Strain identifier

BacDive ID: 159392

Type strain: No

Species: Treponema phagedenis

Strain Designation: B43.1

Strain history: <- P. Kuhnert, Univ. Bern; B43.1

NCBI tax ID(s): 166 (species)

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

@ref: 66215

BacDive-ID: 159392

DSM-Number: 110455

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

description: Treponema phagedenis B43.1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from cow foot with bovine digital dermatitis.

NCBI tax id

  • NCBI tax id: 166
  • Matching level: species

strain history

  • @ref: 66215
  • history: <- P. Kuhnert, Univ. Bern; B43.1

doi: 10.13145/bacdive159392.20230509.8.1

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 phagedenis
  • full scientific name: Treponema phagedenis (ex Brumpt 1922) Kuhnert et al. 2020

@ref: 66215

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Treponemataceae

genus: Treponema

species: Treponema phagedenis

full scientific name: Treponema phagedenis (ex Brumpt 1922) Smibert 1984

strain designation: B43.1

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.074

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66215OTEB-MEDIUM (DSMZ Medium 1245)yeshttps://mediadive.dsmz.de/medium/1245Name: OTEB-MEDIUM (DSMZ Medium 1245) Composition: Proteose peptone no. 2 5.0 g/l Heart Infusion Broth 5.0 g/l Yeast extract 5.0 g/l Sodium Chloride 5.0 g/l Potassium Phosphate 2.0 g/l Fructose 0.8 g/l Sucrose 0.8 g/l Maltose 0.8 g/l Ribose 0.8 g/l Xylose 0.8 g/l Pectin 0.8 g/l Starch 0.8 g/l Sodium pyruvate 0.8 g/l Glucose 0.8 g/l L-Cysteine 0.5 g/l Magnesium sulfate 0.1 g/l Vitamin K1 0.001 g/l Thiamine pyrophosphate 7.5e-05 g/l Fetal bovine serum Acetic acid Propionic acid n-Butyric acid n-Valeric acid Isovaleric acid Isobutyric acid 2-Methylbutyric acid Distilled water
66215OMIZ-PAT (DSMZ Medium 1494)yeshttps://mediadive.dsmz.de/medium/1494Name: . OMIZ-PAT Medium (modified) (DSMZ Medium 1494) Composition: (NH4)6Mo7O24 x 4 H2O 12.4 g/l Yeast extract 3.0 g/l Fe SO4 x 7 H2O 2.78015 g/l D-Glucose 2.0 g/l D-Mannose 2.0 g/l D-Arabinose 2.0 g/l L-Fucose 2.0 g/l D-Trehalose 2.0 g/l D-Sucrose 2.0 g/l L-Rhamnose 2.0 g/l NH4Cl 1.6 g/l Glutathione 1.5366 g/l Ascorbic acid 1.0 g/l NaHCO3 1.0 g/l Ethanol 1.0 g/l KCl 0.968 g/l D-Maltose 0.8 g/l D-glucuronic acid 0.8 g/l D-Mannitol 0.8 g/l D-galacturonic acid 0.8 g/l D-Fructose 0.8 g/l L-Glutamine 0.68 g/l L-Histidine 0.62 g/l NaVO3 0.61 g/l D 0.56 g/l Pyruvic acid 0.55 g/l L-Serine 0.525 g/l Fumaric acid 0.5 g/l HCl 0.3646 g/l L-Cysteine HCl 0.35 g/l L-Glutamic acid 0.3 g/l Formic acid 0.3 g/l ZnSO4 x 7 H2O 0.287 g/l MgSO4 x 7 H2O 0.25 g/l DL-carnitine 0.2 g/l N-Acetylglucosamine 0.2 g/l Citric acid 0.2 g/l L-Lysine HCl 0.182 g/l L-Arginine 0.175 g/l L-Ornithine HCl 0.17 g/l L-Phenylalanine 0.165 g/l CaCl2 x H2O 0.15 g/l L-Methionine 0.15 g/l L-Asparagine 0.15 g/l NaH2PO4 x H2O 0.14 g/l L-Leucine 0.131 g/l L-Isoleucine 0.131 g/l NiSO4 x 6 H2O 0.131 g/l L-Threonine 0.12 g/l L-Aspartic acid 0.118 g/l SnCl2 x 2 H2O 0.118 g/l L-Valine 0.117 g/l L-Proline 0.115 g/l L-Tryptophan 0.102 g/l Nicotinic acid 0.1 g/l Folinic acid 0.1 g/l L-Tyrosine 0.09 g/l NaOH 0.079994 g/l Glycine 0.075 g/l Nicotinamide 0.05 g/l Folic acid 0.05 g/l D-(+)-biotin 0.05 g/l Vitamine B12 0.05 g/l Choline chloride 0.05 g/l Myo-inositol 0.05 g/l L-Alanine 0.045 g/l Hemin 0.026076 g/l N-acetylmuramic acid 0.025 g/l Na2SeO3 0.0173 g/l MnSO4 x H2O 0.0169 g/l Riboflavine 0.01 g/l 2-Mercaptoethanesulfonic acid 0.01 g/l Phenol red 0.01 g/l Putrescine 2 HCl 0.005 g/l Pyridoxal hydrochloride 0.005 g/l Pyridoxal phosphate 0.005 g/l Calcium D-(+)-pantothenate 0.005 g/l Thiamine HCl 0.005 g/l Thiamin pyrophosphate 0.005 g/l Thymidine 0.0024 g/l N-(2-acetamido)-2-aminoethanesulfonic acid 0.0018 g/l Hypoxanthine 0.0014 g/l Uracil 0.0011 g/l Flavin adenine dinucleotide 0.001 g/l ß-nicotinamide adenine dinucleotide 0.001 g/l Coenzym A 0.001 g/l CuSO4 0.000789 g/l Cholesterol Asialofetuin 2-Mercaptoethanol Isovaleric acid Valeric acid 2-Methylbutyric acid Isobutyric acid DL-alpha-lipoic acid Rabbit serum Distilled water

culture temp

  • @ref: 66215
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 99.259

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.998

Isolation, sampling and environmental information

isolation

  • @ref: 66215
  • sample type: cow foot with bovine digital dermatitis
  • geographic location: Bern
  • country: Switzerland
  • origin.country: CHE
  • continent: Europe
  • latitude: 46.9479
  • longitude: 7.4446

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Limb#Foot
#Infection#Disease

taxonmaps

  • @ref: 69479
  • File name: preview.99_230.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_67;96_164;97_176;98_197;99_230&stattab=map
  • Last taxonomy: Treponema phagedenis subclade
  • 16S sequence: MN396624
  • Sequence Identity:
  • Total samples: 1611
  • soil counts: 56
  • aquatic counts: 121
  • animal counts: 1412
  • plant counts: 22

Sequence information

16S sequences

  • @ref: 66215
  • description: Treponema phagedenis strain B43.1 16S ribosomal RNA gene, partial sequence
  • accession: MN396624
  • length: 1546
  • database: ena
  • NCBI tax ID: 162

Genome sequences

  • @ref: 66792
  • description: Treponema phagedenis B43.1
  • accession: GCA_008153345
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 162

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
motileyes74.768no
flagellatedno89.159no
gram-positiveno92.309no
anaerobicyes99.105no
aerobicno98.621no
halophileno67.639no
spore-formingno95.22no
glucose-utilyes85.352no
thermophileno97.477no
glucose-fermentyes71.025no

External links

@ref: 66215

culture collection no.: DSM 110455, NCTC 14362

straininfo link

  • @ref: 111887
  • straininfo: 397395

literature

  • topic: Phylogeny
  • Pubmed-ID: 31999237
  • title: Treponema phagedenis (ex Noguchi 1912) Brumpt 1922 sp. nov., nom. rev., isolated from bovine digital dermatitis.
  • authors: Kuhnert P, Brodard I, Alsaaod M, Steiner A, Stoffel MH, Jores J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004027
  • year: 2020
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cattle, Cattle Diseases/*microbiology, DNA, Bacterial/genetics, Digital Dermatitis/*microbiology, Fatty Acids/chemistry, Humans, *Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Switzerland, Treponema/*classification/isolation & purification
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
66215Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-110455Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110455)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
111887Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397395.1