Strain identifier
BacDive ID: 14349
Type strain: 
Species: Treponema pedis
Strain Designation: T3552B
Strain history: <- N.J. Evans; T3552B <- J. M. Brown <- I. Demirkan
NCBI tax ID(s): 409322 (species)
version 8.1 (current version)
General
@ref: 7659
BacDive-ID: 14349
DSM-Number: 18691
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, animal pathogen
description: Treponema pedis T3552B is an anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from bovine digital dermatitis lesions in Holstein-Friesian cows.
NCBI tax id
- NCBI tax id: 409322
- Matching level: species
strain history
- @ref: 7659
- history: <- N.J. Evans; T3552B <- J. M. Brown <- I. Demirkan
doi: 10.13145/bacdive14349.20230509.8.1
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 pedis
- full scientific name: Treponema pedis Evans et al. 2009
@ref: 7659
domain: Bacteria
phylum: Spirochaetes
class: Spirochaetia
order: Spirochaetales
family: Treponemataceae
genus: Treponema
species: Treponema pedis
full scientific name: Treponema pedis Evans et al. 2009
strain designation: T3552B
type strain: yes
Morphology
cell morphology
- @ref: 28943
- gram stain: negative
- cell length: 10.5 µm
- cell width: 0.25 µm
- motility: yes
pigmentation
- @ref: 28943
- production: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 7659 | 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 |
| 7659 | OTEB-MEDIUM (DSMZ Medium 1245) | yes | https://mediadive.dsmz.de/medium/1245 | Name: OTEB-MEDIUM (DSMZ Medium 1245; with strain-specific modifications) Composition: Fetal bovine serum 100.0 g/l Proteose peptone no. 2 5.0 g/l Sodium Chloride 5.0 g/l Yeast extract 5.0 g/l Heart Infusion Broth 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 Acetic acid Propionic acid n-Butyric acid n-Valeric acid Isovaleric acid Isobutyric acid 2-Methylbutyric acid Distilled water |
culture temp
- @ref: 7659
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 7659 | anaerobe |
| 28943 | anaerobe |
observation
- @ref: 28943
- observation: aggregates in clumps
metabolite utilization
- @ref: 28943
- Chebi-ID: 17754
- metabolite: glycerol
- utilization activity: +
- kind of utilization tested: carbon source
Isolation, sampling and environmental information
isolation
- @ref: 7659
- sample type: bovine digital dermatitis lesions in Holstein-Friesian cows
- country: United Kingdom
- origin.country: GBR
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Inflammation | |
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
taxonmaps
- @ref: 69479
- File name: preview.99_2569.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_67;96_1379;97_1639;98_1991;99_2569&stattab=map
- Last taxonomy: Treponema pedis subclade
- 16S sequence: EF061268
- Sequence Identity:
- Total samples: 2662
- soil counts: 62
- aquatic counts: 36
- animal counts: 2554
- plant counts: 10
Safety information
risk assessment
- @ref: 7659
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7659
- description: Treponema pedis strain T3552B 16S ribosomal RNA gene, partial sequence
- accession: EF061268
- length: 1417
- database: ena
- NCBI tax ID: 409322
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Treponema pedis T3552B | GCA_017161325 | complete | ncbi | 409322 |
| 66792 | Treponema pedis strain T3552B | 409322.5 | complete | patric | 409322 |
| 66792 | Treponema pedis DSM 18691 | 2913380516 | draft | img | 409322 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 89.153 | no |
| gram-positive | no | 94.624 | yes |
| anaerobic | yes | 99.484 | yes |
| aerobic | no | 99.256 | yes |
| halophile | no | 80.511 | no |
| spore-forming | no | 83.067 | no |
| thermophile | no | 95.351 | yes |
| glucose-util | yes | 84.169 | no |
| motile | yes | 86.076 | yes |
| glucose-ferment | yes | 63.569 | no |
External links
@ref: 7659
culture collection no.: DSM 18691, NCTC 13403
straininfo link
- @ref: 83492
- straininfo: 408108
literature
- topic: Phylogeny
- Pubmed-ID: 19406779
- title: Treponema pedis sp. nov., a spirochaete isolated from bovine digital dermatitis lesions.
- authors: Evans NJ, Brown JM, Demirkan I, Murray RD, Birtles RJ, Hart CA, Carter SD
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.002287-0
- year: 2009
- mesh: Animals, Bacterial Typing Techniques, Cattle, Cattle Diseases/*microbiology, DNA, Bacterial/analysis, Dermatitis/microbiology/*veterinary, Flagella/physiology, Flagellin/genetics, Foot Diseases/microbiology/*veterinary, Genes, rRNA/genetics, Genotype, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Treponema/*classification/genetics/isolation & purification/physiology, Treponemal Infections/microbiology/*veterinary
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7659 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18691) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18691 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 28943 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25382 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 83492 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408108.1 | StrainInfo: A central database for resolving microbial strain identifiers |