Strain identifier
BacDive ID: 16783
Type strain: 
Species: Thermoflavimicrobium dichotomicum
Strain Designation: 114, N1595
Strain history: NCIMB 10211 <-- T. Cross CUB 581 <-- M. P. Lechevalier <-- N. S. Agre 114.
NCBI tax ID(s): 46223 (species)
version 8.1 (current version)
General
@ref: 12083
BacDive-ID: 16783
DSM-Number: 44778
keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-positive, human pathogen
description: Thermoflavimicrobium dichotomicum 114 is an aerobe, thermophilic, Gram-positive human pathogen that was isolated from soil.
NCBI tax id
- NCBI tax id: 46223
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12083 | <- JCM <- NCIMB <- T. Cross; CUB 581 <- M. P. Lechevalier <- N. S. Agre; 114 |
| 67771 | <- JCM <- NCIMB <- T. Cross CUB 581 <- M.P. Lechevalier <- N.S. Agre 114 |
| 67770 | NCIMB 10211 <-- T. Cross CUB 581 <-- M. P. Lechevalier <-- N. S. Agre 114. |
doi: 10.13145/bacdive16783.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Thermoflavimicrobium
- species: Thermoflavimicrobium dichotomicum
- full scientific name: Thermoflavimicrobium dichotomicum (Krassilnikov and Agre 1964) Yoon et al. 2005
synonyms
@ref synonym 20215 Actinobifida dichotomica 20215 Thermoactinomyces dichotomica 20215 Thermoactinomyces dichotomicus
@ref: 12083
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Thermoflavimicrobium
species: Thermoflavimicrobium dichotomicum
full scientific name: Thermoflavimicrobium dichotomicum (Krassilnikov and Agre 1964) Yoon et al. 2005
strain designation: 114, N1595
type strain: yes
Morphology
cell morphology
- @ref: 67771
- gram stain: positive
multimedia
- @ref: 12083
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44778.jpg
- caption: Medium 553 45°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 12083 | GYM+S MEDIUM (DSMZ Medium 214) | yes | https://mediadive.dsmz.de/medium/214 | Name: GYM+S MEDIUM (DSMZ Medium 214) Composition: Starch 20.0 g/l Agar 12.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
| 12083 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
| 12083 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water |
| 12083 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 12083 | positive | growth | 45 | thermophilic |
| 67770 | positive | growth | 45 | thermophilic |
| 67771 | positive | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 12083 | soil |
| 67770 | Soil |
| 67771 | From soil |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_170281.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_284;96_44244;97_82385;98_111601;99_170281&stattab=map
- Last taxonomy: Thermoflavimicrobium dichotomicum subclade
- 16S sequence: AF138733
- Sequence Identity:
- Total samples: 2068
- soil counts: 1339
- aquatic counts: 386
- animal counts: 207
- plant counts: 136
Safety information
risk assessment
- @ref: 12083
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermoactinomyces dichotomicus KCTC 3667 16S ribosomal RNA gene, complete sequence | AF138733 | 1475 | ena | 46223 |
| 20218 | Thermoactinomyces dichotomicus 16S ribosomal RNA (16S rRNA) sequence | L16902 | 1463 | ena | 46223 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermoflavimicrobium dichotomicum strain DSM 44778 | 46223.5 | wgs | patric | 46223 |
| 66792 | Thermoflavimicrobium dichotomicum DSM 44778 | 2675903228 | draft | img | 46223 |
| 67770 | Thermoflavimicrobium dichotomicum DSM 44778 | GCA_900114055 | contig | ncbi | 46223 |
GC content
- @ref: 12083
- GC-content: 43
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | yes | 90.76 | yes |
| anaerobic | no | 96.59 | no |
| halophile | no | 94.782 | no |
| spore-forming | yes | 94.463 | no |
| glucose-util | yes | 89.111 | no |
| aerobic | yes | 93.048 | yes |
| flagellated | no | 94.122 | no |
| thermophile | yes | 99.341 | yes |
| motile | no | 86.821 | no |
| glucose-ferment | no | 94.512 | no |
External links
@ref: 12083
culture collection no.: DSM 44778, ATCC 49854, JCM 9688, KCTC 3667, NCIMB 10211, VKM Ac-1435, CUB 581
straininfo link
- @ref: 85799
- straininfo: 42720
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15653907 | Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses. | Yoon JH, Kim IG, Shin YK, Park YH | Int J Syst Evol Microbiol | 10.1099/ijs.0.63203-0 | 2005 | Bacillaceae/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Micromonosporaceae/chemistry/*classification/genetics/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Vitamin K 2/analysis | Phenotype |
| Phylogeny | 31310191 | Thermoflavimicrobium daqui sp. nov., a thermophilic microbe isolated from Moutai-flavour Daqu. | Li DN, Huang W, Qiu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003528 | 2019 | Alcoholic Beverages/*microbiology, Bacillales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 12083 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44778) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44778 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 85799 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42720.1 | StrainInfo: A central database for resolving microbial strain identifiers |