Strain identifier

BacDive ID: 3780

Type strain: Yes

Species: Dyadobacter alkalitolerans

Strain Designation: 12116

Strain history: <- NRRL <- C. Fang, College of Life Sciences, Univ. Wuhan; 12116

NCBI tax ID(s): 1121481 (strain), 492736 (species)

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General

@ref: 17299

BacDive-ID: 3780

DSM-Number: 23607

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

description: Dyadobacter alkalitolerans 12116 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from desert sand.

NCBI tax id

NCBI tax idMatching level
1121481strain
492736species

strain history

  • @ref: 17299
  • history: <- NRRL <- C. Fang, College of Life Sciences, Univ. Wuhan; 12116

doi: 10.13145/bacdive3780.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Dyadobacter
  • species: Dyadobacter alkalitolerans
  • full scientific name: Dyadobacter alkalitolerans Tang et al. 2009

@ref: 17299

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter alkalitolerans

full scientific name: Dyadobacter alkalitolerans Tang et al. 2009

strain designation: 12116

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
28911negativerod-shapedno
69480negative99.977
69480no96.234

pigmentation

  • @ref: 28911
  • production: yes

multimedia

  • @ref: 17299
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23607.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 17299
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17299positivegrowth28mesophilic
28911positivegrowth04-30
28911positiveoptimum21.5psychrophilic

culture pH

@refabilitytypepHPH range
28911positivegrowth05-12alkaliphile
28911positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 28911
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

  • @ref: 28911
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2891122599arabinose+carbon source
2891117057cellobiose+carbon source
2891128757fructose+carbon source
2891128260galactose+carbon source
2891117234glucose+carbon source
2891117716lactose+carbon source
2891117306maltose+carbon source
2891137684mannose+carbon source
2891128053melibiose+carbon source
28911506227N-acetylglucosamine+carbon source
2891116634raffinose+carbon source
2891133942ribose+carbon source
2891117814salicin+carbon source
2891117992sucrose+carbon source
2891127082trehalose+carbon source
2891118222xylose+carbon source
289114853esculin+hydrolysis
2891117632nitrate+reduction

enzymes

@refvalueactivityec
28911acid phosphatase+3.1.3.2
28911alkaline phosphatase+3.1.3.1
28911alpha-galactosidase+3.2.1.22
28911catalase+1.11.1.6
28911cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 17299
  • sample type: desert sand
  • geographic location: Xinjiang
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy
#Condition#Xerophilic

Safety information

risk assessment

  • @ref: 17299
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17299
  • description: Dyadobacter alkalitolerans strain 12116 16S ribosomal RNA gene, partial sequence
  • accession: EU360597
  • length: 1412
  • database: ena
  • NCBI tax ID: 492736

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter alkalitolerans DSM 23607GCA_000428845scaffoldncbi1121481
66792Dyadobacter alkalitolerans DSM 236071121481.4wgspatric1121481
66792Dyadobacter alkalitolerans DSM 236072524023163draftimg1121481

GC content

  • @ref: 28911
  • GC-content: 46.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.514yes
flagellatedno96.965yes
gram-positiveno96.968yes
anaerobicno99.558no
aerobicyes91.622yes
halophileno93.819no
spore-formingno94.86no
glucose-utilyes88.534yes
thermophileno99.273no
glucose-fermentno89.386no

External links

@ref: 17299

culture collection no.: DSM 23607, CCTCC AB 207176, NRRL B-51268

straininfo link

  • @ref: 73292
  • straininfo: 399351

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126724Dyadobacter alkalitolerans sp. nov., isolated from desert sand.Tang Y, Dai J, Zhang L, Mo Z, Wang Y, Li Y, Ji S, Fang C, Zheng CInt J Syst Evol Microbiol10.1099/ijs.0.001404-02009Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Desert Climate, Genes, rRNA, Genotype, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil MicrobiologyGenetics
Phylogeny19717578Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil.Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.017236-02009Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17299Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23607)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23607
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
28911Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2535028776041
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)
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
73292Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399351.1StrainInfo: A central database for resolving microbial strain identifiers