Strain identifier
BacDive ID: 17082
Type strain: 
Species: Thiofilum flexile
Strain Designation: EJ2M-B
Strain history: T. Kohno EJ2M-B.
NCBI tax ID(s): 1123400 (strain), 125627 (species)
version 8.1 (current version)
General
@ref: 5409
BacDive-ID: 17082
DSM-Number: 14609
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Thiofilum flexile EJ2M-B is a mesophilic, Gram-negative bacterium that was isolated from bulking activated sludge.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 125627 | species |
| 1123400 | strain |
strain history
| @ref | history |
|---|---|
| 5409 | <- T. Kohno, Yamanashi Univ., Kofu, Japan |
| 67770 | T. Kohno EJ2M-B. |
doi: 10.13145/bacdive17082.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Leucotrichaceae
- genus: Thiofilum
- species: Thiofilum flexile
- full scientific name: Thiofilum flexile (Aruga et al. 2002) Boden and Scott 2018
synonyms
- @ref: 20215
- synonym: Thiothrix flexilis
@ref: 5409
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Thiofilaceae
genus: Thiofilum
species: Thiofilum flexile
full scientific name: Thiofilum flexile (Aruga et al. 2002) Boden and Scott 2018
strain designation: EJ2M-B
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.997
Culture and growth conditions
culture medium
- @ref: 5409
- name: EGGC (DSMZ Medium 1191)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1191
- composition: Name: EGGC (DSMZ Medium 1191) Composition: Agar 15.0 g/l Glucose 0.6 g/l Casamino acids 0.3 g/l Na-acetate 0.3 g/l Na2HPO4 0.248 g/l NaH2PO4 0.0308 g/l (NH4)2SO4 0.01 g/l MgSO4 x 7 H2O 0.005 g/l KCl 0.005 g/l Thiamine-HCl x 2 H2O 0.0025 g/l Nicotinic acid 0.0025 g/l Pyridoxine hydrochloride 0.0025 g/l Calcium pantothenate 0.0025 g/l CaCl2 x 2 H2O 0.002 g/l CaCO3 0.002 g/l Riboflavin 0.0005 g/l FeCl3 x 6 H2O 5e-05 g/l Vitamin B12 5e-05 g/l Folic acid 1e-05 g/l Biotin 5e-06 g/l Demineralized water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5409 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.969 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 5409 | bulking activated sludge | Japan | JPN | Asia |
| 67770 | Bulking activated sludge of pickle manufacturing wastewater treatment plant of pickle manufacturing | Japan | JPN | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_5482.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_524;96_2654;97_3255;98_4095;99_5482&stattab=map
- Last taxonomy: Thiotrichales
- 16S sequence: AB042545
- Sequence Identity:
- Total samples: 5323
- soil counts: 127
- aquatic counts: 1995
- animal counts: 3155
- plant counts: 46
Safety information
risk assessment
- @ref: 5409
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5409
- description: Thiothrix sp. EJ2M-B gene for 16S ribosomal RNA, partial sequence
- accession: AB042545
- length: 1417
- database: ena
- NCBI tax ID: 125627
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiothrix flexilis DSM 14609 | 1123400.3 | wgs | patric | 1123400 |
| 66792 | Thiofilum flexile DSM 14609 | 2515154111 | draft | img | 1123400 |
| 67770 | Thiofilum flexile DSM 14609 | GCA_000380185 | scaffold | ncbi | 1123400 |
GC content
- @ref: 5409
- GC-content: 44
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 71.085 | no |
| flagellated | no | 80.489 | no |
| gram-positive | no | 98.835 | no |
| anaerobic | no | 96.66 | no |
| aerobic | yes | 79.277 | no |
| halophile | no | 87.346 | no |
| spore-forming | no | 93.587 | no |
| glucose-util | yes | 65.28 | no |
| thermophile | no | 98.212 | yes |
| glucose-ferment | no | 85.197 | no |
External links
@ref: 5409
culture collection no.: DSM 14609, JCM 11135
straininfo link
- @ref: 86082
- straininfo: 101038
literature
- topic: Phylogeny
- Pubmed-ID: 12148645
- title: Characterization of filamentous Eikelboom type 021N bacteria and description of Thiothrix disciformis sp. nov. and Thiothrix flexilis sp. nov.
- authors: Aruga S, Kamagata Y, Kohno T, Hanada S, Nakamura K, Kanagawa T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-4-1309
- year: 2002
- mesh: Bacterial Proteins/analysis, Bacterial Typing Techniques, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gammaproteobacteria/chemistry/*classification/*isolation & purification/physiology, Genotype, *Industrial Waste, Microscopy, Electron, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, *Waste Disposal, Fluid, Water Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 5409 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14609) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14609 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 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 | |
| 86082 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID101038.1 | StrainInfo: A central database for resolving microbial strain identifiers |