Strain identifier

BacDive ID: 159874

Type strain: Yes

Species: Simplicispira suum

Strain Designation: SC1-8

NCBI tax ID(s): 2109915 (species)

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General

@ref: 66615

BacDive-ID: 159874

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

description: Simplicispira suum SC1-8 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from dust from a pig farm.

NCBI tax id

  • NCBI tax id: 2109915
  • Matching level: species

doi: 10.13145/bacdive159874.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Simplicispira
  • species: Simplicispira suum
  • full scientific name: Simplicispira suum Cho et al. 2018

@ref: 66615

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Simplicispira

species: Simplicispira suum

strain designation: SC1-8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
66615negative1.8-2.5 µm0.6-0.7 µmrod-shapedyesmonotrichous, polar
69480yes95.329
69480negative99.999

colony morphology

  • @ref: 66615
  • colony color: white-beige
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A medium

Culture and growth conditions

culture medium

  • @ref: 66615
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66615positiveoptimum28-30mesophilic
66615positivegrowth4-37

culture pH

@refabilitytypepHPH range
66615positiveoptimum7.0-8.0
66615positivegrowth7.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 66615
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.998
69481no100

halophily

@refsaltgrowthtested relationconcentrationhalophily level
66615NaClpositivegrowth0-2 %(w/v)
66615NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6661516024D-mannose-assimilation
66615161933-hydroxybenzoate-assimilation
66615167244-hydroxybutyrate-assimilation
6661516899D-mannitol-assimilation
6661516988D-ribose-assimilation
6661517115L-serine-assimilation
6661517240itaconate-assimilation
6661517268myo-inositol-assimilation
6661517306maltose-assimilation
6661517814salicin-assimilation
6661517924D-sorbitol-assimilation
6661517992sucrose-assimilation
6661518287L-fucose-assimilation
6661518401phenylacetate-assimilation
6661527689decanoate-assimilation
6661528053melibiose-assimilation
6661528087glycogen-assimilation
6661530849L-arabinose-assimilation
66615370543-hydroxybutyrate-assimilation
6661559640N-acetylglucosamine-assimilation
6661562345L-rhamnose-assimilation
66615potassium 2-dehydro-D-gluconate-assimilation
66615potassium 5-dehydro-D-gluconate-assimilation
666159300suberic acid+assimilation
6661515971L-histidine+assimilation
6661516977L-alanine+assimilation
6661517128adipate+assimilation
6661517203L-proline+assimilation
6661517272propionate+assimilation
6661517634D-glucose+assimilation
6661524996lactate+assimilation
6661525115malate+assimilation
6661531011valerate+assimilation
6661532032potassium gluconate+assimilation
6661532954sodium acetate+assimilation
6661553258sodium citrate+assimilation
6661562983sodium malonate+assimilation
6661517234glucose-fermentation
666155291gelatin-hydrolysis
6661515318xanthine-hydrolysis
6661516991dna-hydrolysis
6661528017starch-hydrolysis
6661585146carboxymethylcellulose-hydrolysis
66615casein-hydrolysis
666154853esculin+hydrolysis
6661517368hypoxanthine+hydrolysis
6661518186tyrosine+hydrolysis
6661553426tween 80+hydrolysis
6661517632nitrate+reduction

metabolite production

  • @ref: 66615
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66615acid phosphatase-3.1.3.2
66615alkaline phosphatase-3.1.3.1
66615alpha-chymotrypsin-3.4.21.1
66615alpha-fucosidase-3.2.1.51
66615alpha-galactosidase-3.2.1.22
66615alpha-glucosidase-3.2.1.20
66615alpha-mannosidase-3.2.1.24
66615arginine dihydrolase-3.5.3.6
66615beta-galactosidase-3.2.1.23
66615beta-glucosidase-3.2.1.21
66615beta-glucuronidase-3.2.1.31
66615cystine arylamidase-3.4.11.3
66615lipase (C 14)-
66615N-acetyl-beta-glucosaminidase-3.2.1.52
66615trypsin-3.4.21.4
66615valine arylamidase-
66615catalase+1.11.1.6
66615cytochrome oxidase+1.9.3.1
66615esterase (C 4)+
66615esterase Lipase (C 8)+
66615leucine arylamidase+3.4.11.1
66615naphthol-AS-BI-phosphohydrolase+
66615urease+/-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66615C14:0 2OH1
    66615C16:036
    66615C17:0 cyclo0.6
    66615Unknown ECL 18.846 / C19:1w6c / C19:0w10c cyclo0.7
    66615C17:02.2
    66615C10:0 3OH2.4
    66615C12:02.5
    66615C16:1 w6c / C16:1 w7c45.6
    66615C18:1 w6c / C18:1 w7c7.9
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation time: 1-3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 66615
  • sample type: dust from a pig farm
  • geographic location: Wanju-gun, Jeollabuk-do
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • enrichment culture: R2A
  • enrichment culture duration: 7 days
  • enrichment culture temperature: 28

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Dust
#Engineered#Agriculture#Livestock (Husbandry)
#Host#Mammals#Suidae (Pig,Swine)

Sequence information

16S sequences

  • @ref: 66615
  • description: Simplicispira sp. strain SC1-8 16S ribosomal RNA gene, partial sequence
  • accession: MH032763
  • length: 1523
  • database: ena
  • NCBI tax ID: 2109915

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Simplicispira suum SC1-8GCA_003008595completencbi2109915
66792Simplicispira sp. SC1-82109915.3completepatric2109915

GC content

  • @ref: 66615
  • GC-content: 63.30
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes63.05no
gram-positiveno98.217yes
anaerobicno96.534yes
halophileno92.737no
spore-formingno95.548no
glucose-utilno52.386yes
aerobicyes80.622yes
thermophileno97.411no
motileyes89.727yes
glucose-fermentno90.648yes

External links

@ref: 66615

culture collection no.: KACC 19329, NBRC 113111

literature

  • topic: Phylogeny
  • Pubmed-ID: 29939126
  • title: Simplicispira suum sp. nov., isolated from a dust collector at a pig farm.
  • authors: Cho HY, Heo J, Hong SB, Kim JS, Kwon SW, Kim SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002874
  • year: 2018
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, *Dust, *Farms, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Swine, 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
66615Ha-Young Cho, Jun Heo, Seung-Beom Hong, Jeong-Seon Kim, Soon-Wo Kwon and Soo-Jin KimSimplicispira suum sp. nov., isolated from a dust collector at a pig farm10.1099/ijsem.0.002874IJSEM 68: 2557-2561 201829939126
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