Strain identifier

BacDive ID: 1551

Type strain: Yes

Species: Salimicrobium flavidum

Strain Designation: ISL-25

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 570947 (species)

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General

@ref: 16720

BacDive-ID: 1551

DSM-Number: 23127

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-variable, motile

description: Salimicrobium flavidum ISL-25 is an aerobe, mesophilic, Gram-variable bacterium that was isolated from marine solar saltern sediment.

NCBI tax id

  • NCBI tax id: 570947
  • Matching level: species

strain history

@refhistory
16720<- KCTC <- J. H. Yoon, KRIBB; ISL-25
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive1551.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Salimicrobium
  • species: Salimicrobium flavidum
  • full scientific name: Salimicrobium flavidum Yoon et al. 2009

@ref: 16720

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Salimicrobium

species: Salimicrobium flavidum

full scientific name: Salimicrobium flavidum Yoon et al. 2009

strain designation: ISL-25

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilitycell shapeflagellum arrangementconfidence
29285variable4.9 µm0.85 µmyes
67771yesrod-shapedperitrichous
67771ovoid-shaped
67771positive
69480yes94.139
69480positive100

colony morphology

  • @ref: 61077
  • incubation period: 5 days

pigmentation

  • @ref: 29285
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16720
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 80.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16720positivegrowth35mesophilic
29285positivegrowth04-40
29285positiveoptimum33.5mesophilic
61077positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
29285positivegrowth06-08
29285positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
61077aerobe
67771aerobe

spore formation

@refspore formationconfidence
29285no
69481no96

halophily

@refsaltgrowthtested relationconcentration
29285NaClpositivegrowth01-26 %
29285NaClpositiveoptimum10 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2928528757fructose+carbon source
2928517234glucose+carbon source
2928529864mannitol+carbon source
2928537684mannose+carbon source
2928528053melibiose+carbon source
2928533942ribose+carbon source
2928517992sucrose+carbon source
2928527082trehalose+carbon source
2928553424tween 20+carbon source
2928553423tween 40+carbon source
2928553425tween 60+carbon source
2928553426tween 80+carbon source

enzymes

@refvalueactivityec
29285alkaline phosphatase+3.1.3.1
29285catalase+1.11.1.6
29285cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16720marine solar saltern sedimentYellow SeaRepublic of KoreaKORAsia
61077Marine solar saltern sedimentYellow SeaRepublic of KoreaKORAsia2006
67771From marine solar saltern of the Yellow SeaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_4220.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1295;97_1539;98_1873;99_4220&stattab=map
  • Last taxonomy: Salimicrobium flavidum
  • 16S sequence: FJ357160
  • Sequence Identity:
  • Total samples: 250
  • soil counts: 9
  • aquatic counts: 49
  • animal counts: 191
  • plant counts: 1

Safety information

risk assessment

  • @ref: 16720
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16720
  • description: Salimicrobium sp. ISL-25 16S ribosomal RNA gene, partial sequence
  • accession: FJ357160
  • length: 1524
  • database: ena
  • NCBI tax ID: 570947

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salimicrobium flavidum DSM 23127GCA_900156645scaffoldncbi570947
66792Salimicrobium flavidum strain DSM 23127570947.3wgspatric570947
66792Salimicrobium flavidum DSM 231272681813511draftimg570947

GC content

@refGC-contentmethod
1672049.3high performance liquid chromatography (HPLC)
2928549.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes87no
flagellatedyes82.073yes
gram-positiveyes92.984no
anaerobicno99.06no
aerobicyes91.847no
halophileyes93.831yes
spore-formingno55.185yes
thermophileno97.59yes
glucose-utilyes90.033no
glucose-fermentno79.939no

External links

@ref: 16720

culture collection no.: DSM 23127, CCUG 56755, KCTC 13260, ISL -25

straininfo link

  • @ref: 71196
  • straininfo: 403569

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19628596Salimicrobium flavidum sp. nov., isolated from a marine solar saltern.Yoon JH, Kang SJ, Oh KH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.010215-02009Bacillaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny21596507Salimicrobium salexigens sp. nov., a moderately halophilic bacterium from salted hides.de la Haba RR, Yilmaz P, Sanchez-Porro C, Birbir M, Ventosa ASyst Appl Microbiol10.1016/j.syapm.2011.04.0022011Animals, Animals, Domestic/microbiology, Australia, Bacillaceae/*classification/genetics, Base Sequence, DNA, Bacterial, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry/genetics, Skin/*microbiologyGenetics
Phylogeny25070217Salimicrobium jeotgali sp. nov., isolated from salted, fermented seafood.Choi EJ, Jin HM, Kim KH, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.062042-02014Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seafood/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Vitamin K 2/analogs & derivatives/chemistryBiotechnology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16720Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23127)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23127
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
29285Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2570128776041
61077Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56755)https://www.ccug.se/strain?id=56755
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
71196Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403569.1StrainInfo: A central database for resolving microbial strain identifiers