Strain identifier
BacDive ID: 14090
Type strain: 
Species: Sphaerobacter thermophilus
Strain Designation: S 6022
Strain history: <- W. Demharter, S 6022
NCBI tax ID(s): 479434 (strain), 2057 (species)
version 9.1 (current version)
General
@ref: 9054
BacDive-ID: 14090
DSM-Number: 20745
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-positive, coccus-shaped, colony-forming
description: Sphaerobacter thermophilus S 6022 is an obligate aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from thermophilically treated sewage sludge.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 2057 | species |
| 479434 | strain |
strain history
- @ref: 9054
- history: <- W. Demharter, S 6022
doi: 10.13145/bacdive14090.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/thermomicrobiota
- domain: Bacteria
- phylum: Thermomicrobiota
- class: Thermomicrobia
- order: Sphaerobacterales
- family: Sphaerobacteraceae
- genus: Sphaerobacter
- species: Sphaerobacter thermophilus
- full scientific name: Sphaerobacter thermophilus Demharter et al. 1989
@ref: 9054
domain: Bacteria
phylum: Thermomicrobia
class: Thermomicrobia
order: Sphaerobacterales
family: Sphaerobacteraceae
genus: Sphaerobacter
species: Sphaerobacter thermophilus
full scientific name: Sphaerobacter thermophilus Demharter et al. 1989 emend. Houghton et al. 2015 emend. Nouioui et al. 2018
strain designation: S 6022
type strain: yes
Morphology
cell morphology
- @ref: 43423
- gram stain: positive
- cell length: 1.5-3 µm
- cell width: 1-1.5 µm
- cell shape: coccus-shaped
- motility: no
colony morphology
- @ref: 43423
- colony size: 1-2 mm
- colony color: opaque
- colony shape: circular
- incubation period: 3 days
- medium used: Ottow medium
multimedia
- @ref: 66793
- multimedia content: EM_DSM_20745_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9054 | OTTOW MEDIUM (DSMZ Medium 467) | yes | https://mediadive.dsmz.de/medium/467 | Name: OTTOW MEDIUM (DSMZ Medium 467) Composition: Peptone 7.5 g/l NaCl 5.0 g/l Meat extract 5.0 g/l Casamino acids 2.5 g/l Yeast extract 2.5 g/l Glucose 1.0 g/l Tap water |
| 43423 | Ottow medium | yes |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 9054 | positive | growth | 55 |
| 43423 | positive | growth | 40-65 |
| 43423 | positive | optimum | 55 |
culture pH
- @ref: 43423
- ability: positive
- type: optimum
- pH: 8.5
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 43423
- oxygen tolerance: obligate aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 43423 | no | |
| 69481 | yes | 99 |
murein
- @ref: 9054
- murein short key: A21.10
- type: A3ß L-Orn-ß-Ala
metabolite utilization
| @ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
|---|---|---|---|---|
| 43423 | casein | - | hydrolysis | |
| 43423 | cellulose | - | hydrolysis | 62968 |
| 43423 | gelatin | - | hydrolysis | 5291 |
| 43423 | glucose | - | builds acid from | 17234 |
| 43423 | starch | + | hydrolysis | 28017 |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 43423 | catalase | + | 1.11.1.6 |
| 43423 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 9054 | thermophilically treated sewage sludge | München | Germany | DEU | Europe | |
| 43423 | thermal treated municipal sewage sludge | Muenchen-Grosslappen, Germany | Germany | DEU | Europe | between 1973 and 198 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Sewage sludge |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_6450.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16104;96_3053;97_3751;98_4760;99_6450&stattab=map
- Last taxonomy: Sphaerobacter thermophilus subclade
- 16S sequence: AJ420142
- Sequence Identity:
- Total samples: 5750
- soil counts: 3784
- aquatic counts: 464
- animal counts: 828
- plant counts: 674
Safety information
risk assessment
- @ref: 9054
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Sphaerobacter thermophilus 16S rRNA gene, strain DSM 20745T | AJ420142 | 1500 | nuccore | 479434 |
| 20218 | Sphaerobacter thermophilus (Corynebacterium spec.) partial 16S rRNA | X53210 | 1208 | nuccore | 479434 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphaerobacter thermophilus DSM 20745 | GCA_000024985 | complete | ncbi | 479434 |
| 66792 | Sphaerobacter thermophilus DSM 20745 | 479434.6 | complete | patric | 479434 |
| 66792 | Sphaerobacter thermophilus 4ac11, DSM 20745 | 646311953 | complete | img | 479434 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 9054 | 66.3 | thermal denaturation, midpoint method (Tm) |
| 9054 | 65.7 | high performance liquid chromatography (HPLC) |
| 43423 | 68.1 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 99 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 58.436 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 85.362 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 68.217 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 50.653 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | yes | 67.056 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 64.041 | no |
External links
@ref: 9054
culture collection no.: DSM 20745, ATCC 49802
straininfo link
- @ref: 83258
- straininfo: 49676
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 21304677 | Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). | Pati A, Labutti K, Pukall R, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Mikhailova N, Pitluck S, Bruce D, Goodwin L, Land M, Hauser L, Chang YJ, Jeffries CD, Chen A, Palaniappan K, Chain P, Brettin T, Sikorski J, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A | Stand Genomic Sci | 10.4056/sigs.601105 | 2010 | ||
| Metabolism | 27784229 | Discovery and Biochemical Characterization of the UDP-Xylose Biosynthesis Pathway in Sphaerobacter thermophilus. | Gu B, Laborda P, Wei S, Duan XC, Song HB, Liu L, Voglmeir J | Protein Pept Lett | 10.2174/0929866523666161026115959 | 2016 | Carboxy-Lyases/*metabolism, Chloroflexi/*enzymology/*metabolism, Oxidation-Reduction, Sewage/microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Uridine Diphosphate Glucose Dehydrogenase/*metabolism, Uridine Diphosphate Xylose/*biosynthesis | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9054 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20745) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20745 | |||
| 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 | |
| 43423 | Amrita Pati, Kurt LaButti, Rüdiger Pukall, Matt Nolan, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Alex Copeland, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Sam Pitluck, David Bruce, Lynne Goodwin, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Amy Chen, Krishna Palaniappan, Patrick Chain, Thomas Brettin, Johannes Sikorski, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Alla Lapidus | 10.4056/sigs.601105 | Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022) | Stand Genomic Sci 2: 49-56 2010 | 21304677 | |
| 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 | |
| 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 | |||
| 83258 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49676.1 | StrainInfo: A central database for resolving microbial strain identifiers |