Strain identifier

BacDive ID: 1566

Type strain: Yes

Species: Psychrobacillus psychrodurans

Strain Designation: 68E3, 68000

Strain history: CIP <- 2008, DSMZ <- H.A. Abd El-Rahman, Egypt: strain 68E3

NCBI tax ID(s): 126157 (species)

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

@ref: 4453

BacDive-ID: 1566

DSM-Number: 11713

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

description: Psychrobacillus psychrodurans 68E3 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 126157
  • Matching level: species

strain history

@refhistory
4453<- H. A. Abd El-Rahman; 68E3
122016CIP <- 2008, DSMZ <- H.A. Abd El-Rahman, Egypt: strain 68E3

doi: 10.13145/bacdive1566.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Psychrobacillus
  • species: Psychrobacillus psychrodurans
  • full scientific name: Psychrobacillus psychrodurans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011
  • synonyms

    • @ref: 20215
    • synonym: Bacillus psychrodurans

@ref: 4453

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Psychrobacillus

species: Psychrobacillus psychrodurans

full scientific name: Psychrobacillus psychrodurans (Abd El-Rahman et al. 2002) Krishnamurthi et al. 2011

strain designation: 68E3, 68000

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.72
69480100positive
122016yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4453CASO 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
38231MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122016CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4453positivegrowth25mesophilic
38231positivegrowth25mesophilic
122016positivegrowth22-45
122016nogrowth10psychrophilic
122016nogrowth55thermophilic

culture pH

  • @ref: 122016
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 122016
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
122016yes

halophily

@refsaltgrowthtested relationconcentration
122016NaClpositivegrowth0-6 %
122016NaClnogrowth8 %
122016NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122016citrate-carbon source16947
122016esculin-hydrolysis4853
122016hippurate+hydrolysis606565
122016nitrate+reduction17632
122016nitrite-reduction16301
122016nitrate-respiration17632

antibiotic resistance

  • @ref: 122016
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122016
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12201615688acetoin-
12201617234glucose-

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
122016oxidase+
122016beta-galactosidase-3.2.1.23
122016alcohol dehydrogenase-1.1.1.1
122016gelatinase-
122016amylase-
122016DNase-
122016caseinase+3.4.21.50
122016catalase+1.11.1.6
122016tween esterase+
122016gamma-glutamyltransferase+2.3.2.2
122016lecithinase-
122016lipase-
122016lysine decarboxylase-4.1.1.18
122016ornithine decarboxylase-4.1.1.17
122016protease-
122016urease-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
122016-+++-++---++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122016---------------------+/-------------------------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122016-----------------------------------------------------------+---------------+------------+--+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4453garden soilEl-KanaterEgyptEGYAfrica
122016Environment, SoilEl KanaterEgyptEGYAfrica

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_15779.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_221;97_240;98_269;99_15779&stattab=map
  • Last taxonomy: Psychrobacillus
  • 16S sequence: AJ277984
  • Sequence Identity:
  • Total samples: 8478
  • soil counts: 5352
  • aquatic counts: 817
  • animal counts: 1751
  • plant counts: 558

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44531Risk group (German classification)
1220161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus psychrodurans partial 16S rRNA gene, isolate OS-64.cAM237365956ena126157
4453Bacillus psychrodurans 16S rRNA gene, strain DSM 11713AJ2779841486ena126157

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacillus psychrodurans DSM 11713GCA_900114885contigncbi126157
66792Psychrobacillus psychrodurans strain DSM 11713126157.3wgspatric126157
66792Psychrobacillus psychrodurans DSM 117132675903167draftimg126157
66792Psychrobacillus psychrodurans DSM 11713GCA_027563345scaffoldncbi126157

GC content

  • @ref: 4453
  • GC-content: 36.3
  • method: Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.755no
gram-positiveyes93.728no
anaerobicno98.37no
aerobicyes91.416no
halophileno60.764no
spore-formingyes92.719no
thermophileno99.239yes
glucose-utilyes87.142no
flagellatedyes86.674no
glucose-fermentno87.126no

External links

@ref: 4453

culture collection no.: DSM 11713, ATCC BAA 796, CIP 107791, NCIMB 13837

straininfo link

  • @ref: 71211
  • straininfo: 87967

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508879Two novel psychrotolerant species, Bacillus psychrotolerans sp. nov. and Bacillus psychrodurans sp. nov., which contain ornithine in their cell walls.Abd El-Rahman HA, Fritze D, Sproer C, Claus DInt J Syst Evol Microbiol10.1099/00207713-52-6-21272002Bacillus/*classification/genetics/*metabolism, Base Composition, Cell Wall/metabolism, Cold Temperature, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Ornithine/*metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Phylogeny20650590Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov.Krishnamurthi S, Ruckmani A, Pukall R, Chakrabarti TSyst Appl Microbiol10.1016/j.syapm.2010.06.0032010Bacillus/*classification/cytology/genetics/physiology, *Bacterial Typing Techniques, Base Composition, Base Sequence, Carbohydrates/chemistry, Chemotaxis, Cold Temperature, DNA, Bacterial/genetics, *Gram-Positive Endospore-Forming Rods/classification/cytology/genetics/physiology, Lipids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNA, Species Specificity, Terpenes/chemistryGenetics
Phylogeny28933325Psychrobacillus lasiicapitis sp. nov., isolated from the head of an ant (Lasius fuliginosus).Shen Y, Fu Y, Yu Y, Zhao J, Li J, Li Y, Wang X, Zhang J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0023152017Animals, Ants/*microbiology, Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31985396Psychrobacillus glaciei sp. nov., a psychrotolerant species isolated from an Antarctic iceberg.Choi JY, Lee PCInt J Syst Evol Microbiol10.1099/ijsem.0.0039982020Antarctic Regions, Bacillaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4453Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11713)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11713
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
38231Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5265
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)
68371Automatically annotated from API 50CH acid
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
71211Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87967.1StrainInfo: A central database for resolving microbial strain identifiers
122016Curators of the CIPCollection of Institut Pasteur (CIP 107791)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107791