Strain identifier
BacDive ID: 18132
Type strain:
Species: Rummeliibacillus stabekisii
Strain Designation: KSC-SF6g
Strain history: CIP <- 2009, K. Venkateswaran, Californian Inst. Technol., Pasadena, California, USA: strain KSC-SF6g
NCBI tax ID(s): 241244 (species)
General
@ref: 18050
BacDive-ID: 18132
DSM-Number: 25578
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Rummeliibacillus stabekisii KSC-SF6g is an aerobe, spore-forming, mesophilic bacterium that was isolated from Payload Hazardous Servicing Facility, clean room floor.
NCBI tax id
- NCBI tax id: 241244
- Matching level: species
strain history
@ref | history |
---|---|
18050 | <- NRRL; NRRL-B-51320 <- K. Venkateswaran, Jet Propulsion Laboratory, NASA; KSC-SF6g |
123290 | CIP <- 2009, K. Venkateswaran, Californian Inst. Technol., Pasadena, California, USA: strain KSC-SF6g |
doi: 10.13145/bacdive18132.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Caryophanaceae
- genus: Rummeliibacillus
- species: Rummeliibacillus stabekisii
- full scientific name: Rummeliibacillus stabekisii Vaishampayan et al. 2009
@ref: 18050
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Caryophanaceae
genus: Rummeliibacillus
species: Rummeliibacillus stabekisii
full scientific name: Rummeliibacillus stabekisii Vaishampayan et al. 2009
strain designation: KSC-SF6g
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
29095 | positive | 2.98 µm | 1.105 µm | rod-shaped | yes |
123290 | positive | rod-shaped | yes |
pigmentation
- @ref: 29095
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
18050 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
37908 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123290 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18050 | positive | growth | 30 | mesophilic |
29095 | positive | growth | 28-32 | mesophilic |
29095 | positive | optimum | 30 | mesophilic |
37908 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29095 | aerobe |
123290 | obligate aerobe |
spore formation
- @ref: 29095
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29095 | NaCl | positive | growth | <7 % |
29095 | NaCl | positive | optimum | 3.5 % |
murein
- @ref: 18050
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29095 | 22599 | arabinose | + | carbon source |
29095 | 17057 | cellobiose | + | carbon source |
29095 | 16947 | citrate | + | carbon source |
29095 | 28260 | galactose | + | carbon source |
29095 | 17234 | glucose | + | carbon source |
29095 | 17716 | lactose | + | carbon source |
29095 | 29864 | mannitol | + | carbon source |
29095 | 37684 | mannose | + | carbon source |
29095 | 33942 | ribose | + | carbon source |
29095 | 18222 | xylose | + | carbon source |
123290 | 17632 | nitrate | - | reduction |
123290 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 123290
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
123290 | oxidase | + | |
123290 | catalase | + | 1.11.1.6 |
123290 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123290 | - | + | + | - | - | + | + | - | - | + | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
18050 | Payload Hazardous Servicing Facility, clean room floor | FL, Kennedy Space Center | USA | USA | North America | |
123290 | Kennedy Space Center, clear room | Florida | United States of America | USA | North America | 2005 |
isolation source categories
- Cat1: #Engineered
- Cat2: #Built environment
- Cat3: #Clean room
taxonmaps
- @ref: 69479
- File name: preview.99_765.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_464;97_531;98_611;99_765&stattab=map
- Last taxonomy: Rummeliibacillus stabekisii subclade
- 16S sequence: DQ870754
- Sequence Identity:
- Total samples: 8174
- soil counts: 3047
- aquatic counts: 550
- animal counts: 3634
- plant counts: 943
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
18050 | 1 | Risk group (German classification) |
123290 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rummeliibacillus stabekisii gene for 16S rRNA, partial sequence, strain: NBRC 104870 | AB682217 | 1473 | ena | 241244 |
18050 | Rummeliibacillus stabekisii strain KSC-SF6g 16S ribosomal RNA (rrn) gene, partial sequence | DQ870754 | 1462 | ena | 241244 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rummeliibacillus stabekisii NBRC 104870 | GCA_007988965 | contig | ncbi | 241244 |
66792 | Rummeliibacillus stabekisii DSM 25578 | GCA_014202625 | scaffold | ncbi | 241244 |
66792 | Rummeliibacillus stabekisii strain DSM 25578 | 241244.14 | wgs | patric | 241244 |
66792 | Rummeliibacillus stabekisii strain NBRC 104870 | 241244.13 | wgs | patric | 241244 |
66792 | Rummeliibacillus stabekisii DSM 25578 | 2861577009 | draft | img | 241244 |
GC content
- @ref: 29095
- GC-content: 37.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | yes | 54.271 | no |
gram-positive | yes | 83.407 | no |
anaerobic | no | 98.883 | yes |
aerobic | yes | 90.743 | no |
halophile | yes | 66.324 | yes |
spore-forming | yes | 93.388 | yes |
glucose-util | yes | 88.588 | no |
thermophile | no | 97.667 | yes |
motile | yes | 79.07 | no |
glucose-ferment | no | 89.805 | no |
External links
@ref: 18050
culture collection no.: DSM 25578, NBRC 104870, NRRL B-51320, CIP 110061
straininfo link
- @ref: 87119
- straininfo: 362839
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19406799 | Description of Rummeliibacillus stabekisii gen. nov., sp. nov. and reclassification of Bacillus pycnus Nakamura et al. 2002 as Rummeliibacillus pycnus comb. nov. | Vaishampayan P, Miyashita M, Ohnishi A, Satomi M, Rooney A, La Duc MT, Venkateswaran K | Int J Syst Evol Microbiol | 10.1099/ijs.0.006098-0 | 2009 | Bacillus/*classification, Bacteria, Aerobic/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/*classification/genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 23625232 | Rummeliibacillus suwonensis sp. nov., isolated from soil collected in a mountain area of South Korea. | Her J, Kim J | J Microbiol | 10.1007/s12275-013-3126-5 | 2013 | Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Planococcaceae/classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
18050 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25578) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25578 | ||||
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 | ||
29095 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 25524 | ||
37908 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7876 | |||||
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 | ||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
87119 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID362839.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
123290 | Curators of the CIP | Collection of Institut Pasteur (CIP 110061) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110061 |