Strain identifier

BacDive ID: 18132

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
18050<- NRRL; NRRL-B-51320 <- K. Venkateswaran, Jet Propulsion Laboratory, NASA; KSC-SF6g
123290CIP <- 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

@refgram staincell lengthcell widthcell shapemotility
29095positive2.98 µm1.105 µmrod-shapedyes
123290positiverod-shapedyes

pigmentation

  • @ref: 29095
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18050NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37908MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123290CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18050positivegrowth30mesophilic
29095positivegrowth28-32mesophilic
29095positiveoptimum30mesophilic
37908positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29095aerobe
123290obligate aerobe

spore formation

  • @ref: 29095
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
29095NaClpositivegrowth<7 %
29095NaClpositiveoptimum3.5 %

murein

  • @ref: 18050
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2909522599arabinose+carbon source
2909517057cellobiose+carbon source
2909516947citrate+carbon source
2909528260galactose+carbon source
2909517234glucose+carbon source
2909517716lactose+carbon source
2909529864mannitol+carbon source
2909537684mannose+carbon source
2909533942ribose+carbon source
2909518222xylose+carbon source
12329017632nitrate-reduction
12329016301nitrite-reduction

metabolite production

  • @ref: 123290
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123290oxidase+
123290catalase+1.11.1.6
123290urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123290-++--++--+++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
18050Payload Hazardous Servicing Facility, clean room floorFL, Kennedy Space CenterUSAUSANorth America
123290Kennedy Space Center, clear roomFloridaUnited States of AmericaUSANorth America2005

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

@refbiosafety levelbiosafety level comment
180501Risk group (German classification)
1232901Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rummeliibacillus stabekisii gene for 16S rRNA, partial sequence, strain: NBRC 104870AB6822171473ena241244
18050Rummeliibacillus stabekisii strain KSC-SF6g 16S ribosomal RNA (rrn) gene, partial sequenceDQ8707541462ena241244

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rummeliibacillus stabekisii NBRC 104870GCA_007988965contigncbi241244
66792Rummeliibacillus stabekisii DSM 25578GCA_014202625scaffoldncbi241244
66792Rummeliibacillus stabekisii strain DSM 25578241244.14wgspatric241244
66792Rummeliibacillus stabekisii strain NBRC 104870241244.13wgspatric241244
66792Rummeliibacillus stabekisii DSM 255782861577009draftimg241244

GC content

  • @ref: 29095
  • GC-content: 37.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes54.271no
gram-positiveyes83.407no
anaerobicno98.883yes
aerobicyes90.743no
halophileyes66.324yes
spore-formingyes93.388yes
glucose-utilyes88.588no
thermophileno97.667yes
motileyes79.07no
glucose-fermentno89.805no

External links

@ref: 18050

culture collection no.: DSM 25578, NBRC 104870, NRRL B-51320, CIP 110061

straininfo link

  • @ref: 87119
  • straininfo: 362839

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406799Description 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 KInt J Syst Evol Microbiol10.1099/ijs.0.006098-02009Bacillus/*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 SpecificityGenetics
Phylogeny23625232Rummeliibacillus suwonensis sp. nov., isolated from soil collected in a mountain area of South Korea.Her J, Kim JJ Microbiol10.1007/s12275-013-3126-52013Base 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 MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
18050Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25578)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25578
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29095Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125524
37908Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7876
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68382Automatically annotated from API zym
69479João 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
87119Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362839.1StrainInfo: A central database for resolving microbial strain identifiers
123290Curators of the CIPCollection of Institut Pasteur (CIP 110061)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110061