Strain identifier
BacDive ID: 14325
Type strain: 
Species: Spirochaeta africana
Strain Designation: Z-7692
Strain history: <- T. Zhilina, strain Z-7692
NCBI tax ID(s): 889378 (strain), 46355 (species)
version 8.1 (current version)
General
@ref: 3436
BacDive-ID: 14325
DSM-Number: 8902
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Spirochaeta africana Z-7692 is an anaerobe, mesophilic, Gram-negative bacterium of the family Spirochaetaceae.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 46355 | species |
| 889378 | strain |
strain history
- @ref: 3436
- history: <- T. Zhilina, strain Z-7692
doi: 10.13145/bacdive14325.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/spirochaetota
- domain: Bacteria
- phylum: Spirochaetota
- class: Spirochaetia
- order: Spirochaetales
- family: Spirochaetaceae
- genus: Spirochaeta
- species: Spirochaeta africana
- full scientific name: Spirochaeta africana Zhilina et al. 1996
@ref: 3436
domain: Bacteria
phylum: Spirochaetes
class: Spirochaetia
order: Spirochaetales
family: Spirochaetaceae
genus: Spirochaeta
species: Spirochaeta africana
full scientific name: Spirochaeta africana Zhilina et al. 1996
strain designation: Z-7692
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.877
multimedia
- @ref: 66793
- multimedia content: EM_DSM_8902_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 3436
- name: ALKALIPHILIC SPIROCHAETE MEDIUM (DSMZ Medium 700)
- growth: yes
- link: https://mediadive.dsmz.de/medium/700
- composition: Name: ALKALIPHILIC SPIROCHAETE MEDIUM (DSMZ Medium 700) Composition: NaHCO3 15.0 g/l Na2CO3 10.0 g/l Sucrose 5.0 g/l Na2S x 9 H2O 1.0 g/l NH4Cl 1.0 g/l Yeast extract 0.5 g/l K2HPO4 0.2 g/l KCl 0.2 g/l MgSO4 x 7 H2O 0.003 g/l Nitrilotriacetic acid 0.0015 g/l NaCl 0.001 g/l MnSO4 x H2O 0.0005 g/l CoSO4 x 7 H2O 0.00018 g/l ZnSO4 x 7 H2O 0.00018 g/l FeSO4 x 7 H2O 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l CaCl2 x 2 H2O 0.0001 g/l Calcium D-(+)-pantothenate 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l NiCl2 x 6 H2O 3e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l AlK(SO4)2 x 12 H2O 2e-05 g/l CuSO4 x 5 H2O 1e-05 g/l H3BO3 1e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l Vitamin B12 1e-06 g/l Na2WO4 x 2 H2O 4e-07 g/l Na2SeO3 x 5 H2O 3e-07 g/l Distilled water
culture temp
- @ref: 3436
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 98.22
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 93 |
| 69480 | no | 99.907 |
Isolation, sampling and environmental information
isolation
- @ref: 3436
- geographic location: Lake Magadi
- country: Kenya
- origin.country: KEN
- continent: Africa
taxonmaps
- @ref: 69479
- File name: preview.99_5472.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16673;96_2649;97_3249;98_4087;99_5472&stattab=map
- Last taxonomy: Spirochaeta africana subclade
- 16S sequence: X93928
- Sequence Identity:
- Total samples: 914
- soil counts: 147
- aquatic counts: 696
- animal counts: 57
- plant counts: 14
Safety information
risk assessment
- @ref: 3436
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3436
- description: S.africana 16S ribosomal RNA
- accession: X93928
- length: 1474
- database: ena
- NCBI tax ID: 889378
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Spirochaeta africana DSM 8902 | GCA_000242595 | complete | ncbi | 889378 |
| 66792 | Spirochaeta africana DSM 8902 | 889378.3 | complete | patric | 889378 |
| 66792 | Spirochaeta africana Z-7692, DSM 8902 | 2509276057 | complete | img | 889378 |
GC content
- @ref: 3436
- GC-content: 56.1
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 93 | no |
| motile | yes | 88.345 | no |
| flagellated | no | 69.087 | no |
| gram-positive | no | 93.708 | no |
| anaerobic | yes | 90.692 | no |
| aerobic | no | 94.897 | no |
| halophile | yes | 51.353 | no |
| spore-forming | no | 88.218 | no |
| thermophile | no | 98.368 | yes |
| glucose-util | yes | 86.323 | no |
| glucose-ferment | no | 50 | no |
External links
@ref: 3436
culture collection no.: DSM 8902
straininfo link
- @ref: 83473
- straininfo: 46225
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 8573509 | Spirochaeta alkalica sp. nov., Spirochaeta africana sp. nov., and Spirochaeta asiatica sp. nov., alkaliphilic anaerobes from the Continental Soda Lakes in Central Asia and the East African Rift. | Zhilina TN, Zavarzin GA, Rainey F, Kevbrin VV, Kostrikina NA, Lysenko AM | Int J Syst Bacteriol | 10.1099/00207713-46-1-305 | 1996 | Africa, Eastern, Asia, Central, Bacteria, Anaerobic/classification/isolation & purification/ultrastructure, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Spirochaeta/*classification/isolation & purification/ultrastructure, Water Microbiology | Enzymology |
| Genetics | 23991249 | Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. | Liolos K, Abt B, Scheuner C, Teshima H, Held B, Lapidus A, Nolan M, Lucas S, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Detter JC, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Klenk HP, Kyrpides NC | Stand Genomic Sci | 10.4056/sigs.3607108 | 2013 | ||
| Genetics | 26203324 | Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat. | Ben Hania W, Joseph M, Schumann P, Bunk B, Fiebig A, Sproer C, Klenk HP, Fardeau ML, Spring S | Stand Genomic Sci | 10.1186/1944-3277-10-7 | 2015 | Phylogeny |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3436 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8902) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8902 | |||
| 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 | |
| 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 | |||
| 83473 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46225.1 | StrainInfo: A central database for resolving microbial strain identifiers |