Strain identifier

BacDive ID: 14042

Type strain: Yes

Species: Sanguibacter antarcticus

Strain history: <- SK Hong, KOPRI

NCBI tax ID(s): 372484 (species)

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General

@ref: 7724

BacDive-ID: 14042

DSM-Number: 18966

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, motile, rod-shaped

description: Sanguibacter antarcticus DSM 18966 is a facultative anaerobe, Gram-positive, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 372484
  • Matching level: species

strain history

@refhistory
7724<- H. K. Lee <- S. G. Hong <- I. H. Kim; KOPRI 21702
67770H. K. Lee KOPRI 21702.
67771<- SK Hong, KOPRI

doi: 10.13145/bacdive14042.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Jonesiaceae
  • genus: Sanguibacter
  • species: Sanguibacter antarcticus
  • full scientific name: Sanguibacter antarcticus Hong et al. 2008

@ref: 7724

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Jonesiaceae

genus: Sanguibacter

species: Sanguibacter antarcticus

full scientific name: Sanguibacter antarcticus Hong et al. 2008 emend. Pikuta et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32142positive22.6 µm0.5 µmrod-shapedyes
67771positive

colony morphology

@refincubation periodmedium usedcolony color
1832810-14 daysISP 2
1832810-14 daysISP 3Zinc yellow (1018)
1832810-14 daysISP 4
1832810-14 daysISP 5
1832810-14 daysISP 6
1832810-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18328noISP 2
18328noISP 3
18328noISP 4
18328noISP 5
18328noISP 6
18328noISP 7

pigmentation

  • @ref: 32142
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7724TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18328ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18328ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18328ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18328ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18328ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18328ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperature
7724positivegrowth28
18328positiveoptimum28
32142positivegrowth04-30
32142positiveoptimum24.5
67770positivegrowth25
67771positivegrowth25

culture pH

@refabilitytypepHPH range
32142positivegrowth04-09alkaliphile
32142positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32142facultative anaerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
32142NaClpositivegrowth0-7 %
32142NaClpositiveoptimum3.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3214216947citrate+carbon source
3214217632nitrate+reduction
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
6837116443D-tagatose-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
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

enzymes

@refvalueactivityec
32142catalase+1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18328++----+++--+++++-++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18328-++-++---+-+---++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7724----+++---++++----+-----++++++-++---++-+++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7724soilAntartica, King George Island
67770Sea sand from King George IslandAntarcticaATAAntarctica
67771From soilAntarcticRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_10557.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3136;97_3840;98_7862;99_10557&stattab=map
  • Last taxonomy: Sanguibacter antarcticus subclade
  • 16S sequence: EF211071
  • Sequence Identity:
  • Total samples: 13750
  • soil counts: 4220
  • aquatic counts: 1906
  • animal counts: 6269
  • plant counts: 1355

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183281German classification
77241Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7724
  • description: Sanguibacter antarcticus strain KOPRI 21702 16S ribosomal RNA gene, partial sequence
  • accession: EF211071
  • length: 1468
  • database: nuccore
  • NCBI tax ID: 372484

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sanguibacter antarcticus strain DSM 18966372484.4wgspatric372484
66792Sanguibacter antarcticus DSM 189662627853609draftimg372484
67770Sanguibacter antarcticus DSM 18966GCA_002564005contigncbi372484

GC content

@refGC-contentmethod
772469.5
6777069.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno83no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.268yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.454yes
69480spore-formingspore-formingAbility to form endo- or exosporesno61.465no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes65.876no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.967yes
69480flagellatedmotile2+Ability to perform flagellated movementno65.371no

External links

@ref: 7724

culture collection no.: DSM 18966, JCM 14623, KCTC 13143, Kopri 21702

straininfo link

  • @ref: 83211
  • straininfo: 323996

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175681Sanguibacter antarcticus sp. nov., isolated from Antarctic sea sand.Hong SG, Lee YK, Yim JH, Chun J, Lee HKInt J Syst Evol Microbiol10.1099/ijs.0.65031-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Species SpecificityGenetics
Pathogenicity20100576Expression of recombinant endochitinase from the Antarctic bacterium, Sanguibacter antarcticus KOPRI 21702 in Pichia pastoris by codon optimization.Lee SG, Koh HY, Han SJ, Park H, Na DC, Kim IC, Lee HK, Yim JHProtein Expr Purif10.1016/j.pep.2010.01.0172010Amino Acid Sequence, Antarctic Regions, Bacteria/drug effects/*enzymology, Base Sequence, Bioreactors/microbiology, Chitinases/chemistry/genetics/isolation & purification/*metabolism, Chromatography, Thin Layer, Codon/*genetics, *Genetic Techniques, Hydrogen-Ion Concentration/drug effects, Methanol/pharmacology, Molecular Sequence Data, Pichia/*metabolism, Recombinant Proteins/*metabolism, Recombination, Genetic/drug effects, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7724Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18966)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18966
18328Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18966.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
32142Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2838628776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
83211Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323996.1StrainInfo: A central database for resolving microbial strain identifiers