Strain identifier
BacDive ID: 6135
Type strain: 
Species: Herpetosiphon geysericola
Strain Designation: GC-42, Hp gy1
Strain history: <- H. Reichenbach, Hp gy1 <- ATCC <- R.A. Lewin, GC-42; identity of the strain not clear
NCBI tax ID(s): 70996 (species)
version 9.1 (current version)
General
@ref: 3010
BacDive-ID: 6135
DSM-Number: 7119
keywords: genome sequence, 16S sequence, Bacteria, aerobe
description: Herpetosiphon geysericola GC-42 is an aerobe bacterium that was isolated from hot spring.
NCBI tax id
- NCBI tax id: 70996
- Matching level: species
strain history
- @ref: 3010
- history: <- H. Reichenbach, Hp gy1 <- ATCC <- R.A. Lewin, GC-42; identity of the strain not clear
doi: 10.13145/bacdive6135.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/chloroflexota
- domain: Bacteria
- phylum: Chloroflexota
- class: Chloroflexia
- order: Herpetosiphonales
- family: Herpetosiphonaceae
- genus: Herpetosiphon
- species: Herpetosiphon geysericola
- full scientific name: Herpetosiphon geysericola (Copeland 1936) Lewin 1970 (Approved Lists 1980)
synonyms
@ref synonym 20215 Leptolyngbya geysericola 20215 Phormidium geysericola
@ref: 3010
domain: Bacteria
phylum: Chloroflexi
class: Chloroflexia
order: Herpetosiphonales
family: Herpetosiphonaceae
genus: Herpetosiphon
species: Herpetosiphon geysericola
full scientific name: Herpetosiphon geysericola (Copeland 1936) Lewin 1970 emend. Nouioui et al. 2018
strain designation: GC-42, Hp gy1
type strain: no
Morphology
colony morphology
- @ref: 58308
- incubation period: 5 days
Culture and growth conditions
culture medium
- @ref: 3010
- name: CY-AGAR (DSMZ Medium 67)
- growth: yes
- link: https://mediadive.dsmz.de/medium/67
- composition: Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 3010 | positive | growth | 25 |
| 58308 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 58308
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 3010 | hot spring | Guadalupe Canon | Mexico | MEX | North America |
| 58308 | Rocks bedside a hot spring |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 3010
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Herpetosiphon geysericola 16S ribosomal RNA gene, partial sequence
- accession: AF039293
- length: 1417
- database: nuccore
- NCBI tax ID: 70996
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Herpetosiphon geysericola DSM 7119 | GCA_001306135 | contig | ncbi | 70996 |
| 66792 | Herpetosiphon geysericola strain DSM 7119 | 70996.7 | wgs | patric | 70996 |
| 66792 | Herpetosiphon geysericola DSM 7119 | 2645728042 | draft | img | 70996 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 58.643 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.458 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 60.146 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 81.579 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 80.172 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 71.912 | no |
External links
@ref: 3010
culture collection no.: DSM 7119, ATCC 23076, CCUG 48727
straininfo link
- @ref: 75622
- straininfo: 37896
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 26586889 | Draft Genome Sequence of Herpetosiphon geysericola GC-42, a Nonphototrophic Member of the Chloroflexi Class Chloroflexia. | Ward LM, Hemp J, Pace LA, Fischer WW | Genome Announc | 10.1128/genomeA.01352-15 | 2015 | ||
| Phylogeny | 28741992 | Herpetosiphon gulosus sp. nov., a filamentous predatory bacterium isolated from sandy soil and Herpetosiphon giganteus sp. nov., nom. rev. | Pan X, Kage H, Martin K, Nett M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002141 | 2017 | Bacterial Typing Techniques, Base Composition, Chloroflexi/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Nepal, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silicon Dioxide, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3010 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7119) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7119 | |||
| 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 | |
| 58308 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 48727) | https://www.ccug.se/strain?id=48727 | |||
| 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) | |||
| 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 | |||
| 75622 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID37896.1 | StrainInfo: A central database for resolving microbial strain identifiers |