Strain identifier

BacDive ID: 158573

Type strain: Yes

Species: Oceanibaculum nanhaiense

Strain Designation: L54-1-50

Strain history: <- Zongze Shao and Qiliang Lai, The Third istitute Oceanic Administration(SOA)

NCBI tax ID(s): 1909734 (species)

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General

@ref: 65276

BacDive-ID: 158573

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

description: Oceanibaculum nanhaiense L54-1-50 is an aerobe, Gram-negative, motile bacterium that was isolated from From sediment sample.

NCBI tax id

  • NCBI tax id: 1909734
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zongze Shao and Qiliang Lai, The Third istitute Oceanic Administration(SOA)

doi: 10.13145/bacdive158573.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Thalassobaculaceae
  • genus: Oceanibaculum
  • species: Oceanibaculum nanhaiense
  • full scientific name: Oceanibaculum nanhaiense Du et al. 2017

@ref: 65276

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodospirillales

family: Rhodospirillaceae

genus: Oceanibaculum

species: Oceanibaculum nanhaiense

strain designation: L54-1-50

type strain: yes

Morphology

cell morphology

  • @ref: 65276
  • gram stain: negative
  • cell length: 1.5-2.5 µm
  • cell width: 0.8-1 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 65276
  • colony size: 1 mm
  • colony color: grey
  • incubation period: 4 days
  • medium used: MA

Culture and growth conditions

culture medium

  • @ref: 65276
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65276positivegrowth10-45
65276positiveoptimum25-37mesophilic
65276nogrowth4psychrophilic
65276nogrowth50thermophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
65276NaClpositivegrowth0-9 %(w/v)
65276NaClpositiveoptimum2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65276309162-oxoglutarate+respiration
65276286442-oxopentanoate+respiration
65276370543-hydroxybutyrate+respiration
6527630089acetate+respiration
6527617128adipate+assimilation
6527627613amygdalin-fermentation
6527622599arabinose-fermentation
6527629016arginine-hydrolysis
6527627689decanoate-carbon source
6527617634D-glucose-carbon source
6527616899D-mannitol-carbon source
6527616024D-mannose-carbon source
6527633801D-saccharate+respiration
652764853esculin-hydrolysis
6527617234glucose-fermentation
6527673804glycyl L-aspartic acid+respiration
6527617268myo-inositol-fermentation
6527630849L-arabinose-carbon source
6527629985L-glutamate+respiration
6527617203L-proline+respiration
6527624996lactate+respiration
6527625115malate+assimilation
6527617306maltose-carbon source
6527629864mannitol-fermentation
6527628053melibiose-fermentation
65276506227N-acetylglucosamine-carbon source
6527673784glycyl-l-glutamate+respiration
6527617632nitrate+reduction
6527618401phenylacetate-carbon source
6527632032potassium gluconate-carbon source
6527626546rhamnose-fermentation
6527653258sodium citrate-carbon source
6527630911sorbitol-fermentation
65276143136succinamate+respiration
6527630031succinate+respiration
6527617992sucrose-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6527615688acetoinyes
6527616136hydrogen sulfideno
6527635581indoleno

metabolite tests

  • @ref: 65276
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
65276catalase+1.11.1.6
65276cytochrome oxidase+1.9.3.1
65276alkaline phosphatase+3.1.3.1
65276valine aminopeptidase+
65276acid phosphatase+3.1.3.2
65276gelatinase+
65276esterase (C 4)+
65276cystine aminopeptidase+3.4.11.3
65276lipase (C 14)-
65276alpha-galactosidase-3.2.1.22
65276beta-glucuronidase-3.2.1.31
65276beta-glucosidase-3.2.1.21
65276alpha-mannosidase-3.2.1.24
65276alpha-fucosidase-3.2.1.51
65276esterase Lipase (C 8)-
65276leucine aminopeptidase-3.4.1.1
65276naphthol-AS-BI-phosphohydrolase-
65276trypsin-3.4.21.4
65276alpha-chymotrypsin-3.4.21.1
65276alpha-glucosidase-3.2.1.20
65276N-acetyl-beta-glucosaminidase-3.2.1.52
65276arginine dihydrolase-3.5.3.6
65276lysine decarboxylase-4.1.1.18
65276ornithine decarboxylase-4.1.1.17
65276tryptophan deaminase-4.1.99.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    65276C14:01
    65276C16:08.3
    65276C18:03
    65276C11:0 iso0.5
    65276C15:1 iso G0.8
    65276C8:0 3OH0.6
    65276C11:0 3OH0.5
    65276C16:0 3OH2.6
    65276C18:0 3OH0.7
    65276C18:1 2OH7.4
    65276C16:1ω5c1.1
    65276C17:1ω7c0.8
    65276C18:1ω9c3.2
    65276cyclo C19:0ω8c4.2
    65276C18:1ω7c 11-methy0.8
    65276C14:0 3OH and/or C16:1 iso I2.4
    65276C16:1ω7c and/or C16:1ω6c3.6
    65276unknown 18.846 and/or C19:1ω6c0.519
    65276C18:1ω7c and/or C18:1ω6c55.3
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
67771From sediment samplethe South China SeaChinaCHNAsia
65276surface seawater samplesouth china seaChinaCHNAsia2016-1018.2666111marine agar 22161 week25The surface seawater was diluted and spread on marine agar 2216 medium. After 1 week aerobic incubation at 25°C, the colonies were picked out

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_40490.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_231;96_859;97_1004;98_1185;99_40490&stattab=map
  • Last taxonomy: Oceanibaculum nanhaiense
  • 16S sequence: KX870046
  • Sequence Identity:
  • Total samples: 534
  • soil counts: 146
  • aquatic counts: 352
  • animal counts: 21
  • plant counts: 15

Sequence information

16S sequences

  • @ref: 65276
  • description: 16S rRNA gene sequences
  • accession: KX870046
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oceanibaculum nanhaiense L54-1-50GCA_002148795contigncbi1909734
66792Oceanibaculum nanhaiense L54-1-502791354911draftimg1909734

GC content

  • @ref: 65276
  • GC-content: 65.1
  • method: genome sequence analysis

External links

@ref: 65276

culture collection no.: KCTC 52312, MCCC 1A05150

literature

  • topic: Phylogeny
  • Pubmed-ID: 29022547
  • title: Oceanibaculum nanhaiense sp. nov., isolated from surface seawater.
  • authors: Du Y, Liu X, Lai Q, Li W, Sun F, Shao Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002388
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65276Yaping Du, Xiupian Liu, Qiliang Lai, Weiwei Li, Fengqin Sun, Zongze ShaoOceanibaculum nanhaiense sp. nov., isolated from surface seawater10.1099/ijsem.0.002388IJSEM 67: 4842-4845 201729022547
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/