Strain identifier
BacDive ID: 1327
Type strain:
Species: Halobacillus halophilus
Strain Designation: 3
Strain history: IAM 13060 <-- M. V. Hao and K. Komagata HK 814 <-- CCM 3527 <-- DSM 2266 <-- H. J. Rolf 3.
NCBI tax ID(s): 866895 (strain), 1570 (species)
General
@ref: 1011
BacDive-ID: 1327
DSM-Number: 2266
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, moderately halophilic, chemoorganotroph, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, pigmented
description: Halobacillus halophilus 3 is an obligate aerobe, moderately halophilic, chemoorganotroph bacterium that has a orange pigmentation and was isolated from salt marsh soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1570 | species |
866895 | strain |
strain history
@ref | history |
---|---|
1011 | <- H.J. Rolf, 3 |
67770 | IAM 13060 <-- M. V. Hao and K. Komagata HK 814 <-- CCM 3527 <-- DSM 2266 <-- H. J. Rolf 3. |
doi: 10.13145/bacdive1327.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Halobacillus
- species: Halobacillus halophilus
- full scientific name: Halobacillus halophilus (Claus et al. 1984) Spring et al. 1996
synonyms
- @ref: 20215
- synonym: Sporosarcina halophila
@ref: 1011
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Halobacillus
species: Halobacillus halophilus
full scientific name: Halobacillus halophilus (Claus et al. 1984) Spring et al. 1996
strain designation: 3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
22983 | positive | rod-shaped | yes | |
69480 | yes | 94.579 | ||
69480 | positive | 100 |
pigmentation
- @ref: 22983
- production: yes
- color: orange
Culture and growth conditions
culture medium
- @ref: 1011
- name: MARINE AGAR (DSMZ Medium 123)
- growth: yes
- link: https://mediadive.dsmz.de/medium/123
- composition: Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1011 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 22983
- oxygen tolerance: obligate aerobe
nutrition type
- @ref: 22983
- type: chemoorganotroph
spore formation
@ref | type of spore | spore formation | confidence |
---|---|---|---|
22983 | endospore | yes | |
69481 | yes | 100 | |
69480 | yes | 99.999 |
halophily
- @ref: 22983
- halophily level: moderately halophilic
murein
- @ref: 1011
- murein short key: A21.04
- type: A4ß L-Orn-D-Asp
metabolite utilization
- @ref: 22983
- Chebi-ID: 17632
- metabolite: nitrate
- utilization activity: -
- kind of utilization tested: reduction
metabolite production
- @ref: 22983
- Chebi-ID: 15688
- metabolite: acetoin
- production: no
metabolite tests
- @ref: 22983
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
22983 | catalase | + | 1.11.1.6 |
22983 | cytochrome oxidase | + | 1.9.3.1 |
22983 | DNase | + | |
22983 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
1011 | salt marsh soil | Sylt | Germany | DEU | Europe |
67770 | Salt marsh soil | Germany | DEU | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Salt marsh |
#Environmental | #Terrestrial | #Soil |
#Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_3747.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_469;97_536;98_617;99_3747&stattab=map
- Last taxonomy: Halobacillus
- 16S sequence: AB681790
- Sequence Identity:
- Total samples: 448
- soil counts: 116
- aquatic counts: 246
- animal counts: 13
- plant counts: 73
Safety information
risk assessment
- @ref: 1011
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: A492 | AB367151 | 492 | ena | 866895 |
20218 | Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: B492 | AB367152 | 492 | ena | 866895 |
20218 | Halobacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 740 | AB367153 | 740 | ena | 866895 |
67770 | Halobacillus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 102448 | AB681790 | 1492 | ena | 1570 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halobacillus halophilus DSM 2266 type strain: DSM 2266 | GCA_000284515 | complete | ncbi | 866895 |
66792 | Halobacillus halophilus DSM 2266 | 866895.3 | complete | patric | 866895 |
66792 | Halobacillus halophilus DSM 2266 strain type strain: DSM 2266 | 866895.15 | plasmid | patric | 866895 |
66792 | Halobacillus halophilus DSM 2266 strain type strain: DSM 2266 | 866895.14 | plasmid | patric | 866895 |
66792 | Halobacillus halophilus DSM 2266 | 2513237186 | complete | img | 866895 |
GC content
@ref | GC-content |
---|---|
22983 | 40-43 |
1011 | 40.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 86.855 | no |
flagellated | yes | 80.834 | no |
gram-positive | yes | 88.278 | yes |
anaerobic | no | 98.806 | no |
aerobic | yes | 95.318 | yes |
halophile | yes | 94.114 | no |
spore-forming | yes | 91.973 | no |
thermophile | no | 99.193 | yes |
glucose-util | yes | 89.239 | no |
glucose-ferment | no | 86.087 | no |
External links
@ref: 1011
culture collection no.: DSM 2266, ATCC 35676, NCIMB 2269, JCM 20832, CCM 3527, CECT 5013, IAM 12846, IAM 13060, KCTC 3685, LMG 17431, NBRC 102448
straininfo link
- @ref: 70977
- straininfo: 9982
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23194807 | Sporosarcina halophila sp. nov., an Obligate, Slightly Halophilic Bacterium from Salt Marsh Soils. | Claus D, Fahmy F, Rolf HJ, Tosunoglu N | Syst Appl Microbiol | 10.1016/S0723-2020(83)80007-1 | 1983 | ||
Phylogeny | 25795064 | Halobacillus andaensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soil. | Wang K, Zhang L, Yang Y, Pan Y, Meng L, Liu H, Hong S, Huang H, Jiang J | Int J Syst Evol Microbiol | 10.1099/ijs.0.000198 | 2015 | Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Halobacillus/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1011 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2266) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2266 | |||
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 | |
22983 | S. SPRING,W. LUDWIG,M. C. MARQUEZ,A. VENTOSA,K.-H. SCHLEIFER | 10.1099/00207713-46-2-492 | Halobacillus gen. nov., with Descriptions of Halobacillus litoralis sp. nov. and Halobacillus trueperi sp. nov., and Transfer of Sporosarcina halophila to Halobacillus halophilus comb. nov. | IJSEM 46: 492-496 1996 | ||
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) | |||
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 | |
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) | |||
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 | |||
70977 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9982.1 | StrainInfo: A central database for resolving microbial strain identifiers |