Strain identifier

BacDive ID: 133774

Type strain: Yes

Species: Sphingobacterium detergens

Strain Designation: 6.2S

NCBI tax ID(s): 1145106 (species)

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General

@ref: 30465

BacDive-ID: 133774

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

description: Sphingobacterium detergens 6.2S is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1145106
  • Matching level: species

doi: 10.13145/bacdive133774.20230509.8.1

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 detergens
  • full scientific name: Sphingobacterium detergens Marqués et al. 2012

@ref: 30465

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium detergens

strain designation: 6.2S

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30465negative2.15 µm0.9 µmrod-shapedno
69480no90.108
69480negative99.985

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30465positivegrowth15-37
30465positiveoptimum33.5mesophilic

culture pH

@refabilitytypepH
30465positivegrowth6-7.5
30465positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30465
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30465no
69481no100
69480no99.98

halophily

  • @ref: 30465
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3046522599arabinose+carbon source
3046517234glucose+carbon source
3046517754glycerol+carbon source
3046517306maltose+carbon source
3046537684mannose+carbon source
3046528053melibiose+carbon source
30465506227N-acetylglucosamine+carbon source
3046526546rhamnose+carbon source
304654853esculin+hydrolysis

enzymes

@refvalueactivityec
30465catalase+1.11.1.6
30465gelatinase+
30465cytochrome oxidase+1.9.3.1
30465urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 30465
  • sample type: soil

isolation source categories

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

Sequence information

16S sequences

  • @ref: 30465
  • description: Sphingobacterium detergens strain 6.2S 16S ribosomal RNA gene, partial sequence
  • accession: JN015213
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 1145106

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium detergens CECT 7938GCA_003610355scaffoldncbi1145106
66792Sphingobacterium detergens strain CECT 79381145106.3wgspatric1145106
66792Sphingobacterium detergens CECT 79382772190801draftimg1145106

GC content

  • @ref: 30465
  • GC-content: 40

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.573yes
flagellatedno96.649yes
gram-positiveno97.014yes
anaerobicno99.645yes
aerobicyes89.768yes
halophileno93.999no
spore-formingno94.51yes
glucose-utilyes88.892yes
thermophileno99.334yes
glucose-fermentno91.5no

External links

@ref: 30465

culture collection no.: CECT 7938, LMG 26465

straininfo link

  • @ref: 91592
  • straininfo: 377581

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22307508Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil.Marques AM, Burgos-Diaz C, Aranda FJ, Teruel JA, Manresa A, Ortiz A, Farfan MInt J Syst Evol Microbiol10.1099/ijs.0.036707-02012Azores, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Surface-Active Agents/*metabolismGenetics
Phylogeny23148100Sphingobacterium caeni sp. nov., isolated from activated sludge.Sun LN, Zhang J, Chen Q, He J, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.046987-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/analysisGenetics

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
30465Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172680028776041
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
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
91592Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID377581.1