Strain identifier

BacDive ID: 1135

Type strain: Yes

Species: Alkalicoccobacillus gibsonii

Strain Designation: PN 109

Strain history: CIP <- 1996, DSM <- H. Outtrup, Novo Nordisk A/S: strain PN 109

NCBI tax ID(s): 79881 (species)

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General

@ref: 3365

BacDive-ID: 1135

DSM-Number: 8722

keywords: 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Alkalicoccobacillus gibsonii PN 109 is an obligate aerobe, spore-forming, mesophilic bacterium of the family Bacillaceae.

NCBI tax id

  • NCBI tax id: 79881
  • Matching level: species

strain history

@refhistory
3365<- H. Outtrup, Novo Nordisk A/S; PD 138
119612CIP <- 1996, DSM <- H. Outtrup, Novo Nordisk A/S: strain PN 109

doi: 10.13145/bacdive1135.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Alkalicoccobacillus
  • species: Alkalicoccobacillus gibsonii
  • full scientific name: Alkalicoccobacillus gibsonii (Nielsen et al. 1995) Kim et al. 2023

  • synonyms

    @refsynonym
    20215Shouchella gibsonii
    20215Alkalihalobacillus gibsonii
    20215Bacillus gibsonii

@ref: 3365

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Shouchella

species: Shouchella gibsonii

full scientific name: Shouchella gibsonii (Nielsen et al. 1995) Joshi et al. 2022

strain designation: PN 109

type strain: yes

Morphology

cell morphology

  • @ref: 119612
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3365ALKALINE NUTRIENT AGAR (DSMZ Medium 31)yeshttps://mediadive.dsmz.de/medium/31Name: ALKALINE NUTRIENT AGAR (DSMZ Medium 31; with strain-specific modifications) Composition: Agar 15.0 g/l Na2CO3 anhydrous 5.3 g/l Peptone 5.0 g/l NaCl 5.0 g/l NaHCO3 4.2 g/l Meat extract 3.0 g/l Distilled water
35234MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119612CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3365positivegrowth30mesophilic
35234positivegrowth30mesophilic
119612positivegrowth10-37
119612nogrowth45thermophilic
119612nogrowth55thermophilic

culture pH

  • @ref: 119612
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119612
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 119612
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
119612NaClpositivegrowth0-6 %
119612NaClnogrowth8 %
119612NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371N-acetylglucosamine-builds acid from59640
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
119612citrate-carbon source16947
119612nitrite-reduction16301
119612nitrate-respiration17632

metabolite production

  • @ref: 119612
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 119612
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
119612oxidase+
119612gelatinase+
119612amylase-
119612DNase+
119612caseinase+3.4.21.50
119612catalase+1.11.1.6
119612lecithinase-
119612lysine decarboxylase-4.1.1.18
119612ornithine decarboxylase-4.1.1.17
119612urease-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
119612-+++-+-+-++-++-++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119612----------------------+/--+/------+/-------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119612+++++-+++++++++++++++-+--+-----+-+++-----+-------+---++-----+-------------------+-----+----+-------

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_8522.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3955;97_4866;98_6230;99_8522&stattab=map
  • Last taxonomy: Alkalihalobacillus gibsonii
  • 16S sequence: X76446
  • Sequence Identity:
  • Total samples: 25187
  • soil counts: 13715
  • aquatic counts: 2140
  • animal counts: 5354
  • plant counts: 3978

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
33651Risk group (German classification)
1196121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bacillus gibsonii DSM 8722, 16S rRNA gene
  • accession: X76446
  • length: 1506
  • database: ena
  • NCBI tax ID: 79881

GC content

  • @ref: 3365
  • GC-content: 41.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.369no
anaerobicno94.327no
halophileno91.168no
spore-formingno93.822no
glucose-utilyes93.979no
thermophileno99.103no
flagellatedno60.892no
motileyes88.88no
aerobicyes88.459no
glucose-fermentyes91.688no

External links

@ref: 3365

culture collection no.: DSM 8722, ATCC 700164, CIP 104720, PD 138

straininfo link

  • @ref: 70806
  • straininfo: 10539

literature

  • topic: Phylogeny
  • Pubmed-ID: 18048744
  • title: Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6.
  • authors: Borchert MS, Nielsen P, Graeber I, Kaesler I, Szewzyk U, Pape T, Antranikian G, Schafer T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65177-0
  • year: 2007
  • mesh: Animals, Bacillus/chemistry/*classification/genetics/*isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Germany, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plakortis/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3365Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8722)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8722
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
35234Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16660
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
70806Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10539.1StrainInfo: A central database for resolving microbial strain identifiers
119612Curators of the CIPCollection of Institut Pasteur (CIP 104720)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104720