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Strain identifier

BacDive ID: 14341

Type strain: Yes

Species: Treponema saccharophilum

Strain Designation: PB

Strain history: DSM 2985 <-- E. Canale-Parola; PB <-- B. J. Paster and E. Canale-Parola.

NCBI tax ID(s): 907348 (strain), 165 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1268

BacDive-ID: 14341

DSM-Number: 2985

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Treponema saccharophilum PB is an anaerobe, mesophilic bacterium that was isolated from bovine rumen.

NCBI tax id

NCBI tax idMatching level
907348strain
165species

strain history

doi: 10.13145/bacdive14341.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Treponemataceae
  • genus: Treponema
  • species: Treponema saccharophilum
  • full scientific name: Treponema saccharophilum Paster and Canale-Parola 1986

@ref: 1268

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Treponemataceae

genus: Treponema

species: Treponema saccharophilum

full scientific name: Treponema saccharophilum Paster and Canale-Parola 1986

strain designation: PB

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 94.653

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_2985_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2985_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2985_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2985_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2985_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 1268
  • name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/323
  • composition: Name: TREPONEMA SACCHAROPHILUM MEDIUM (DSMZ Medium 323) Composition: Agar 12.0 g/l Na2CO3 2.5 g/l D-Glucose 2.0 g/l Trypticase peptone 2.0 g/l Yeast extract 2.0 g/l L-Cysteine HCl x H2O 1.0 g/l (NH4)2SO4 0.9 g/l NaCl 0.9 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l MgSO4 x 7 H2O 0.19 g/l CaCl2 x 2 H2O 0.12 g/l Sodium resazurin 0.0005 g/l n-Butyric acid iso-Butyric acid DL-2-Methylbutyric acid n-Valeric acid iso-Valeric acid Distilled water

culture temp

@refgrowthtypetemperaturerange
1268positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1268anaerobe
69480anaerobe99.323

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.855

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 99.615

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1268bovine rumenMassachusetts, AmherstUSAUSANorth America
67770Rumen fluid sample obtained from a fistulated cow (Holstein breed) housed at the University of Massachusetts Dairy FacilitySouth Deerfield, MAUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Rumen

Safety information

risk assessment

  • @ref: 1268
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Treponema saccharophilum strain ATCC 43261 16S ribosomal RNA gene, partial sequence
  • accession: M71238
  • length: 1497
  • database: ena
  • NCBI tax ID: 165

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Treponema saccharophilum DSM 2985907348.3wgspatric907348
66792Treponema saccharophilum PB, DSM 29852509276055draftimg907348
67770Treponema saccharophilum DSM 2985 DSM 2985GCA_000255555contigncbi907348

GC content

@refGC-contentmethod
126854.0
6777053-55thermal denaturation, midpoint method (Tm)

External links

@ref: 1268

culture collection no.: DSM 2985, ATCC 43261, JCM 32279

straininfo link

@refpassport
20218http://www.straininfo.net/strains/158254
20218http://www.straininfo.net/strains/121151

literature

  • topic: Phylogeny
  • Pubmed-ID: 24289046
  • title: Monitoring the rumen pectinolytic bacteria Treponema saccharophilum using real-time PCR.
  • authors: Liu J, Wang JK, Zhu W, Pu YY, Guan LL, Liu JX
  • journal: FEMS Microbiol Ecol
  • DOI: 10.1111/1574-6941.12246
  • year: 2013
  • mesh: Animal Feed, Animals, Cattle/microbiology, DNA Primers/genetics, DNA, Bacterial/genetics/isolation & purification, Female, Lolium/chemistry, Pectins/*metabolism, RNA, Ribosomal, 16S/genetics, Real-Time Polymerase Chain Reaction, Rumen/*microbiology, Sensitivity and Specificity, Sequence Analysis, DNA, Treponema/genetics/*isolation & purification, Zea mays/chemistry
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1268Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2985)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2985
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
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)