Strain identifier

BacDive ID: 17785

Type strain: Yes

Species: Pyramidobacter piscolens

Strain Designation: W5455

Strain history: <- DSM <- J Downes, W5455 <- L Fernandes-Naglik

NCBI tax ID(s): 638849 (species)

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General

@ref: 15564

BacDive-ID: 17785

DSM-Number: 21147

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

description: Pyramidobacter piscolens W5455 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from aspirate from oral abscess.

NCBI tax id

  • NCBI tax id: 638849
  • Matching level: species

strain history

@refhistory
15564<- J. Downes; W5455 <- L. Fernandes-Naglik {2000}
67770CCUG 55836 <-- J. Downes W5455.
67771<- DSM <- J Downes, W5455 <- L Fernandes-Naglik

doi: 10.13145/bacdive17785.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/synergistota
  • domain: Bacteria
  • phylum: Synergistota
  • class: Synergistia
  • order: Synergistales
  • family: Synergistaceae
  • genus: Pyramidobacter
  • species: Pyramidobacter piscolens
  • full scientific name: Pyramidobacter piscolens Downes et al. 2009

@ref: 15564

domain: Bacteria

phylum: Synergistetes

class: Synergistia

order: Synergistales

family: Synergistaceae

genus: Pyramidobacter

species: Pyramidobacter piscolens

full scientific name: Pyramidobacter piscolens Downes et al. 2009

strain designation: W5455

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
28882negative1.5 µm0.75 µmrod-shapedno
67771no
67771negative

colony morphology

  • @ref: 60748
  • incubation period: 2 days

pigmentation

  • @ref: 28882
  • production: no

Culture and growth conditions

culture medium

  • @ref: 15564
  • 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
15564positivegrowth37mesophilic
28882positiveoptimum30mesophilic
60748positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15564anaerobe
28882anaerobe
60748anaerobe
67771anaerobe

observation

  • @ref: 28882
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2888230089acetate+carbon source
2888218401phenylacetate+carbon source
2888217272propionate+carbon source
2888230031succinate+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
2888216136hydrogen sulfideyes
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
15564------------------------++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15564aspirate from oral abscessLondonUnited KingdomGBREurope
60748Human abscess aspirate,oral odontogenicLondonUnited KingdomGBREurope2000-12-19
67770Human oral cavity
67771From human odontogenic abscessLondonUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Mouth
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_33986.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_438;96_2022;97_2435;98_25129;99_33986&stattab=map
  • Last taxonomy: Pyramidobacter piscolens subclade
  • 16S sequence: EU309492
  • Sequence Identity:
  • Total samples: 10874
  • soil counts: 174
  • aquatic counts: 264
  • animal counts: 10378
  • plant counts: 58

Safety information

risk assessment

  • @ref: 15564
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
15564Pyramidobacter piscolens W5455 16S ribosomal RNA gene, partial sequenceEU3094921445ena352165
67770Pyramidobacter piscolens gene for 16S ribosomal RNA, partial sequenceAB5654801484ena352165

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pyramidobacter piscolens W5455352165.18wgspatric352165
66792Pyramidobacter piscolens W5455647000302draftimg352165
67770Pyramidobacter piscolens W5455GCA_000177335contigncbi352165

GC content

@refGC-contentmethod
1556459high performance liquid chromatography (HPLC)
2888259
6777159.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno95.764yes
anaerobicyes99.614yes
halophileno80.498no
spore-formingno89.449no
glucose-utilyes63.051no
motileno91.733yes
flagellatedno98.416yes
aerobicno98.315yes
thermophileno92.077yes
glucose-fermentno56.883no

External links

@ref: 15564

culture collection no.: DSM 21147, CCUG 55836, KCTC 15164, JCM 16336

straininfo link

  • @ref: 86776
  • straininfo: 408315

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406777Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity.Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T, Yu WH, Sutcliffe IC, Wade WGInt J Syst Evol Microbiol10.1099/ijs.0.000364-02009Bacteria, Anaerobic/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Gingivitis/*microbiology, Gram-Negative Bacteria/*classification/genetics/isolation & purification/physiology, Gram-Negative Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Mouth/*microbiology, Periodontal Pocket/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny32353874Characterization and survey in cattle of a rumen Pyrimadobacter sp. which degrades the plant toxin fluoroacetate.Kang S, Khan S, Webb R, Denman S, McSweeney CFEMS Microbiol Ecol10.1093/femsec/fiaa0772020Animals, Arginine, Australia, Bacteria, Base Composition, Cattle, DNA, Bacterial/genetics, *Fluoroacetates, Humans, Leucine, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rumen, Sequence Analysis, DNA, Surveys and QuestionnairesPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15564Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21147)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21147
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
28882Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2532228776041
60748Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55836)https://www.ccug.se/strain?id=55836
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
86776Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408315.1StrainInfo: A central database for resolving microbial strain identifiers