Strain identifier
BacDive ID: 159392
Type strain:
Species: Treponema phagedenis
Strain Designation: B43.1
Strain history: <- P. Kuhnert, Univ. Bern; B43.1
NCBI tax ID(s): 166 (species)
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
@ref | name | growth | link | composition |
---|---|---|---|---|
66215 | OTEB-MEDIUM (DSMZ Medium 1245) | yes | https://mediadive.dsmz.de/medium/1245 | Name: 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 |
66215 | OMIZ-PAT (DSMZ Medium 1494) | yes | https://mediadive.dsmz.de/medium/1494 | Name: . 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 82 | no |
motile | yes | 74.768 | no |
flagellated | no | 89.159 | no |
gram-positive | no | 92.309 | no |
anaerobic | yes | 99.105 | no |
aerobic | no | 98.621 | no |
halophile | no | 67.639 | no |
spore-forming | no | 95.22 | no |
glucose-util | yes | 85.352 | no |
thermophile | no | 97.477 | no |
glucose-ferment | yes | 71.025 | no |
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
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
66215 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-110455 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110455) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
69479 | João 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 beta | https://microbeatlas.org/ | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
111887 | Reimer, 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 identifiers | 10.60712/SI-ID397395.1 |