Strain identifier

BacDive ID: 133167

Type strain: Yes

Species: Shinella curvata

Strain Designation: C3

Strain history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; C3.

NCBI tax ID(s): 1817964 (species)

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General

@ref: 24941

BacDive-ID: 133167

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

description: Shinella curvata C3 is a chemoorganoheterotroph, Gram-negative, rod-shaped bacterium that was isolated from hydrocarbon-contaminated desert sands.

NCBI tax id

  • NCBI tax id: 1817964
  • Matching level: species

strain history

  • @ref: 67770
  • history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; C3.

doi: 10.13145/bacdive133167.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Shinella
  • species: Shinella curvata
  • full scientific name: Shinella curvata Subhash and Lee 2016

@ref: 24941

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Shinella

species: Shinella curvata

strain designation: C3

type strain: yes

Morphology

cell morphology

  • @ref: 24941
  • gram stain: negative
  • cell length: 1.9-2.8 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 24941
  • colony color: cream

Culture and growth conditions

culture temp

@refgrowthtypetemperature
24941positivegrowth4-45
24941positiveoptimum28-35
67770positivegrowth30

culture pH

@refabilitytypepHPH range
24941positivegrowth6.1-8.8alkaliphile
24941positiveoptimum6.9-7.7

Physiology and metabolism

nutrition type

  • @ref: 24941
  • type: chemoorganoheterotroph

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 99

halophily

@refsaltgrowthtested relationconcentration
24941NaClpositivemaximum3.5 %(w/v)
24941NaClpositivegrowth0.5 %(w/v)
24941NaClpositivegrowth0-3.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2494117057cellobiose-carbon source
2494117057cellobiose-builds acid from
2494117029chitin-hydrolysis
2494116991dna-hydrolysis
249414853esculin-hydrolysis
249415291gelatin-hydrolysis
2494117234glucose-fermentation
2494130849L-arabinose-carbon source
2494130849L-arabinose-builds acid from
2494162345L-rhamnose-carbon source
2494162345L-rhamnose-builds acid from
2494117306maltose-builds acid from
2494116634raffinose-carbon source
2494116634raffinose-builds acid from
2494127897tryptophan-energy source
2494153426tween 80-hydrolysis
2494116199urea-hydrolysis
2494131206ammonium chloride+nitrogen source
2494135391aspartate+carbon source
24941casein+hydrolysis
2494115824D-fructose+builds acid from
2494117634D-glucose+carbon source
2494117634D-glucose+builds acid from
2494116899D-mannitol+carbon source
2494116988D-ribose+carbon source
2494117924D-sorbitol+carbon source
2494128757fructose+carbon source
2494129987glutamate+carbon source
2494125115malate+carbon source
2494117306maltose+carbon source
2494128053melibiose+carbon source
2494128053melibiose+builds acid from
2494115361pyruvate+carbon source
2494128017starch+hydrolysis
2494117992sucrose+carbon source
2494153424tween 20+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
2494128971ampicillinyesyes
24941100147nalidixic acidyesyes
2494117698chloramphenicolyesyes
2494118208penicillin gyesyes
2494128077rifampicinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2494115688acetoinno
2494135581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
2494117234glucose-
2494115688acetoin-
2494135581indole-

enzymes

@refvalueactivityec
24941acid phosphatase+3.1.3.2
24941alkaline phosphatase+3.1.3.1
24941alpha-chymotrypsin-3.4.21.1
24941alpha-fucosidase+3.2.1.51
24941alpha-galactosidase-3.2.1.22
24941alpha-glucosidase-3.2.1.20
24941alpha-mannosidase-3.2.1.24
24941arginine decarboxylase-4.1.1.19
24941beta-galactosidase+3.2.1.23
24941beta-glucosidase+3.2.1.21
24941beta-glucuronidase-3.2.1.31
24941catalase+1.11.1.6
24941cystine arylamidase+3.4.11.3
24941cytochrome oxidase+1.9.3.1
24941esterase (C 4)+
24941esterase lipase (C 8)-
24941leucine arylamidase+3.4.11.1
24941lipase (C 14)-
24941lysine decarboxylase-4.1.1.18
24941N-acetyl-beta-glucosaminidase+3.2.1.52
24941naphthol-AS-BI-phosphohydrolase-
24941trypsin-3.4.21.4
24941tryptophan deaminase-4.1.99.1
24941valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
24941hydrocarbon-contaminated desert sandsKuwaitKWTAsia
67770Hydrocarbon-contaminated desert sands

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_2772.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1474;97_1759;98_2152;99_2772&stattab=map
  • Last taxonomy: Shinella
  • 16S sequence: LT545981
  • Sequence Identity:
  • Total samples: 2083
  • soil counts: 353
  • aquatic counts: 1019
  • animal counts: 568
  • plant counts: 143

Sequence information

16S sequences

  • @ref: 24941
  • description: Shinella sp. C3 partial 16S rRNA gene, strain C3
  • accession: LT545981
  • length: 1423
  • database: nuccore
  • NCBI tax ID: 1817964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shinella curvata strain JCM 312391817964.4wgspatric1817964
66792Shinella curvata JCM 312392891339218draftimg1817964
67770Shinella curvata JCM 31239GCA_010994455contigncbi1817964
66792Shinella curvata C3GCA_022899935scaffoldncbi1817964

GC content

  • @ref: 24941
  • GC-content: 65.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno99no
69480gram-positivegram-positivePositive reaction to Gram-stainingno83.627yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.805no
69480spore-formingspore-formingAbility to form endo- or exosporesno62.719no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes61.706no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.25yes
69480flagellatedmotile2+Ability to perform flagellated movementyes68.84no

External links

@ref: 24941

culture collection no.: KEMB 2255-446, JCM 31239

literature

  • topic: Phylogeny
  • Pubmed-ID: 27393556
  • title: Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands.
  • authors: Subhash Y, Lee SS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001290
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, *Hydrocarbons, Kuwait, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants
  • 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
24941Y. L. Subhash, Sang-SeobShinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands10.1099/ijsem.0.001290IJSEM 66: 3929-3934 201627393556
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