Strain identifier
BacDive ID: 413
Type strain: 
Species: Alicyclobacillus herbarius
Strain Designation: CP-1
Strain history: IAM 14883 <-- K. Goto CP-1.
NCBI tax ID(s): 1120972 (strain), 122960 (species)
version 8.1 (current version)
General
@ref: 5110
BacDive-ID: 413
DSM-Number: 13609
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, thermophilic, motile
description: Alicyclobacillus herbarius CP-1 is a spore-forming, thermophilic, motile bacterium that was isolated from dry flower of Hibiscus.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 122960 | species |
| 1120972 | strain |
strain history
| @ref | history |
|---|---|
| 5110 | <- K. Goto |
| 67770 | IAM 14883 <-- K. Goto CP-1. |
doi: 10.13145/bacdive413.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Alicyclobacillaceae
- genus: Alicyclobacillus
- species: Alicyclobacillus herbarius
- full scientific name: Alicyclobacillus herbarius Goto et al. 2002
@ref: 5110
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Alicyclobacillaceae
genus: Alicyclobacillus
species: Alicyclobacillus herbarius
full scientific name: Alicyclobacillus herbarius Goto et al. 2002
strain designation: CP-1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 91.466 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 5110
- name: BACILLUS ACIDOCALDARIUS MEDIUM (DSMZ Medium 13)
- growth: yes
- link: https://mediadive.dsmz.de/medium/13
- composition: Name: BACILLUS ACIDOCALDARIUS MEDIUM (DSMZ Medium 13; with strain-specific modifications) Composition: Agar 20.0 g/l Glucose 1.0 g/l Yeast extract 1.0 g/l KH2PO4 0.6 g/l MgSO4 x 7 H2O 0.5 g/l CaCl2 x 2 H2O 0.25 g/l (NH4)2SO4 0.2 g/l MnSO4 0.01 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 5110 | positive | growth | 55 | thermophilic | |
| 67770 | positive | growth | 55 | thermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 99.704
observation
- @ref: 67770
- observation: quinones: MK-7, MK-3, MK-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species |
|---|---|---|
| 5110 | dry flower of Hibiscus | Hibiscus |
| 67770 | Herbal tea of hibiscus |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | |
| #Host Body-Site | #Plant | #Flower |
taxonmaps
- @ref: 69479
- File name: preview.99_22570.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_313;96_2685;97_13791;98_17004;99_22570&stattab=map
- Last taxonomy: Alicyclobacillus herbarius subclade
- 16S sequence: AB681266
- Sequence Identity:
- Total samples: 3896
- soil counts: 1750
- aquatic counts: 197
- animal counts: 1427
- plant counts: 522
Safety information
risk assessment
- @ref: 5110
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Alicyclobacillus herbarius gene for 16S ribosomal RNA, partial sequence | AB042055 | 1529 | ena | 122960 |
| 20218 | Alicyclobacillus herbarius isolate Ah5 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EU723612 | 514 | ena | 122960 |
| 20218 | Alicyclobacillus herbarius isolate Ah11 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EU723613 | 514 | ena | 122960 |
| 20218 | Alicyclobacillus herbarius isolate Ah20 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EU723614 | 564 | ena | 122960 |
| 20218 | Alicyclobacillus herbarius gene for 16S rRNA, partial sequence, strain: NBRC 100860 | AB681266 | 1471 | ena | 122960 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Alicyclobacillus herbarius DSM 13609 | 1120972.3 | wgs | patric | 1120972 |
| 66792 | Alicyclobacillus herbarius DSM 13609 | 2523533552 | draft | img | 1120972 |
| 67770 | Alicyclobacillus herbarius DSM 13609 | GCA_000430585 | scaffold | ncbi | 1120972 |
GC content
- @ref: 67770
- GC-content: 56.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 86 | no |
| motile | yes | 80.963 | no |
| flagellated | no | 69.58 | no |
| gram-positive | yes | 79.182 | no |
| anaerobic | no | 98.774 | no |
| aerobic | yes | 89.568 | no |
| halophile | no | 94.917 | no |
| spore-forming | yes | 95.801 | no |
| glucose-util | yes | 90.549 | no |
| thermophile | yes | 99.999 | yes |
| glucose-ferment | no | 88.965 | no |
External links
@ref: 5110
culture collection no.: DSM 13609, IAM 14883, NRIC 0477, JCM 21376, NBRC 100860
straininfo link
- @ref: 70093
- straininfo: 49496
literature
- topic: Phylogeny
- Pubmed-ID: 11837292
- title: Alicyclobacillus herbarius sp. nov., a novel bacterium containing omega-cycloheptane fatty acids, isolated from herbal tea.
- authors: Goto K, Matsubara H, Mochida K, Matsumura T, Hara Y, Niwa M, Yamasato K
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/00207713-52-1-109
- year: 2002
- mesh: Beverages/*microbiology, Cycloheptanes/*analysis, DNA, Ribosomal/analysis, Fatty Acids/*analysis, Gram-Positive Endospore-Forming Rods/*chemistry/*classification/genetics/isolation & purification, Hot Temperature, Hydrogen-Ion Concentration, Malvaceae/*microbiology, Molecular Sequence Data, Phylogeny, Plant Structures/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Stress
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5110 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13609) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13609 | |||
| 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 | |
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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) | |||
| 70093 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49496.1 | StrainInfo: A central database for resolving microbial strain identifiers |