Strain identifier

BacDive ID: 1257

Type strain: Yes

Species: Heyndrickxia shackletonii

Strain Designation: B1724

Strain history: CIP <- 2002, N.A. Logan, Caledonian Univ., Glasgow, Scotland, UK: strain B1724

NCBI tax ID(s): 157838 (species)

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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: Heyndrickxia 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

@refhistory
7755<- CIP <- N. A. Logan; B1724
382292002, N.A. Logan, Glasgow, UK: strain B1724
122577CIP <- 2002, N.A. Logan, Caledonian Univ., Glasgow, Scotland, UK: strain B1724

doi: 10.13145/bacdive1257.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Heyndrickxia
  • species: Heyndrickxia shackletonii
  • full scientific name: Heyndrickxia shackletonii (Logan et al. 2004) Narsing Rao et al. 2023

  • synonyms

    @refsynonym
    20215Margalitia shackletonii
    20215Bacillus 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
69480yes96.552
69480positive100
122577positiverod-shapedyes

colony morphology

  • @ref: 122577

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)
122577CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7755positivegrowth30mesophilic
29918positivegrowth15-55
29918positiveoptimum37mesophilic
38229positivegrowth30mesophilic
122577positivegrowth22-45
122577nogrowth10psychrophilic
122577nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
29918positivegrowth4.5-9.0alkaliphile
29918positiveoptimum7
122577positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29918aerobe
122577obligate aerobe

spore formation

@refspore formationconfidence
29918yes
69481yes100
69480yes100
122577yes

halophily

@refsaltgrowthtested relationconcentration
122577NaClpositivegrowth0-4 %
122577NaClnogrowth6 %
122577NaClnogrowth8 %
122577NaClnogrowth10 %

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
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
683714853esculin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12257716947citrate-carbon source
1225774853esculin+hydrolysis
122577606565hippurate+hydrolysis
12257717632nitrate-reduction
12257716301nitrite-reduction
12257717632nitrate-respiration

metabolite production

  • @ref: 122577
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12257715688acetoin-
12257717234glucose-

enzymes

@refvalueactivityec
29918catalase+1.11.1.6
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
122577oxidase+
122577beta-galactosidase+3.2.1.23
122577alcohol dehydrogenase-1.1.1.1
122577gelatinase-
122577amylase-
122577DNase-
122577caseinase+3.4.21.50
122577catalase+1.11.1.6
122577tween esterase+
122577gamma-glutamyltransferase-2.3.2.2
122577lecithinase-
122577lipase-
122577lysine decarboxylase-4.1.1.18
122577ornithine decarboxylase-4.1.1.17
122577protease-
122577urease-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
122577-+++-+--+++++----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122577+/----+/-----+/-+++/-----+/----+/-+/-+/-++/-+/-+/----+----+-+--+/--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122577------------------+-------------------+-----------------------------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
7755volcanic soil
122577Environment, Volcanic soilIcelandISLEurope1997

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

@refbiosafety levelbiosafety level comment
77551Risk group (German classification)
1225771Risk group (French 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
66792Heyndrickxia shackletonii LMG 18435GCA_001420715scaffoldncbi157838
66792Heyndrickxia shackletonii LMG 18435GCA_011008805contigncbi157838
66792Bacillus shackletonii strain LMG 18435157838.3wgspatric157838
66792Bacillus shackletonii strain LMG 18435157838.12wgspatric157838

GC content

  • @ref: 7755
  • GC-content: 35.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes65.599no
gram-positiveyes60.771yes
anaerobicno98.151yes
aerobicyes88.561yes
halophileno65.918no
spore-formingyes96.083yes
thermophileno94.867yes
glucose-utilyes89.335no
motileyes91.244yes
glucose-fermentno88.762no

External links

@ref: 7755

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

straininfo link

  • @ref: 70913
  • straininfo: 12024

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/urltitleID_cross_referencepubmedjournal
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
29918Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2628928776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
70913Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12024.1StrainInfo: A central database for resolving microbial strain identifiers
122577Curators of the CIPCollection of Institut Pasteur (CIP 107762)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107762