Strain identifier

BacDive ID: 18153

Type strain: Yes

Species: Solimonas variicoloris

Strain Designation: MN28

Strain history: <- M. M. Friedrich and A. Lipski, University Osnabrueck; MN28

NCBI tax ID(s): 1123256 (strain), 254408 (species)

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General

@ref: 6088

BacDive-ID: 18153

DSM-Number: 15731

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

description: Solimonas variicoloris MN28 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hexane degrading biofilter.

NCBI tax id

NCBI tax idMatching level
1123256strain
254408species

strain history

  • @ref: 6088
  • history: <- M. M. Friedrich and A. Lipski, University Osnabrueck; MN28

doi: 10.13145/bacdive18153.20230509.8.1

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 variicoloris
  • full scientific name: Solimonas variicoloris (Friedrich and Lipski 2008) Sheu et al. 2011

  • synonyms

    @refsynonym
    20215Sinobacter variicoloris
    20215Singularimonas variicoloris

@ref: 6088

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Nevskiaceae

genus: Solimonas

species: Solimonas variicoloris

full scientific name: Solimonas variicoloris (Friedrich and Lipski 2008) Sheu et al. 2011

strain designation: MN28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
32452negative0.9 µm0.6 µmrod-shaped
69480negative99.998

colony morphology

  • @ref: 62482
  • incubation period: 2 days

pigmentation

  • @ref: 32452
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6088
  • name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/220
  • composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6088positivegrowth30mesophilic
32452positivegrowth23-37
32452positiveoptimum30mesophilic
62482positivegrowth30mesophilic

culture pH

@refabilitytypepH
32452positivegrowth7
32452positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32452aerobe
62482aerobe

spore formation

@refspore formationconfidence
32452no
69481no100
69480no99.997

observation

  • @ref: 32452
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3245217234glucose+carbon source
3245229987glutamate+carbon source
3245251850methyl pyruvate+carbon source
3245230031succinate+carbon source
3245226986threonine+carbon source
324524853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
32452catalase+1.11.1.6
32452gelatinase+
32452cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
62482-+---+----++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
62482-----+--+-----------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6088hexane degrading biofilterHammGermanyDEUEurope
62482Biofilter,industrialHammGermanyDEUEurope2007

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioremediation
  • Cat3: #Biofilter

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: AJ555478
  • Sequence Identity:
  • Total samples: 1541
  • soil counts: 394
  • aquatic counts: 617
  • animal counts: 324
  • plant counts: 206

Safety information

risk assessment

  • @ref: 6088
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6088
  • description: Gamma proteobacterium MN 28 partial 16S rRNA gene, strain MN 28
  • accession: AJ555478
  • length: 1487
  • database: ena
  • NCBI tax ID: 1123256

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solimonas variicoloris DSM 15731GCA_000382285scaffoldncbi1123256
66792Singularimonas variicoloris DSM 157311123256.3wgspatric1123256
66792Solimonas variicoloris DSM 157312521172650draftimg1123256

GC content

  • @ref: 6088
  • GC-content: 64.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes77.939no
flagellatedno66.07no
gram-positiveno98.9yes
anaerobicno99.089no
aerobicyes88.856yes
halophileno94.383no
spore-formingno95.781no
thermophileno92.342yes
glucose-utilyes86.569yes
glucose-fermentno93.418no

External links

@ref: 6088

culture collection no.: DSM 15731, LMG 22844, CCUG 60888

straininfo link

  • @ref: 87137
  • straininfo: 135576

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842850Alkanibacter difficilis gen. nov., sp. nov. and Singularimonas variicoloris gen. nov., sp. nov., hexane-degrading bacteria isolated from a hexane-treated biofilter.Friedrich MM, Lipski AInt J Syst Evol Microbiol10.1099/ijs.0.65517-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/*genetics/isolation & purification/metabolism, Genes, Bacterial, Genes, rRNA, Hexanes/*metabolism, Industrial Waste, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryMetabolism
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6088Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15731
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
32452Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2867428776041
62482Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60888)https://www.ccug.se/strain?id=60888
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)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
87137Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135576.1StrainInfo: A central database for resolving microbial strain identifiers