Strain identifier

BacDive ID: 5639

Type strain: Yes

Species: Salegentibacter salegens

Strain history: CIP <- 1994, ACAM <- S.J. Dobson

NCBI tax ID(s): 143223 (species)

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General

@ref: 2161

BacDive-ID: 5639

DSM-Number: 5424

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Salegentibacter salegens DSM 5424 is a mesophilic, Gram-negative bacterium of the family Flavobacteriaceae.

NCBI tax id

  • NCBI tax id: 143223
  • Matching level: species

strain history

@refhistory
2161<- P.D. Franzmann <- S.J. Dobson <- R. Garric
122363CIP <- 1994, ACAM <- S.J. Dobson

doi: 10.13145/bacdive5639.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Salegentibacter
  • species: Salegentibacter salegens
  • full scientific name: Salegentibacter salegens (Dobson et al. 1993) McCammon and Bowman 2000

  • synonyms

    • @ref: 20215
    • synonym: Flavobacterium salegens

@ref: 2161

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Salegentibacter

species: Salegentibacter salegens

full scientific name: Salegentibacter salegens (Dobson et al. 1993) McCammon and Bowman 2000

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.983
122363negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2161BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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
34460Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122363CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2161positivegrowth28mesophilic
34460positivegrowth30mesophilic
51525positivegrowth30mesophilic
122363positivegrowth10-30
122363nogrowth5psychrophilic
122363nogrowth37mesophilic
122363nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
122363NaClnogrowth0 %
122363NaClnogrowth2 %
122363NaClnogrowth4 %
122363NaClnogrowth6 %
122363NaClnogrowth8 %
122363NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1223634853esculin+hydrolysis
12236317632nitrate+reduction
12236316301nitrite-reduction
122363132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 122363
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122363oxidase+
122363beta-galactosidase+3.2.1.23
122363alcohol dehydrogenase-1.1.1.1
122363gelatinase-
122363DNase+
122363catalase+1.11.1.6
122363lecithinase-
122363lysine decarboxylase-4.1.1.18
122363ornithine decarboxylase-4.1.1.17
122363tryptophan deaminase-
122363urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51525C15:02.915
    51525C16:00.716
    51525C15:0 2OH2.716.217
    51525C15:0 3OH1.216.504
    51525C15:0 ANTEISO7.214.711
    51525C15:0 ISO8.314.621
    51525C15:0 ISO 3OH216.135
    51525C15:1 ANTEISO A1.214.526
    51525C15:1 ISO G1114.441
    51525C15:1 ω6c2.214.856
    51525C16:0 3OH1.217.52
    51525C16:0 iso4.215.626
    51525C16:0 iso 3OH3.717.145
    51525C16:1 ISO H315.461
    51525C16:1 ω7c9.515.819
    51525C16:1 ω7c/C15:0 ISO 2OH6.715.85
    51525C17:0 2OH5.818.249
    51525C17:0 iso 3OH10.618.161
    51525C17:1 ω6c5.116.862
    51525C17:1 ω9c ANTEISO1.916.525
    51525C17:1 ω9c ISO3.516.416
    51525Unidentified3.515.947
    51525unknown 13.566113.566
    51525unknown 16.580116.58
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122363---++-------------+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentgeographic locationsample type
34460AntarcticaATAAntarctica
51525AntarcticaATAAustralia and OceaniaVestfold Hills
122363AntarcticaATAAntarcticaEnvironment, Organic lake

taxonmaps

  • @ref: 69479
  • File name: preview.99_419.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_114;97_121;98_135;99_419&stattab=map
  • Last taxonomy: Salegentibacter salegens
  • 16S sequence: M92279
  • Sequence Identity:
  • Total samples: 755
  • soil counts: 55
  • aquatic counts: 646
  • animal counts: 43
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
21611Risk group (German classification)
1223631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Flavobacterium salegens 16S ribosomal RNA gene
  • accession: M92279
  • length: 1471
  • database: ena
  • NCBI tax ID: 143223

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salegentibacter salegens DSM 5424GCA_003001895scaffoldncbi143223
66792Salegentibacter salegens strain DSM 5424143223.5wgspatric143223
66792Salegentibacter salegens DSM 54242593339299draftimg143223

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.418no
gram-positiveno98.42no
anaerobicno99.242no
aerobicyes89.037no
halophileyes68.761no
spore-formingno94.679no
glucose-utilyes89.65no
thermophileno98.945yes
motileno88.862no
glucose-fermentno88.909no

External links

@ref: 2161

culture collection no.: DSM 5424, ACAM 48, ATCC 51522, CCUG 33447, LMG 13193, CIP 104041

straininfo link

  • @ref: 75122
  • straininfo: 7702

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7678983Direct sequencing of the polymerase chain reaction-amplified 16S rRNA gene of Flavobacterium gondwanense sp. nov. and Flavobacterium salegens sp. nov., two new species from a hypersaline Antarctic lake.Dobson SJ, Colwell RR, McMeekin TA, Franzmann PDInt J Syst Bacteriol10.1099/00207713-43-1-771993Antarctic Regions, Bacterial Typing Techniques, Base Sequence, Flavobacterium/*classification/*genetics, *Genes, Bacterial, Molecular Sequence Data, Phylogeny, *Polymerase Chain Reaction/methods, RNA, Bacterial/*analysis, RNA, Ribosomal, 16S/*analysis/genetics, Sequence Analysis, Sodium Chloride, *Water MicrobiologyGenetics
Phylogeny15280277Salegentibacter holothuriorum sp. nov., isolated from the edible holothurian Apostichopus japonicus.Nedashkovskaya OI, Suzuki M, Vancanneyt M, Cleenwerck I, Zhukova NV, Vysotskii MV, Mikhailov VV, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02987-02004Aerobiosis, Animals, Catalase/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Oxidoreductases/metabolism, Pacific Ocean, Phenazines, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sea Cucumbers/*microbiology, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Staining and Labeling, Water Microbiology, beta-Galactosidase/metabolismMetabolism
Phylogeny15653880Salegentibacter mishustinae sp. nov., isolated from the sea urchin Strongylocentrotus intermedius.Nedashkovskaya OI, Kim SB, Lysenko AM, Mikhailov VV, Bae KS, Kim ISInt J Syst Evol Microbiol10.1099/ijs.0.63297-02005Animals, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2161Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5424)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5424
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
34460Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15905
51525Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33447)https://www.ccug.se/strain?id=33447
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)
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
75122Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7702.1StrainInfo: A central database for resolving microbial strain identifiers
122363Curators of the CIPCollection of Institut Pasteur (CIP 104041)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104041