Strain identifier
BacDive ID: 1450
Type strain: 
Species: Geobacillus lituanicus
Strain Designation: N-3
Strain history: <- N. Kuisiene, Vilnius Univ.; N-3
NCBI tax ID(s): 169283 (species)
version 8.1 (current version)
General
@ref: 5846
BacDive-ID: 1450
DSM-Number: 15325
keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, spore-forming, thermophilic, Gram-positive, motile, rod-shaped, colony-forming
description: Geobacillus lituanicus N-3 is an aerobe, chemoorganotroph, spore-forming bacterium that forms circular colonies and was isolated from oilfield.
NCBI tax id
- NCBI tax id: 169283
- Matching level: species
strain history
- @ref: 5846
- history: <- N. Kuisiene, Vilnius Univ.; N-3
doi: 10.13145/bacdive1450.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Geobacillus
- species: Geobacillus lituanicus
- full scientific name: Geobacillus lituanicus Kuisiene et al. 2004
@ref: 5846
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Geobacillus
species: Geobacillus lituanicus
full scientific name: Geobacillus lituanicus Kuisiene et al. 2004
strain designation: N-3
type strain: yes
Morphology
cell morphology
- @ref: 23036
- gram stain: positive
- cell length: 4.4-5.8 µm
- cell width: 1.1-1.4 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: peritrichous
colony morphology
- @ref: 23036
- colony color: tawny
- colony shape: circular
Culture and growth conditions
culture medium
- @ref: 5846
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5846 | positive | growth | 55 | thermophilic |
| 23036 | maximum | 70.0 | thermophilic | |
| 23036 | minimum | 55.0 | thermophilic | |
| 23036 | positive | optimum | 55.0-60.0 | thermophilic |
| 23036 | thermophilic |
culture pH
- @ref: 23036
- ability: positive
- type: growth
- pH: 6.5
Physiology and metabolism
oxygen tolerance
- @ref: 23036
- oxygen tolerance: aerobe
nutrition type
- @ref: 23036
- type: chemoorganotroph
spore formation
- @ref: 23036
- spore description: oval,subterminal,in slightly distended sporangia
- type of spore: endospore
- spore formation: yes
halophily
- @ref: 23036
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0.0-0.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23036 | 17632 | nitrate | - | builds gas from |
| 23036 | 22599 | arabinose | + | builds acid from |
| 23036 | 17057 | cellobiose | + | builds acid from |
| 23036 | 28260 | galactose | + | builds acid from |
| 23036 | 29864 | mannitol | + | builds acid from |
| 23036 | 33942 | ribose | + | builds acid from |
| 23036 | 18222 | xylose | + | builds acid from |
| 23036 | 17632 | nitrate | + | electron acceptor |
| 23036 | casein | + | hydrolysis | |
| 23036 | 3815 | collagen | + | hydrolysis |
| 23036 | 28017 | starch | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 23036 | catalase | + | 1.11.1.6 |
| 23036 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature |
|---|---|---|---|---|---|---|---|
| 5846 | oilfield | Lithuania | LTU | Europe | |||
| 23036 | crude oil of a high-temperature oilfield | Czapek agar | 2 days | 60.0 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Geologic |
| #Condition | #Thermophilic (>45°C) | |
| #Engineered | #Industrial | #Oil reservoir |
taxonmaps
- @ref: 69479
- File name: preview.99_1030.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_79;96_191;97_207;98_231;99_1030&stattab=map
- Last taxonomy: Geobacillus
- 16S sequence: AY044055
- Sequence Identity:
- Total samples: 3714
- soil counts: 485
- aquatic counts: 635
- animal counts: 2412
- plant counts: 182
Safety information
risk assessment
- @ref: 5846
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 01 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF645695 | 521 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 17 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF645696 | 657 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 23 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF645697 | 756 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 28 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF645698 | 882 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 30 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF645699 | 752 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 36 16S ribosomal RNA gene, partial sequence; and 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence | EF645700 | 1033 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone 39 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF645701 | 712 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone GL-M 16S-23S ribosomal RNA intergenic spacer and tRNA-Ile gene, partial sequence; and tRNA-Ala gene, complete sequence | EU157946 | 543 | ena | 169283 |
| 20218 | Geobacillus lituanicus strain DSM 15325 clone GL-D 16S-23S ribosomal RNA intergenic spacer and tRNA-Ile gene, partial sequence; and tRNA-Ala gene, complete sequence | EU157947 | 700 | ena | 169283 |
| 5846 | Geobacillus lituanicus 16S ribosomal RNA gene, complete sequence | AY044055 | 1523 | ena | 169283 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geobacillus lituanicus N-3 | GCA_002243605 | complete | ncbi | 169283 |
| 66792 | Geobacillus lituanicus N-3 | 2758568037 | complete | img | 169283 |
GC content
- @ref: 5846
- GC-content: 52.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | yes | 90.195 | yes |
| gram-positive | yes | 86.096 | yes |
| anaerobic | no | 96.828 | no |
| aerobic | yes | 87.834 | no |
| halophile | no | 97.345 | no |
| spore-forming | yes | 97.212 | yes |
| glucose-util | yes | 91.259 | no |
| thermophile | yes | 99.999 | yes |
| motile | yes | 88.466 | yes |
| glucose-ferment | no | 90.028 | no |
External links
@ref: 5846
culture collection no.: DSM 15325
straininfo link
- @ref: 71100
- straininfo: 134424
literature
- topic: Phylogeny
- Pubmed-ID: 15545423
- title: Geobacillus lituanicus sp. nov.
- authors: Kuisiene N, Raugalas J, Chitavichius D
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02976-0
- year: 2004
- mesh: Aerobiosis, Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Deoxyribonucleases, Type II Site-Specific, Genes, rRNA, Hot Temperature, Lithuania, Molecular Sequence Data, Phylogeny, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, Proteins/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5846 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15325) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15325 | |||
| 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 | |
| 23036 | Nomeda Kuisiene,Juozas Raugalas,Donaldas Chitavichius | 10.1099/ijs.0.02976-0 | Geobacillus lituanicus sp. nov. | IJSEM 54: 1991-1995 2004 | 15545423 | |
| 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) | |||
| 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 | |||
| 71100 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID134424.1 | StrainInfo: A central database for resolving microbial strain identifiers |