Strain identifier

BacDive ID: 133474

Type strain: Yes

Species: Microbulbifer variabilis

Strain Designation: Ni-2088

NCBI tax ID(s): 1279017 (strain), 266805 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 29108

BacDive-ID: 133474

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

description: Microbulbifer variabilis Ni-2088 is an aerobe, Gram-negative, ovoid-shaped bacterium that was isolated from marine algae.

NCBI tax id

NCBI tax idMatching level
266805species
1279017strain

doi: 10.13145/bacdive133474.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Microbulbiferaceae
  • genus: Microbulbifer
  • species: Microbulbifer variabilis
  • full scientific name: Microbulbifer variabilis Nishijima et al. 2009

@ref: 29108

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cellvibrionales

family: Microbulbiferaceae

genus: Microbulbifer

species: Microbulbifer variabilis

strain designation: Ni-2088

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29108negative0.85 µm0.6 µmovoid-shapedno
69480negative99.661

pigmentation

  • @ref: 29108
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29108positivegrowth12-42
29108positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
29108positivegrowth6.0-9.0alkaliphile
29108positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 29108
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29108no
69481no100
69480no99.6

halophily

@refsaltgrowthtested relationconcentration
29108NaClpositivegrowth0.5-7 %
29108NaClpositiveoptimum2 %

observation

  • @ref: 29108
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2910817306maltose+carbon source
2910837684mannose+carbon source
2910853426tween 80+carbon source
291084853esculin+hydrolysis
2910817632nitrate+reduction

enzymes

@refvalueactivityec
29108acid phosphatase+3.1.3.2
29108alkaline phosphatase+3.1.3.1
29108catalase+1.11.1.6
29108cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 29108
  • sample type: marine algae

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_5878.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_1073;97_3457;98_4371;99_5878&stattab=map
  • Last taxonomy: Microbulbifer
  • 16S sequence: AB167354
  • Sequence Identity:
  • Total samples: 434
  • soil counts: 25
  • aquatic counts: 389
  • animal counts: 19
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 29108
  • description: Microbulbifer variabilis gene for 16S rRNA, partial sequence
  • accession: AB167354
  • length: 1492
  • database: nuccore
  • NCBI tax ID: 266805

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbulbifer variabilis ATCC 700307GCA_000380565contigncbi1279017
66792Microbulbifer variabilis ATCC 7003071279017.3wgspatric1279017
66792Microbulbifer variabilis ATCC 7003072519899636draftimg1279017

GC content

  • @ref: 29108
  • GC-content: 48.75

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.128yes
gram-positiveno98.454no
anaerobicno98.898no
aerobicyes89.233no
halophileyes65.932no
spore-formingno94.94yes
thermophileno98.746yes
glucose-utilyes89.974no
flagellatedno90.339no
glucose-fermentno87.019no

External links

@ref: 29108

culture collection no.: MBIC 01082, ATCC 700307

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542114Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod-coccus cell cycle in association with the growth phase.Nishijima M, Takadera T, Imamura N, Kasai H, An KD, Adachi K, Nagao T, Sano H, Yamasato KInt J Syst Evol Microbiol10.1099/ijs.0.006452-02009Alteromonadaceae/*classification/genetics/growth & development/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Eukaryota/classification/*microbiology, Fatty Acids/analysis, Genes, rRNA, Genotype, Japan, *Marine Biology, Molecular Sequence Data, Pacific Ocean, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny27959777Microbulbifer echini sp. nov., isolated from the gastrointestinal tract of a purple sea urchin, Heliocidaris crassispina.Lee JY, Kim PS, Hyun DW, Kim HS, Shin NR, Jung MJ, Yun JH, Kim MS, Whon TW, Bae JWInt J Syst Evol Microbiol10.1099/ijsem.0.0017312017Alteromonadaceae/*classification/genetics/isolation & purification, Animals, Anthocidaris/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny35945400Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk Sea.Romanenko L, Kurilenko V, Otstavnykh N, Velansky P, Isaeva M, Mikhailov VArch Microbiol10.1007/s00203-022-03161-92022*Alteromonadaceae/genetics, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Geologic Sediments/microbiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

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
29108Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172553628776041
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
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