Strain identifier

BacDive ID: 13906

Type strain: Yes

Species: Shinella fusca

Strain Designation: DC-196

Strain history: <- C. M. Manaia, Escola Superior de Biotecnol., Univ. Católica Portuguesa, Porto, Portugal <- I. Vaz-Moreira et al.; DC.196

NCBI tax ID(s): 544480 (species)

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General

@ref: 15612

BacDive-ID: 13906

DSM-Number: 21319

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Shinella fusca DC-196 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Domestic wastes compost.

NCBI tax id

  • NCBI tax id: 544480
  • Matching level: species

strain history

  • @ref: 15612
  • history: <- C. M. Manaia, Escola Superior de Biotecnol., Univ. Católica Portuguesa, Porto, Portugal <- I. Vaz-Moreira et al.; DC.196

doi: 10.13145/bacdive13906.20230509.8.1

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 fusca
  • full scientific name: Shinella fusca Vaz-Moreira et al. 2010

@ref: 15612

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Shinella

species: Shinella fusca

full scientific name: Shinella fusca Vaz-Moreira et al. 2010

strain designation: DC-196

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29251negative1.19 µm0.45 µmrod-shapedyes
69480yes91.521
69480negative99.986

pigmentation

  • @ref: 29251
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15612
  • name: PLATE COUNT AGAR (DSMZ Medium 464)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/464
  • composition: Name: PLATE COUNT AGAR (DSMZ Medium 464) Composition: Agar 15.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Dextrose 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15612positivegrowth28mesophilic
29251positivegrowth10-40

culture pH

  • @ref: 29251
  • ability: positive
  • type: growth
  • pH: 06-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 29251
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

  • @ref: 29251
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2925117128adipate+carbon source
2925115963ribitol+carbon source
2925122599arabinose+carbon source
2925118403L-arabitol+carbon source
2925117057cellobiose+carbon source
2925116947citrate+carbon source
2925133984fucose+carbon source
2925128260galactose+carbon source
2925117234glucose+carbon source
2925117754glycerol+carbon source
2925117306maltose+carbon source
2925129864mannitol+carbon source
2925137684mannose+carbon source
29251506227N-acetylglucosamine+carbon source
2925126546rhamnose+carbon source
2925133942ribose+carbon source
2925117992sucrose+carbon source
2925127082trehalose+carbon source
2925117151xylitol+carbon source
2925118222xylose+carbon source
292514853esculin+hydrolysis
2925117632nitrate+reduction

enzymes

@refvalueactivityec
29251acid phosphatase+3.1.3.2
29251alkaline phosphatase+3.1.3.1
29251catalase+1.11.1.6
29251cytochrome oxidase+1.9.3.1
29251urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15612Domestic wastes compostPortoPortugalPRTEurope
60744Domestic wastes compostPortoPortugalPRTEurope2005

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Waste#Domestic waste

taxonmaps

  • @ref: 69479
  • File name: preview.99_31811.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1474;97_1759;98_23614;99_31811&stattab=map
  • Last taxonomy: Shinella
  • 16S sequence: FM177879
  • Sequence Identity:
  • Total samples: 104
  • soil counts: 30
  • aquatic counts: 53
  • animal counts: 14
  • plant counts: 7

Safety information

risk assessment

  • @ref: 15612
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15612
  • description: Shinella fusca partial 16S rRNA gene, type strain DC-196T
  • accession: FM177879
  • length: 1437
  • database: ena
  • NCBI tax ID: 544480

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shinella fusca DSM 21319GCA_014203155scaffoldncbi544480
66792Shinella fusca strain DSM 21319544480.7wgspatric544480
66792Shinella fusca DSM 213192861721846draftimg544480

GC content

@refGC-contentmethod
1561266.2high performance liquid chromatography (HPLC)
2925166

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno70.905no
gram-positiveno98.371no
anaerobicno95.957yes
aerobicyes87.824no
halophileno88.702no
spore-formingno94.929no
glucose-utilyes94.8yes
thermophileno99.022yes
motileyes87.639yes
glucose-fermentno89.298no

External links

@ref: 15612

culture collection no.: DSM 21319, CCUG 55808, LMG 24714

straininfo link

  • @ref: 83081
  • straininfo: 366460

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648331Shinella fusca sp. nov., isolated from domestic waste compost.Vaz-Moreira I, Faria C, Lopes AR, Svensson LA, Moore ERB, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.009498-02009Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/*isolation & purification/metabolism, Sewage/*microbiologyMetabolism
Phylogeny20870886Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant.Lee M, Woo SG, Ten LNInt J Syst Evol Microbiol10.1099/ijs.0.026435-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Nitrates/*metabolism, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny27393556Shinella curvata sp. nov., isolated from hydrocarbon-contaminated desert sands.Subhash Y, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0012902016Bacterial 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 PollutantsTranscriptome
Phylogeny29949500Shinella pollutisoli sp. nov., isolated from tetrabromobisphenol A-contaminated soil.Mu Y, Jia WB, Ke Z, Zhuang W, Wang HM, Jiang JD, Chen K, Chen QInt J Syst Evol Microbiol10.1099/ijsem.0.0028832018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Polybrominated Biphenyls, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15612Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21319)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21319
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29251Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2567128776041
60744Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55808)https://www.ccug.se/strain?id=55808
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83081Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID366460.1StrainInfo: A central database for resolving microbial strain identifiers