Strain identifier
BacDive ID: 14343
Type strain: 
Species: Treponema brennaborense
Strain Designation: DD5/3
Strain history: <- K. Schrank, Freie Univ. Berlin; DD5/3
NCBI tax ID(s): 906968 (strain), 81028 (species)
version 8.1 (current version)
General
@ref: 4631
BacDive-ID: 14343
DSM-Number: 12168
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, animal pathogen
description: Treponema brennaborense DD5/3 is an anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from ulcerative lesion of a bovine foot infected with digital dermatitis.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 81028 | species |
| 906968 | strain |
strain history
- @ref: 4631
- history: <- K. Schrank, Freie Univ. Berlin; DD5/3
doi: 10.13145/bacdive14343.20230509.8.1
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 brennaborense
- full scientific name: Treponema brennaborense Schrank et al. 1999
@ref: 4631
domain: Bacteria
phylum: Spirochaetes
class: Spirochaetia
order: Spirochaetales
family: Treponemataceae
genus: Treponema
species: Treponema brennaborense
full scientific name: Treponema brennaborense Schrank et al. 1999
strain designation: DD5/3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.915
multimedia
- @ref: 66793
- multimedia content: EM_DSM_12168_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 4631 | 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 |
| 4631 | CHOPPED MEAT MEDIUM FOR TREPONEMA SP. (DSMZ Medium 78a) | yes | https://mediadive.dsmz.de/medium/78a | Name: CHOPPED MEAT MEDIUM FOR TREPONEMA SP. (DSMZ Medium 78a) Composition: Ground beef 473.934 g/l Casitone 28.436 g/l Agar 14.218 g/l Yeast extract 4.73934 g/l K2HPO4 4.73934 g/l L-Glutamine 0.663507 g/l L-Histidine 0.56872 g/l L-Cysteine HCl 0.473934 g/l L-Serine 0.473934 g/l Ethanol 0.180095 g/l Vitamin K3 0.0473934 g/l Hemin 0.00473934 g/l Resazurin 0.000947867 g/l p-Aminobenzoic acid 0.000236967 g/l Vitamin B12 0.000236967 g/l Pantothenic acid 0.000236967 g/l Riboflavin 0.000236967 g/l alpha-lipoic acid 0.000236967 g/l Thiamine-HCl x 2 H2O 0.000236967 g/l Nicotine amide 0.000118483 g/l Nicotinic acid 0.000118483 g/l Biotin 9.47867e-05 g/l Folic acid 9.47867e-05 g/l Pyridoxamine hydrochloride 4.73934e-05 g/l NaOH Vitamin K1 Distilled water |
culture temp
- @ref: 4631
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 4631 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.982 |
Isolation, sampling and environmental information
isolation
- @ref: 4631
- sample type: ulcerative lesion of a bovine foot infected with digital dermatitis
- geographic location: Brandenburg, Dretzen
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 52.2134
- longitude: 12.2834
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Disease | |
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host Body-Site | #Other | #Wound |
| #Host Body-Site | #Limb | #Foot |
Safety information
risk assessment
- @ref: 4631
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4631
- description: Treponema brennaborense 16S rRNA gene
- accession: Y16568
- length: 1497
- database: ena
- NCBI tax ID: 81028
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Treponema brennaborense DSM 12168 | GCA_000212415 | complete | ncbi | 906968 |
| 66792 | Treponema brennaborense DSM 12168 | 906968.3 | complete | patric | 906968 |
| 66792 | Treponema brennaborense DD5/3, DSM 12168 | 650716100 | complete | img | 906968 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 79.115 | no |
| flagellated | no | 77.564 | no |
| gram-positive | no | 91.981 | no |
| anaerobic | yes | 99.514 | no |
| aerobic | no | 99.097 | yes |
| halophile | no | 87.221 | no |
| spore-forming | no | 93 | no |
| thermophile | no | 93.976 | no |
| glucose-util | yes | 83.182 | no |
| glucose-ferment | yes | 79.255 | no |
External links
@ref: 4631
culture collection no.: DSM 12168
straininfo link
- @ref: 83488
- straininfo: 49244
literature
- topic: Phylogeny
- Pubmed-ID: 10028246
- title: Treponema brennaborense sp. nov., a novel spirochaete isolated from a dairy cow suffering from digital dermatitis.
- authors: Schrank K, Choi BK, Grund S, Moter A, Heuner K, Nattermann H, Gobel UB
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-49-1-43
- year: 1999
- mesh: Animals, Bacterial Proteins/analysis, Base Sequence, Cattle, Cattle Diseases/*microbiology, DNA, Ribosomal/chemistry, Dermatitis/microbiology/*veterinary, Female, In Situ Hybridization, Fluorescence, Molecular Sequence Data, Phylogeny, Rabbits, Treponema/classification/genetics/*isolation & purification
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 4631 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12168) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12168 | |||
| 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 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 83488 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49244.1 | StrainInfo: A central database for resolving microbial strain identifiers |