We are hiring!

Strain identifier

BacDive ID: 1257

Type strain: Yes

Species: Margalitia shackletonii

Strain Designation: B1724

Strain history: 2002, N.A. Logan, Glasgow, UK: strain B1724

NCBI tax ID(s): 157838 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7.1 (current version):
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 7.1 (current version)

General

@ref: 7755

BacDive-ID: 1257

DSM-Number: 18868

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

description: Margalitia shackletonii B1724 is an aerobe, spore-forming, mesophilic bacterium that was isolated from volcanic soil.

NCBI tax id

  • NCBI tax id: 157838
  • Matching level: species

strain history

doi: 10.13145/bacdive1257.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Margalitia
  • species: Margalitia shackletonii
  • full scientific name: Margalitia shackletonii (Logan et al. 2004) Gupta et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Bacillus shackletonii

@ref: 7755

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Margalitia

species: Margalitia shackletonii

full scientific name: Margalitia shackletonii (Logan et al. 2004) Gupta et al. 2020

strain designation: B1724

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29918variable3.5 µm0.8 µmrod-shapedyes
69480yes80.68
69480positive91.543

pigmentation

  • @ref: 29918
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7755NUTRIENT 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
38229MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
7755positivegrowth30mesophilic
29918positivegrowth15-55
29918positiveoptimum37mesophilic
38229positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29918positivegrowth4.5-9.0alkaliphile
29918positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29918
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29918yes
69480yes98.222

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 93.328

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2991828260galactose+carbon source
2991817716lactose+carbon source
2991837684mannose+carbon source
2991833942ribose+carbon source
2991827082trehalose+carbon source
299184853esculin+hydrolysis

enzymes

  • @ref: 29918
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 7755
  • sample type: volcanic soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Volcanic
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3213.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1672;97_2002;98_2462;99_3213&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: AJ250318
  • Sequence Identity:
  • Total samples: 378
  • soil counts: 166
  • aquatic counts: 54
  • animal counts: 127
  • plant counts: 31

Safety information

risk assessment

  • @ref: 7755
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7755
  • description: Bacterium LMG 18435 16S rRNA gene, strain LMG 18435
  • accession: AJ250318
  • length: 1503
  • database: ena
  • NCBI tax ID: 157838

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Margalitia shackletonii LMG 18435GCA_001420715scaffoldncbi157838
66792Margalitia shackletonii LMG 18435GCA_011008805contigncbi157838
66792Bacillus shackletonii strain LMG 18435157838.3wgspatric157838
66792Bacillus shackletonii strain LMG 18435157838.12wgspatric157838
66792Maritimibacter sp. HL-12 HL-12GCA_900177545scaffoldpatric1162418

GC content

  • @ref: 7755
  • GC-content: 35.4

External links

@ref: 7755

culture collection no.: DSM 18868, CIP 107762, KCTC 13003, LMG 18435

straininfo link

@refpassport
20218http://www.straininfo.net/strains/692107
20218http://www.straininfo.net/strains/377586
20218http://www.straininfo.net/strains/840260
20218http://www.straininfo.net/strains/45745

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023945Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago.Logan NA, Lebbe L, Verhelst A, Goris J, Forsyth G, Rodriguez-Diaz M, Heyndrickx M, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.02661-02004Antarctic Regions, Bacillus/*classification/genetics/growth & development/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Restriction Mapping, *Soil Microbiology, Volcanic EruptionsGenetics
Phylogeny25603996Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil.Cui X, Wang Y, Liu J, Chang M, Zhao Y, Zhou S, Zhuang LArch Microbiol10.1007/s00203-015-1082-72015Bacillus/*genetics/*growth & development/isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Cardiolipins/analysis, Chromium/*metabolism, DNA, Bacterial/genetics, Drug Resistance, Bacterial, Fatty Acids/analysis, Metals, Heavy, Microbial Sensitivity Tests, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/*chemistry, *Soil Microbiology, Soil Pollutants/chemistry/metabolismMetabolism
Phylogeny26559004Bacillus ectoiniformans sp. nov., a halotolerant bacterium isolated from deep-sea sediments.Zhu D, Zhang P, Niu L, Xie C, Li P, Sun J, Hang FInt J Syst Evol Microbiol10.1099/ijsem.0.0007632015
Genetics26847895Draft Genome Sequence of Bacillus shackletonii LMG 18435T, Isolated from Volcanic Mossy Soil.Wang JP, Liu B, Liu GH, Ge CB, Xiao RF, Zheng XF, Shi HGenome Announc10.1128/genomeA.01689-152016Phylogeny
Metabolism27084709Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern.Zhou YX, Liu GH, Liu B, Chen GJ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-016-0692-72016Alginates/*metabolism, Bacillus/genetics/*isolation & purification/*metabolism, Cell Wall/metabolism, China, Fatty Acids/metabolism, Genotype, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Nucleic Acid Hybridization, Peptidoglycan/metabolism, Phenotype, Phosphatidylethanolamines/metabolism, Phylogeny, Sequence Analysis, DNA, Sodium Chloride, Soil/chemistry, *Soil Microbiology, Vitamin K 2/metabolismPhylogeny
Phylogeny32375947Bacillus aquiflavi sp. nov., isolated from yellow water of strongly flavored Chinese baijiu.Xie J, Cheng K, Zhao D, Yang G, Qiao Z, Qiu S, Yu X, Liu H, Li T, Feng H, Yao S, Zhai LInt J Syst Evol Microbiol10.1099/ijsem.0.0041852020Alcoholic Beverages/*microbiology, Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, WaterTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7755Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18868)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18868
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
2628910.1099/ijs.0.02661-015023945
29918Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126289
38229Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5233
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
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)