Strain identifier

BacDive ID: 133925

Type strain: Yes

Species: Idiomarina indica

Strain Designation: SW104

Strain history: L. Song SW104.

NCBI tax ID(s): 1159017 (species)

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General

@ref: 30884

BacDive-ID: 133925

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Idiomarina indica SW104 is an aerobe, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 1159017
  • Matching level: species

strain history

  • @ref: 67770
  • history: L. Song SW104.

doi: 10.13145/bacdive133925.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Idiomarinaceae
  • genus: Idiomarina
  • species: Idiomarina indica
  • full scientific name: Idiomarina indica Song et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Pseudidiomarina indica

@ref: 30884

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Idiomarina

species: Idiomarina indica

strain designation: SW104

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30884negative4.75 µm0.45 µmrod-shapedyes
69480yes94.15
69480negative99.995

pigmentation

  • @ref: 30884
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30884positivegrowth12-50
30884positiveoptimum36mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
30884positivegrowth6.0-9.0alkaliphile
30884positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 30884
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30884no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
30884NaClpositivegrowth0.5-10 %
30884NaClpositiveoptimum2.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3088422599arabinose+carbon source
3088417234glucose+carbon source
3088429987glutamate+carbon source
3088417596inosine+carbon source
3088429864mannitol+carbon source
3088426271proline+carbon source
3088430911sorbitol+carbon source
3088417992sucrose+carbon source
3088417632nitrate+reduction

enzymes

@refvalueactivityec
30884acid phosphatase+3.1.3.2
30884alkaline phosphatase+3.1.3.1
30884catalase+1.11.1.6
30884cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample type
30884seawater
67770Seawater from the Indian Ocean

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_146614.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_197;96_17874;97_22031;98_97087;99_146614&stattab=map
  • Last taxonomy: Pseudidiomarina indica subclade
  • 16S sequence: JN867053
  • Sequence Identity:
  • Total samples: 777
  • soil counts: 104
  • aquatic counts: 146
  • animal counts: 467
  • plant counts: 60

Sequence information

16S sequences

  • @ref: 30884
  • description: Idiomarina indica strain SW104 16S ribosomal RNA gene, partial sequence
  • accession: JN867053
  • length: 1536
  • database: nuccore
  • NCBI tax ID: 1159017

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Idiomarina indica strain CGMCC 1.108241159017.3wgspatric1159017
66792Pseudidiomarina indica CGMCC 1.108242596583643draftimg1159017
67770Pseudidiomarina indica CGMCC 1.10824GCA_900104245scaffoldncbi1159017

GC content

  • @ref: 67770
  • GC-content: 49.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.271yes
gram-positiveno98.991yes
anaerobicno98.811yes
aerobicyes88.299no
halophileno61.961no
spore-formingno96.914yes
flagellatedno83.577no
thermophileno99.582no
glucose-utilyes70.035no
glucose-fermentno80.943no

External links

@ref: 30884

culture collection no.: CGMCC 1.10824, JCM 18138

literature

  • topic: Phylogeny
  • Pubmed-ID: 23223816
  • title: Idiomarina indica sp. nov., isolated from seawater.
  • authors: Song L, Ren F, Huang Y, Dai X, Zhou Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.046789-0
  • year: 2012
  • mesh: Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
30884Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172721428776041
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/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1