Strain identifier

BacDive ID: 1234

Type strain: Yes

Species: Shouchella patagoniensis

Strain history: CIP <- 2005, DSMZ <- N. Olivera, PROIMI, Tucuman, Argentina: strain PAT 05

NCBI tax ID(s): 228576 (species)

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General

@ref: 6303

BacDive-ID: 1234

DSM-Number: 16117

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, motile

description: Shouchella patagoniensis DSM 16117 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil .

NCBI tax id

  • NCBI tax id: 228576
  • Matching level: species

strain history

@refhistory
6303<- N. Olivera; PAT 05
121628CIP <- 2005, DSMZ <- N. Olivera, PROIMI, Tucuman, Argentina: strain PAT 05

doi: 10.13145/bacdive1234.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Shouchella
  • species: Shouchella patagoniensis
  • full scientific name: Shouchella patagoniensis (Olivera et al. 2005) Joshi et al. 2022

  • synonyms

    @refsynonym
    20215Alkalihalobacillus patagoniensis
    20215Bacillus patagoniensis

@ref: 6303

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Shouchella

species: Shouchella patagoniensis

full scientific name: Shouchella patagoniensis (Olivera et al.2005) Joshi et al. 2022

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes91.185
69480100positive
121628nopositiverod-shaped

colony morphology

  • @ref: 121628
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6303CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
38288MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121628CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6303positivegrowth30mesophilic
38288positivegrowth30mesophilic
121628positivegrowth10-30
121628nogrowth37mesophilic
121628nogrowth45thermophilic
121628nogrowth55thermophilic

culture pH

  • @ref: 121628
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 121628
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
121628yes

halophily

@refsaltgrowthtested relationconcentration
121628NaClpositivegrowth6-10 %
121628NaClnogrowth0 %
121628NaClnogrowth2 %
121628NaClnogrowth4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12162816947citrate-carbon source
1216284853esculin+hydrolysis
121628606565hippurate-hydrolysis
12162817632nitrate-reduction
12162816301nitrite-reduction
12162817632nitrate-respiration

metabolite production

  • @ref: 121628
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12162815688acetoin-
12162817234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
121628oxidase+
121628beta-galactosidase+3.2.1.23
121628alcohol dehydrogenase-1.1.1.1
121628gelatinase+
121628amylase-
121628DNase+
121628caseinase-3.4.21.50
121628catalase+1.11.1.6
121628tween esterase-
121628gamma-glutamyltransferase+2.3.2.2
121628lecithinase-
121628lipase-
121628lysine decarboxylase-4.1.1.18
121628ornithine decarboxylase-4.1.1.17
121628urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121628--++-+-----+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121628++-++-+++-+----+++-+--++-+-----+-++++----+-----++++--+--+--++---+----------+--+++-----+-+---++--+++

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6303soil (rhizosphere of shrub Atriplex lampa)Atriplex lampanorth-eastern PatagoniaArgentinaARGMiddle and South America
121628Environment, Soil, rhizosphere of the perennial shrub Atriplex lampaNorth eastern PatagoniaArgentinaARGMiddle and South America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_1235.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_719;97_841;98_977;99_1235&stattab=map
  • Last taxonomy: Alkalihalobacillus patagoniensis subclade
  • 16S sequence: AY258614
  • Sequence Identity:
  • Total samples: 587
  • soil counts: 337
  • aquatic counts: 34
  • animal counts: 158
  • plant counts: 58

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63031Risk group (German classification)
1216281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6303
  • description: Bacillus patagoniensis strain PAT 05 16S ribosomal RNA gene, partial sequence
  • accession: AY258614
  • length: 1402
  • database: ena
  • NCBI tax ID: 228576

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shouchella patagoniensis DSM 16117GCA_002019705scaffoldncbi228576
66792Bacillus patagoniensis strain DSM 16117228576.3wgspatric228576
66792Bacillus patagoniensis DSM 161172916853388draftimg228576

GC content

  • @ref: 6303
  • GC-content: 39.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes75.544no
gram-positiveyes92.951no
anaerobicno99.053no
aerobicyes94.317no
halophileyes88.361no
spore-formingyes95.458no
glucose-utilyes91.321no
thermophileno99.439yes
motileyes88.858no
glucose-fermentno89.864no

External links

@ref: 6303

culture collection no.: DSM 16117, ATCC BAA 965, CIP 108678, PAT 05

straininfo link

  • @ref: 70890
  • straininfo: 135104

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653916Bacillus patagoniensis sp. nov., a novel alkalitolerant bacterium from the rhizosphere of Atriplex lampa in Patagonia, Argentina.Olivera N, Sineriz F, Breccia JDInt J Syst Evol Microbiol10.1099/ijs.0.63348-02005Atriplex/*microbiology, Bacillus/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25008165Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.Lei Z, Qiu P, Ye R, Tian J, Liu Y, Wang L, Tang SK, Li WJ, Tian YJ Gen Appl MicrobiolDN/JST.JSTAGE/jgam/60.1012014Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny25294189Bacillus lonarensis sp. nov., an alkalitolerant bacterium isolated from a soda lake.Reddy SV, Thirumala M, Farooq M, Sasikala C, Ramana CVArch Microbiol10.1007/s00203-014-1040-92014Bacillus/*classification/cytology/*isolation & purification/physiology, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, India, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, Spores, Bacterial/physiology, TemperatureGenetics
Phylogeny31951191Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus.Shin B, Park C, Lee BH, Lee KE, Park WInt J Syst Evol Microbiol10.1099/ijsem.0.0039822020Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Enzymology32888092Proteomic analysis and optimized production of Alkalihalobacillus patagoniensis PAT 05(T) extracellular proteases.Olivera NL, Sequeiros C, Iglesias M, Nievas MBioprocess Biosyst Eng10.1007/s00449-020-02436-z2020Bacillaceae/*enzymology, *Bacterial Proteins/biosynthesis/chemistry/isolation & purification, *Peptide Hydrolases/biosynthesis/chemistry/isolation & purification, *ProteomicsPhylogeny

Reference

@idauthorscataloguedoi/urltitle
6303Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16117)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16117
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
38288Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6333
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)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70890Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135104.1StrainInfo: A central database for resolving microbial strain identifiers
121628Curators of the CIPCollection of Institut Pasteur (CIP 108678)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108678