37mesophilic
32539positiveoptimum37mesophilic
60573positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
32539positivegrowth7
32539positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8356anaerobe
32539anaerobe
60573anaerobe

spore formation

  • @ref: 32539
  • spore formation: no

observation

  • @ref: 32539
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3253922599arabinose+carbon source
3253917057cellobiose+carbon source
3253917716lactose+carbon source
3253937684mannose+carbon source
3253916634raffinose+carbon source
3253917814salicin+carbon source
3253917992sucrose+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
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-
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
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8356--+/-+++---+---+--++-+----+--+/--
8356--++++---+++-+--++-+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
8356human oral squamous cell carcinoma tissueUnited KingdomGBREurope
60573Human oral tissue,squamous cell carcinomaUnited KingdomGBREurope2004Cardiff
67770Human oral cavity

isolation source categories

Cat1Cat2
#Host#Human
#Host Body-Site

taxonmaps

  • @ref: 69479
  • File name: preview.99_3080.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_87;97_92;98_2367;99_3080&stattab=map
  • Last taxonomy: Prevotella histicola subclade
  • 16S sequence: AB547685
  • Sequence Identity:
  • Total samples: 84211
  • soil counts: 1242
  • aquatic counts: 1647
  • animal counts: 80804
  • plant counts: 518

Safety information

risk assessment

  • @ref: 8356
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8356Prevotella histicola strain T05-04 16S ribosomal RNA gene, partial sequenceEU1266611453ena470565
67770Prevotella histicola gene for 16S ribosomal RNA, partial sequence, strain: JCM 15637AB5476851480ena470565

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella histicola JCM 15637 = DNF00424GCA_000759075contigncbi1236504
66792Prevotella histicola JCM 15637 = DNF004241236504.5wgspatric1236504
67770Prevotella histicola JCM 15637 = DNF00424GCA_000613925contigncbi1236504

GC content

@refGC-contentmethod
835643high performance liquid chromatography (HPLC)
3253943
835641.2sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.31yes
gram-positiveno97.418yes
anaerobicyes97.731no
aerobicno98.204yes
halophileno84.458no
spore-formingno96.855yes
glucose-utilyes89.332no
flagellatedno96.824yes
thermophileno97.667yes
glucose-fermentyes57.179no

External links

@ref: 8356

culture collection no.: DSM 19854, CCUG 55407, JCM 15637

straininfo link

  • @ref: 81774
  • straininfo: 396876

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18676457Prevotella histicola sp. nov., isolated from the human oral cavity.Downes J, Hooper SJ, Wilson MJ, Wade WGInt J Syst Evol Microbiol10.1099/ijs.0.65656-02008Acetic Acid/metabolism, Bacterial Typing Techniques, Base Composition, Carcinoma, Squamous Cell/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Humans, Molecular Sequence Data, Mouth Mucosa/*microbiology, Mouth Neoplasms/*microbiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, Prevotella/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species Specificity, Succinic Acid/metabolismGenetics
Phylogeny23793857Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease.Hedberg ME, Israelsson A, Moore ERB, Svensson-Stadler L, Wai SN, Pietz G, Sandstrom O, Hernell O, Hammarstrom ML, Hammarstrom SInt J Syst Evol Microbiol10.1099/ijs.0.052647-02013Acetic Acid/metabolism, Bacterial Typing Techniques, Base Composition, Celiac Disease/*microbiology, Cell Line, Tumor, Child, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Epithelial Cells/microbiology, Fatty Acids/chemistry, Female, Humans, Intestine, Small/cytology/*microbiology, Molecular Sequence Data, *Phylogeny, Prevotella/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Succinic Acid/metabolism, SwedenMetabolism
Metabolism34017324Prevotella histicola Protects From Arthritis by Expansion of Allobaculum and Augmenting Butyrate Production in Humanized Mice.Balakrishnan B, Luckey D, Bodhke R, Chen J, Marietta E, Jeraldo P, Murray J, Taneja VFront Immunol10.3389/fimmu.2021.6096442021Adaptation, Physiological, Animals, Arthritis, Rheumatoid/diagnosis/etiology/metabolism/therapy, Bile Acids and Salts/pharmacology, Biological Therapy/*methods, Butyrates/*metabolism, Disease Models, Animal, Fatty Acids, Volatile/metabolism, Gastric Juice, Gastrointestinal Microbiome, Humans, Hydrogen-Ion Concentration, Mice, Mice, Transgenic, Prevotella/classification/drug effects/genetics/*physiology, *SymbiosisPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8356Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19854)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19854
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
32539Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2875728776041
60573Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55407)https://www.ccug.se/strain?id=55407
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
81774Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396876.1StrainInfo: A central database for resolving microbial strain identifiers