Strain identifier

BacDive ID: 18154

Type strain: Yes

Species: Solimonas flava

Strain Designation: CW-KD 4

Strain history: <- Y Zhou, Nanjing Agricultiral Univ, China

NCBI tax ID(s): 1123257 (strain), 415849 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7812

BacDive-ID: 18154

DSM-Number: 18980

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

description: Solimonas flava CW-KD 4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface layer of a polluted farmland soil.

NCBI tax id

NCBI tax idMatching level
1123257strain
415849species

strain history

@refhistory
7812<- Y. Zhou, Nanjing Agric. Univ., China; CW-KD 4 <- Y. Zhou and R. Lai
67771<- Y Zhou, Nanjing Agricultiral Univ, China

doi: 10.13145/bacdive18154.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Nevskiales
  • family: Nevskiaceae
  • genus: Solimonas
  • species: Solimonas flava
  • full scientific name: Solimonas flava (Zhou et al. 2008) Sheu et al. 2011

  • synonyms

    • @ref: 20215
    • synonym: Sinobacter flavus

@ref: 7812

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Nevskiaceae

genus: Solimonas

species: Solimonas flava

full scientific name: Solimonas flava (Zhou et al. 2008) Sheu et al. 2011

strain designation: CW-KD 4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32277negative2.6 µm0.45 µmrod-shapedno
67771negative
69480negative99.987

pigmentation

  • @ref: 32277
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7812
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7812positivegrowth28mesophilic
32277positivegrowth10-35
32277positiveoptimum27.5mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
32277positivegrowth05-08
32277positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32277aerobe
67771aerobe

spore formation

@refspore formationconfidence
32277no
69481no100
69480no99.985

halophily

  • @ref: 32277
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3227717057cellobiose+carbon source
322775417glucosamine+carbon source
3227717234glucose+carbon source
32277506227N-acetylglucosamine+carbon source
3227733942ribose+carbon source
3227717992sucrose+carbon source

enzymes

@refvalueactivityec
32277cytochrome oxidase+1.9.3.1
32277urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7812surface layer of a polluted farmland soilJiangsu Province, NanjingChinaCHNAsia
67771From soilJiangsu ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4429.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_146;96_1648;97_1972;98_3329;99_4429&stattab=map
  • Last taxonomy: Solimonas
  • 16S sequence: EF154515
  • Sequence Identity:
  • Total samples: 1541
  • soil counts: 394
  • aquatic counts: 617
  • animal counts: 324
  • plant counts: 206

Safety information

risk assessment

  • @ref: 7812
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7812
  • description: Solimonas flava DSM 18980 strain CW-KD 4 16S ribosomal RNA gene, partial sequence
  • accession: EF154515
  • length: 1487
  • database: ena
  • NCBI tax ID: 1123257

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solimonas flava DSM 18980GCA_000426685scaffoldncbi1123257
66792Sinobacter flavus DSM 189801123257.3wgspatric1123257
66792Solimonas flava DSM 189802526164694draftimg1123257

GC content

  • @ref: 32277
  • GC-content: 65.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes75.375yes
flagellatedno72no
gram-positiveno98.793no
anaerobicno99.298yes
aerobicyes91.099yes
halophileno93.46no
spore-formingno95.601yes
glucose-utilyes87.7yes
thermophileno96.418yes
glucose-fermentno92.732no

External links

@ref: 7812

culture collection no.: DSM 18980, CCTCC AB 206145, KCTC 12881

straininfo link

  • @ref: 87138
  • straininfo: 402783

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175707Description of Sinobacter flavus gen. nov., sp. nov., and proposal of Sinobacteraceae fam. nov.Zhou Y, Zhang YQ, Zhi XY, Wang X, Dong J, Chen Y, Lai R, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.65244-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil PollutantsGenetics
Phylogeny20971835Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli.Sheu SY, Cho NT, Arun AB, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.023010-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Flagella/physiology, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Taiwan, TemperatureGenetics
Phylogeny22407788Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008.Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ERB, Lawson PAInt J Syst Evol Microbiol10.1099/ijs.0.037127-02012Arkansas, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny24421276Solimonas terrae sp. nov., isolated from soil.Kim SJ, Moon JY, Weon HY, Ahn JH, Chen WM, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.055574-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny30016233Solimonas fluminis sp. nov., isolated from a freshwater river.Lee Y, Lee B, Lee K, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0028652018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7812Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18980)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18980
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
32277Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2851728776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
87138Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402783.1StrainInfo: A central database for resolving microbial strain identifiers