Strain identifier
BacDive ID: 14350
Type strain: 
Species: Sphaerochaeta coccoides
Strain Designation: SPN1
Strain history: <- S. Dröge, Johannes Gutenberg-Universität Mainz, Germany; SPN1 <- S. Dröge
NCBI tax ID(s): 760011 (strain), 273376 (species)
version 8.1 (current version)
General
@ref: 6842
BacDive-ID: 14350
DSM-Number: 17374
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Sphaerochaeta coccoides SPN1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from hindgut of the termite Neotermes castaneus.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 273376 | species |
| 760011 | strain |
strain history
- @ref: 6842
- history: <- S. Dröge, Johannes Gutenberg-Universität Mainz, Germany; SPN1 <- S. Dröge
doi: 10.13145/bacdive14350.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/spirochaetota
- domain: Bacteria
- phylum: Spirochaetota
- class: Spirochaetia
- order: Spirochaetales
- family: Sphaerochaetaceae
- genus: Sphaerochaeta
- species: Sphaerochaeta coccoides
- full scientific name: Sphaerochaeta coccoides (Dröge et al. 2006) Abt et al. 2012
synonyms
@ref synonym 20215 Parasphaerochaeta coccoides 20215 Spirochaeta coccoides
@ref: 6842
domain: Bacteria
phylum: Spirochaetes
class: Spirochaetia
order: Spirochaetales
family: Sphaerochaetaceae
genus: Sphaerochaeta
species: Sphaerochaeta coccoides
full scientific name: Sphaerochaeta coccoides (Dröge et al. 2006) Abt et al. 2012
strain designation: SPN1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.807
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_17374_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17374_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17374_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17374_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17374_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_17374_6.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 6842
- name: SPHAEROCHAETA MEDIUM (DSMZ Medium 1204)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1204
- composition: Name: SPHAEROCHAETA MEDIUM (DSMZ Medium 1204) Composition: Yeast extract 4.0 g/l Casein peptone 2.0 g/l Maltose monohydrate 2.0 g/l Na2CO3 1.0 g/l NaCl 1.0 g/l DL-Dithiothreitol 0.8 g/l KCl 0.5 g/l MgCl2 x 6 H2O 0.4 g/l NH4Cl 0.3 g/l KH2PO4 0.2 g/l Na2SO4 0.15 g/l CaCl2 x 2 H2O 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
- @ref: 6842
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6842 | anaerobe | |
| 69480 | anaerobe | 98.651 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
Isolation, sampling and environmental information
isolation
- @ref: 6842
- sample type: hindgut of the termite Neotermes castaneus
- host species: Neotermes castaneus
- country: Cuba
- origin.country: CUB
- continent: Middle and South America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Arthropoda | #Insecta |
| #Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_472.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16386;96_311;97_345;98_390;99_472&stattab=map
- Last taxonomy: Sphaerochaeta coccoides subclade
- 16S sequence: AJ698092
- Sequence Identity:
- Total samples: 174
- soil counts: 33
- aquatic counts: 41
- animal counts: 84
- plant counts: 16
Safety information
risk assessment
- @ref: 6842
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6842
- description: Spirochaeta sp. SPN1 partial 16S rRNA gene, type strain SPN1T
- accession: AJ698092
- length: 1500
- database: ena
- NCBI tax ID: 760011
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Parasphaerochaeta coccoides DSM 17374 | GCA_000208385 | complete | ncbi | 760011 |
| 66792 | Sphaerochaeta coccoides DSM 17374 | 760011.3 | complete | patric | 760011 |
| 66792 | Sphaerochaeta coccoides SPN1, DSM 17374 | 2503904012 | complete | img | 760011 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 86.011 | no |
| flagellated | no | 97.935 | no |
| gram-positive | no | 90.533 | no |
| anaerobic | yes | 97.929 | yes |
| aerobic | no | 98.63 | yes |
| halophile | no | 75.061 | no |
| spore-forming | no | 94.807 | no |
| glucose-util | yes | 89.563 | no |
| thermophile | no | 86.547 | no |
| glucose-ferment | yes | 70.63 | no |
External links
@ref: 6842
culture collection no.: DSM 17374, ATCC BAA 1237
straininfo link
- @ref: 83493
- straininfo: 297328
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6842 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17374) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17374 | |||
| 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 | |
| 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 | |||
| 83493 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297328.1 | StrainInfo: A central database for resolving microbial strain identifiers |