Strain identifier

BacDive ID: 133656

Type strain: Yes

Species: Microbulbifer yueqingensis

Strain Designation: Y226

Strain history: D.-S. Zhang Y226.

NCBI tax ID(s): 658219 (species)

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General

@ref: 29975

BacDive-ID: 133656

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

description: Microbulbifer yueqingensis Y226 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 658219
  • Matching level: species

strain history

  • @ref: 67770
  • history: D.-S. Zhang Y226.

doi: 10.13145/bacdive133656.20230509.8.1

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 yueqingensis
  • full scientific name: Microbulbifer yueqingensis Zhang et al. 2012

@ref: 29975

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Cellvibrionales

family: Microbulbiferaceae

genus: Microbulbifer

species: Microbulbifer yueqingensis

strain designation: Y226

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29975negative2.5-5.0 µm0.3-0.5 µmrod-shapedno
69480negative99.998

pigmentation

  • @ref: 29975
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29975positivegrowth15-45
29975positiveoptimum30-37mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29975positivegrowth05-10alkaliphile
29975positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 29975
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
29975NaClpositivegrowth0-10 %
29975NaClpositiveoptimum2-3 %

observation

  • @ref: 67770
  • observation: quinones: Q-8, Q-7, Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2997530089acetate+carbon source
2997516449alanine+carbon source
2997529016arginine+carbon source
2997517057cellobiose+carbon source
2997517234glucose+carbon source
2997529987glutamate+carbon source
2997527570histidine+carbon source
2997525115malate+carbon source
2997537684mannose+carbon source
2997518257ornithine+carbon source
2997515361pyruvate+carbon source
2997530031succinate+carbon source
2997527082trehalose+carbon source
2997553426tween 80+carbon source
299754853esculin+hydrolysis
2997517632nitrate+reduction

enzymes

@refvalueactivityec
29975catalase+1.11.1.6
29975cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29975marine sediment
67770Marine sediment sample from Yueqing BayZhejiang ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_44440.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_1255;97_3475;98_30212;99_44440&stattab=map
  • Last taxonomy: Microbulbifer yueqingensis subclade
  • 16S sequence: GQ262813
  • Sequence Identity:
  • Total samples: 87
  • soil counts: 19
  • aquatic counts: 62
  • animal counts: 6

Sequence information

16S sequences

  • @ref: 29975
  • description: Microbulbifer yueqingensis strain Y226 16S ribosomal RNA gene, partial sequence
  • accession: GQ262813
  • length: 1498
  • database: nuccore
  • NCBI tax ID: 658219

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbulbifer yueqingensis strain CGMCC 1.10658658219.4wgspatric658219
66792Microbulbifer yueqingensis CGMCC 1.106582667528184draftimg658219
67770Microbulbifer yueqingensis CGMCC 1.10658GCA_900100355scaffoldncbi658219

GC content

@refGC-contentmethod
2997556.7
6777056.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.648yes
anaerobicno99.069no
halophileyes73.14no
spore-formingno97.726no
glucose-utilyes85.126yes
thermophileno97.773yes
flagellatedno94.354yes
motileno87.577yes
aerobicyes90.72yes
glucose-fermentno90.12no

External links

@ref: 29975

culture collection no.: CGMCC 1.10658, JCM 17212

literature

  • topic: Phylogeny
  • Pubmed-ID: 21478393
  • title: Microbulbifer marinus sp. nov. and Microbulbifer yueqingensis sp. nov., isolated from marine sediment.
  • authors: Zhang DS, Huo YY, Xu XW, Wu YH, Wang CS, Xu XF, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.027714-0
  • year: 2011
  • mesh: Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
  • topic2: Genetics

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
29975Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172634328776041
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/
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