Strain identifier

BacDive ID: 134347

Type strain: Yes

Species: Sphingobacterium siyangense

Strain Designation: SY1

Strain history: H. Liu SY1.

NCBI tax ID(s): 459529 (species)

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General

@ref: 32563

BacDive-ID: 134347

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

description: Sphingobacterium siyangense SY1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 459529
  • Matching level: species

strain history

  • @ref: 67770
  • history: H. Liu SY1.

doi: 10.13145/bacdive134347.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium siyangense
  • full scientific name: Sphingobacterium siyangense Liu et al. 2008

@ref: 32563

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium siyangense

strain designation: SY1

type strain: yes

Morphology

cell morphology

  • @ref: 32563
  • gram stain: negative
  • cell length: 1.25 µm
  • cell width: 0.8 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 32563
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32563positivegrowth04-42
32563positiveoptimum33.5mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32563positivegrowth03-10alkaliphile
32563positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32563
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32563
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32563NaClpositivegrowth0-4 %
32563NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3256315963ribitol+carbon source
3256322599arabinose+carbon source
3256318403L-arabitol+carbon source
3256317057cellobiose+carbon source
3256323652dextrin+carbon source
3256328757fructose+carbon source
3256328260galactose+carbon source
3256324265gluconate+carbon source
3256317234glucose+carbon source
3256317754glycerol+carbon source
3256317716lactose+carbon source
3256317306maltose+carbon source
3256329864mannitol+carbon source
3256337684mannose+carbon source
3256328053melibiose+carbon source
32563506227N-acetylglucosamine+carbon source
3256316634raffinose+carbon source
3256326546rhamnose+carbon source
3256333942ribose+carbon source
3256317814salicin+carbon source
3256330911sorbitol+carbon source
3256317992sucrose+carbon source
3256327082trehalose+carbon source
3256317151xylitol+carbon source
3256318222xylose+carbon source
325634853esculin+hydrolysis
3256317632nitrate+reduction

enzymes

@refvalueactivityec
32563catalase+1.11.1.6
32563cytochrome oxidase+1.9.3.1
32563urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
32563soil
67770Farm soil sampleJiangsu ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_39368.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_911;97_1061;98_3597;99_39368&stattab=map
  • Last taxonomy: Sphingobacterium
  • 16S sequence: EU046272
  • Sequence Identity:
  • Total samples: 715
  • soil counts: 44
  • aquatic counts: 94
  • animal counts: 98
  • plant counts: 479

Sequence information

16S sequences

  • @ref: 32563
  • description: Sphingobacterium siyangense strain SY1 16S ribosomal RNA gene, partial sequence
  • accession: EU046272
  • length: 1489
  • database: nuccore
  • NCBI tax ID: 459529

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium siyangense CGMCC 1.6855GCA_007830445scaffoldncbi459529
66792Sphingobacterium siyangense strain CGMCC 1.6855459529.5wgspatric459529
66792Sphingobacterium siyangensis CGMCC 1.68552596583573draftimg459529

GC content

@refGC-contentmethod
3256338.5
6777038.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.106no
flagellatedno95.696yes
gram-positiveno97.389yes
anaerobicno99.238yes
aerobicyes87.3yes
halophileno92.903yes
spore-formingno94.661yes
thermophileno99.705no
glucose-utilyes89.118yes
glucose-fermentno87.788no

External links

@ref: 32563

culture collection no.: KCTC 22131, CGMCC 1.6855, JCM 14866

literature

  • topic: Phylogeny
  • Pubmed-ID: 18523194
  • title: Sphingobacterium siyangense sp. nov., isolated from farm soil.
  • authors: Liu R, Liu H, Zhang CX, Yang SY, Liu XH, Zhang KY, Lai R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65696-0
  • year: 2008
  • mesh: *Agriculture, Bacterial Typing Techniques, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Sphingobacterium/*classification/genetics/*isolation & purification/physiology
  • 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
32563Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877928776041
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/