Strain identifier

BacDive ID: 133099

Type strain: Yes

Species: Sanguibacter gelidistatuariae

Strain Designation: ISLP-3

Strain history: E. V. Pikuta; Athens State Univ., USA; ISLP-3.

NCBI tax ID(s): 1814289 (species)

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General

@ref: 24887

BacDive-ID: 133099

DSM-Number: 100501

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

description: Sanguibacter gelidistatuariae ISLP-3 is a facultative anaerobe, Gram-positive, motile bacterium that forms circular colonies and was isolated from naturally formed ice sculpture .

NCBI tax id

  • NCBI tax id: 1814289
  • Matching level: species

strain history

@refhistory
24887<- E. Pikuta, Athens State Univ., USA; ISLP-3
67770E. V. Pikuta; Athens State Univ., USA; ISLP-3.

doi: 10.13145/bacdive133099.20230509.8.1

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 gelidistatuariae
  • full scientific name: Sanguibacter gelidistatuariae Pikuta et al. 2017

@ref: 24887

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Jonesiaceae

genus: Sanguibacter

species: Sanguibacter gelidistatuariae

full scientific name: Sanguibacter gelidistatuariae Pikuta et al. 2017

strain designation: ISLP-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25305positive1.2-3.5 µm0.4-0.5 µmrod-shapedyes
25305no
69480positive100

colony morphology

  • @ref: 25305
  • colony size: 1-3 mm
  • colony color: cream to brownish
  • colony shape: circular
  • medium used: anaerobic medium (AM) agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25305anaerobic medium (AM) agaryes
24887TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
25305positivegrowth3-35
25305positiveoptimum22-24psychrophilic
24887positivegrowth25mesophilic
67770positivegrowth24psychrophilic

culture pH

@refabilitytypepHPH range
25305positivegrowth6.0-9.5alkaliphile
25305positiveoptimum7.4-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25305
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
25305no
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
25305NaClpositivegrowth0-2 %(w/v)
25305NaCloptimum0.25 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2530530089acetate-growth
2530515347acetone-growth
2530517750betaine-growth
2530517968butyrate-growth
25305casamino acids-growth
2530516947citrate-growth
2530516899D-mannitol-growth
2530516236ethanol-growth
2530515740formate-growth
2530517754glycerol-growth
2530524996lactate-growth
2530517790methanol-growth
2530530623oxalate-growth
2530517309pectin-growth
25305peptone-growth
2530517272propionate-growth
2530515361pyruvate-growth
2530518139trimethylamine-growth
25305yeast extract-growth
2530517029chitin+growth
2530517108D-arabinose+growth
2530517057cellobiose+growth
2530515824D-fructose+growth
2530517634D-glucose+growth
2530516024D-mannose+growth
2530516988D-ribose+growth
2530516551D-trehalose+growth
2530517716lactose+growth
2530517306maltose+growth
25305506227N-acetylglucosamine+growth
2530528017starch+growth
2530517992sucrose+growth
2530535026triethylamine+growth

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
2530528971ampicillinyesyes250 µg/mL
2530517833gentamicinyesyes250 µg/mL
2530528077rifampicinyesyes250 µg/mL
2530527902tetracyclineyesyes250 µg/mL
253056104kanamycinyesyes250 µg/mL
2530517698chloramphenicolyesyes100 µg/mL

enzymes

  • @ref: 25305
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25305C13:0 anteiso2.3
    25305C15:0 anteiso47.3
    25305C17:0 anteiso3.4
    25305C13:0 3OH / C15:1 isoH1.1
    25305C14:08
    25305C15:03.4
    25305C15:0 2OH1.1
    25305C16:08.5
    25305C18:0 / C17:0 cyclo2.3
    25305C13:0 iso2.9
    25305C14:0 iso2.4
    25305C15:0 iso6
    25305C16:0 iso8.5
  • type of FA analysis: whole cell analysis
  • incubation medium: AM
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: QTSA 1
  • system: MIS MIDI
  • instrument: Agilent Technologies 6890 N
  • method/protocol: Miller 1982
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture composition
24887naturally formed ice sculpture (70° 44' 31'' S 11° 47' 39'' E)Schirmacher Hills of Dronning Queen Maud Land, shore of Lake PodprudnoyeAntarcticaATAAustralia and Oceania-70.741911.7942
25305sample of glacier containing small embedded stonesanaerobic medium (AM)NaCl 5.0 g/l, KCl 0.3 g/l, KH2PO4 0.3 g/l, NH4Cl 1.0 g/l, MgSO4*7H2O 0.1 g/l, CaSO4*7H2O 0.0125 g/l, NaHCO3 0.2 g/l, Na2S*9H2O 0.5 g/l, resazurin 0.005 % (w/v), 2 ml vitamin solution, 1 ml trace element solution, yeast extract 0.1 g/l, D-Glucose 5 g/l, pH 7.2
67770Shore of Lake Podprudnoye in Antarctica

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Ice
#Environmental#Terrestrial#Glacier

taxonmaps

  • @ref: 69479
  • File name: preview.99_59544.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_3136;97_3840;98_4877;99_59544&stattab=map
  • Last taxonomy: Sanguibacter
  • 16S sequence: KM406784
  • Sequence Identity:
  • Total samples: 191
  • soil counts: 63
  • aquatic counts: 88
  • animal counts: 34
  • plant counts: 6

Safety information

risk assessment

  • @ref: 24887
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24887
  • description: Sanguibacter gelidistatuariae strain ISLP-3 16S ribosomal RNA gene, partial sequence
  • accession: KM406784
  • length: 1381
  • database: ena
  • NCBI tax ID: 1814289

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sanguibacter gelidistatuariae ISLP-32657245272draftimg1814289
67770Sanguibacter gelidistatuariae ISLP-3GCA_900096585scaffoldncbi1814289

GC content

@refGC-contentmethod
2488769.5sequence analysis
6777069.5genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 75
  • training_data: no

External links

@ref: 24887

culture collection no.: DSM 100501, ATCC TSD-17, JCM 30887

straininfo link

  • @ref: 91363
  • straininfo: 402633

literature

  • topic: Phylogeny
  • Pubmed-ID: 28150571
  • title: Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions of the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S. soli and S. suarezii.
  • authors: Pikuta EV, Lyu Z, Williams MD, Patel NB, Liu Y, Hoover RB, Busse HJ, Lawson PA, Whitman WB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001838
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ice, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sculpture, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24887Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100501Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100501)
25305E. V. L. Pikuta, Z.,Williams, M. D.,Patel, N. B.,Liu, Y.,Hoover, R. B.,Busse, H. J.,Lawson, P. A.,Whitman, W. B.Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions of the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S. soli and S. suarezii10.1099/ijsem.0.001838IJSEM 67: 1442-1450 201728150571
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
91363Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402633.1