Strain identifier
BacDive ID: 16787
Type strain: 
Species: Kroppenstedtia eburnea
Strain Designation: JFMB-ATE, thermophiler Actinomycet
Strain history: <- K. Koettnitz, Germany; JFMB-ATE
NCBI tax ID(s): 714067 (species)
version 8.1 (current version)
General
@ref: 15690
BacDive-ID: 16787
DSM-Number: 45196
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive, human pathogen
description: Kroppenstedtia eburnea JFMB-ATE is an aerobe, spore-forming, thermophilic human pathogen that was isolated from plastic surface in grade C.
NCBI tax id
- NCBI tax id: 714067
- Matching level: species
strain history
- @ref: 15690
- history: <- K. Koettnitz, Germany; JFMB-ATE
doi: 10.13145/bacdive16787.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Kroppenstedtia
- species: Kroppenstedtia eburnea
- full scientific name: Kroppenstedtia eburnea von Jan et al. 2011
@ref: 15690
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Kroppenstedtia
species: Kroppenstedtia eburnea
full scientific name: Kroppenstedtia eburnea von Jan et al. 2011
strain designation: JFMB-ATE, thermophiler Actinomycet
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
multimedia
- @ref: 15690
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45196.jpg
- caption: Medium 215 45°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 15690 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
| 15690 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15690 | positive | growth | 45 | thermophilic |
| 61875 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 61875
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | sampling date | geographic location |
|---|---|---|---|---|---|---|
| 15690 | plastic surface in grade C | Germany | DEU | Europe | ||
| 61875 | Environmental sample | Germany | DEU | Europe | 2008-04-01 | Southern Germany |
isolation source categories
- Cat1: #Engineered
- Cat2: #Industrial
- Cat3: #Engineered product
taxonmaps
- @ref: 69479
- File name: preview.99_2932.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_1547;97_1846;98_2266;99_2932&stattab=map
- Last taxonomy: Kroppenstedtia eburnea subclade
- 16S sequence: FN665656
- Sequence Identity:
- Total samples: 4457
- soil counts: 2401
- aquatic counts: 380
- animal counts: 1244
- plant counts: 432
Safety information
risk assessment
- @ref: 15690
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15690
- description: Thermoactinomycetaceae bacterium JFMB-ATE 16S rRNA gene, strain JFMB-ATE
- accession: FN665656
- length: 1607
- database: ena
- NCBI tax ID: 714067
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kroppenstedtia eburnea DSM 45196 | GCA_013282215 | complete | ncbi | 714067 |
| 66792 | Kroppenstedtia eburnea DSM 45196 | GCA_900156615 | contig | ncbi | 714067 |
| 66792 | Kroppenstedtia eburnea strain DSM 45196 | 714067.7 | complete | patric | 714067 |
| 66792 | Kroppenstedtia eburnea strain DSM 45196 | 714067.3 | wgs | patric | 714067 |
| 66792 | Kroppenstedtia eburnea DSM 45196 | 2681813512 | draft | img | 714067 |
GC content
- @ref: 15690
- GC-content: 54.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 81.753 | no |
| flagellated | no | 91.307 | no |
| gram-positive | yes | 91.814 | no |
| anaerobic | no | 99.044 | no |
| aerobic | yes | 95.217 | no |
| halophile | no | 76.806 | no |
| spore-forming | yes | 93.859 | no |
| glucose-util | yes | 90.581 | no |
| thermophile | yes | 97.899 | no |
| glucose-ferment | no | 93.978 | no |
External links
@ref: 15690
culture collection no.: DSM 45196, CCUG 59226, NRRL B-24804
straininfo link
- @ref: 85803
- straininfo: 406820
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20971832 | Kroppenstedtia eburnea gen. nov., sp. nov., a thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009. | von Jan M, Riegger N, Potter G, Schumann P, Verbarg S, Sproer C, Rohde M, Lauer B, Labeda DP, Klenk HP | Int J Syst Evol Microbiol | 10.1099/ijs.0.026179-0 | 2010 | Bacillales/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, *Environmental Microbiology, Germany, Hydrogen-Ion Concentration, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology, Temperature | Genetics |
| Phylogeny | 23728375 | Kroppenstedtia guangzhouensis sp. nov., a thermoactinomycete isolated from soil. | Yang G, Qin D, Wu C, Yuan Y, Zhou S, Cai Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.051011-0 | 2013 | Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 26910402 | Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients. | Bell ME, Lasker BA, Klenk HP, Hoyles L, Sproer C, Schumann P, Brown JM | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0663-z | 2016 | Adolescent, Aged, Bacterial Typing Techniques, DNA, Bacterial/genetics, Female, Gram-Positive Bacterial Infections/blood/cerebrospinal fluid/*microbiology, Humans, Lung/microbiology, Male, Middle Aged, Phylogeny, RNA, Ribosomal, 16S/genetics, Spores, Bacterial/cytology, Thermoactinomyces/classification/cytology/genetics/*isolation & purification | Pathogenicity |
| Phylogeny | 27671055 | Paludifilum halophilum gen. nov., sp. nov., a thermoactinomycete isolated from superficial sediment of a solar saltern. | Frikha-Dammak D, Fardeau ML, Cayol JL, Ben Fguira-Fourati L, Najeh S, Ollivier B, Maalej S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001523 | 2016 | Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Tunisia, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| 33122418 | Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data. | Gulvik CA, Batra D, Rowe LA, Sheth M, Humrighouse BW, Howard DT, Lee J, McQuiston JR, Lasker BA | Microbiol Resour Announc | 10.1128/MRA.00650-20 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15690 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45196) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45196 | |
| 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 | |
| 61875 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 59226) | https://www.ccug.se/strain?id=59226 | |
| 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 | |
| 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 | |
| 85803 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406820.1 | StrainInfo: A central database for resolving microbial strain identifiers |