Strain identifier

BacDive ID: 133466

Type strain: Yes

Species: Pseudidiomarina tainanensis

Strain Designation: 908087

Strain history: X.-W. Xu 908087.

NCBI tax ID(s): 519453 (species)

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General

@ref: 29079

BacDive-ID: 133466

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

description: Pseudidiomarina tainanensis 908087 is an aerobe, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 519453
  • Matching level: species

strain history

  • @ref: 67770
  • history: X.-W. Xu 908087.

doi: 10.13145/bacdive133466.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Idiomarinaceae
  • genus: Pseudidiomarina
  • species: Pseudidiomarina tainanensis
  • full scientific name: Pseudidiomarina tainanensis Jean et al. 2009

  • synonyms

    @refsynonym
    20215Idiomarina tainanensis
    20215Pseudidiomarina maritima
    20215Idiomarina maritima

@ref: 29079

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Pseudidiomarina

species: Pseudidiomarina maritima

strain designation: 908087

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29079negative1.75 µm0.5 µmrod-shapedyes
125438negative98.744

pigmentation

  • @ref: 29079
  • production: no

Culture and growth conditions

culture temp

@refgrowthtypetemperature
29079positivegrowth10-45
29079positiveoptimum37
67770positivegrowth30

culture pH

@refabilitytypepHPH range
29079positivegrowth6.5-10.0alkaliphile
29079positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29079aerobe
125439obligate aerobe99.7

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 93.563

halophily

@refsaltgrowthtested relationconcentration
29079NaClpositivegrowth0.5-15 %
29079NaClpositiveoptimum3 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2907953424tween 20+carbon source
2907953426tween 80+carbon source

enzymes

@refvalueactivityec
29079catalase+1.11.1.6
29079cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
29079seawater
67770Coastal seawater sample collected from the East China SeaChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_26495.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_197;96_3743;97_4602;98_5910;99_26495&stattab=map
  • Last taxonomy: Pseudidiomarina
  • 16S sequence: EU600203
  • Sequence Identity:
  • Total samples: 522
  • soil counts: 13
  • aquatic counts: 337
  • animal counts: 168
  • plant counts: 4

Sequence information

16S sequences

  • @ref: 29079
  • description: Pseudidiomarina maritima strain 908087 16S ribosomal RNA gene, partial sequence
  • accession: EU600203
  • length: 1507
  • database: nuccore
  • NCBI tax ID: 519453

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Idiomarina maritima strain CGMCC 1.7285519453.3wgspatric519453
66792Idiomarina maritima CGMCC 1.72852617270903draftimg519453
67770Pseudidiomarina maritima CGMCC 1.7285GCA_900115255contigncbi519453

GC content

@refGC-contentmethod
2907945.2
6777045.2high performance liquid chromatography (HPLC)
6777047.4genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.744yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.606yes
125438spore-formingspore-formingAbility to form endo- or exosporesno93.563no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.014yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.475no
125438motile2+flagellatedAbility to perform flagellated movementno54.491no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno85.7
125439BacteriaNetmotilityAbility to perform movementyes65.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative80.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.7

External links

@ref: 29079

culture collection no.: CGMCC 1.7285, JCM 15534

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502309Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea.Wu YH, Shen YQ, Xu XW, Wang CS, Oren A, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.005702-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny23223816Idiomarina indica sp. nov., isolated from seawater.Song L, Ren F, Huang Y, Dai X, Zhou YInt J Syst Evol Microbiol10.1099/ijs.0.046789-02012Alteromonadaceae/*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/analysisGenetics
Phylogeny25078320Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea.Poddar A, Lepcha RT, Mukherjee D, Bhattacharyya D, Das SKRes Microbiol10.1016/j.resmic.2014.07.0082014Aerobiosis, Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny31486762Pseudidiomarina maritima Wu et al. 2009 is a later heterotypic synonym of Pseudidiomarina tainanensis Jean et al. 2009 and emended description of the species.Liu Y, Lai Q, Shao Z, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0036782019Alteromonadaceae/*classification/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny31697639Pseudidiomarina gelatinasegens sp. nov., isolated from surface sediment of the Terra Nova Bay, Antarctica.Li A, Zhang M, Xu S, Chen M, Yao Q, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0037602020Alteromonadaceae/*classification/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Bays, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
29079Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172550928776041
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
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG