Strain identifier

BacDive ID: 140929

Type strain: Yes

Species: Massilia violacea

Strain Designation: CAVIO

NCBI tax ID(s): 1715466 (species)

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General

@ref: 43801

BacDive-ID: 140929

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Massilia violacea CAVIO is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from A soil sample collected from the riverbank of Zahuapan River at Las Cascadas de Atlihuetzia.

NCBI tax id

  • NCBI tax id: 1715466
  • Matching level: species

doi: 10.13145/bacdive140929.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Massilia
  • species: Massilia violacea
  • full scientific name: Massilia violacea Embarcadero-Jiménez et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella violacea

@ref: 43801

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia violacea

strain designation: CAVIO

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43801negative2-2.6 µm0.5-0.7 µmrod-shapedyespolar
69480yes97.499
69480negative100

colony morphology

  • @ref: 43801
  • colony size: 2-5 mm
  • colony color: Pale violet
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43801
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43801positivegrowth10-35
43801positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
43801positivegrowth5.8-9.2alkaliphile
43801positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 43801
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43801no
69481no99
69480no99.988

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43801NaClpositivegrowth0-1 %(w/v)
43801NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4380116899D-mannitol-assimilation
4380116024D-mannose-assimilation
4380132032potassium gluconate-assimilation
4380132735guanidinium chloride-growth
4380148607lithium chloride-growth
4380175273niaproof-growth
4380175248potassium tellurite-growth
4380175229sodium bromate-growth
4380164103sodium butyrate-growth
4380185146carboxymethylcellulose-hydrolysis
438014853esculin-hydrolysis
4380128017starch-hydrolysis
4380115588D-malate-respiration
43801167632-oxobutanoate-respiration
43801739183-O-methyl-D-glucose-respiration
43801181014-hydroxyphenylacetic acid-respiration
4380113705acetoacetate-respiration
43801645522-hydroxybutyrate-respiration
4380136219alpha-lactose-respiration
4380118333D-arabitol-respiration
4380115824D-fructose-respiration
4380128847D-fucose-respiration
4380115895D-galactonic acid lactone-respiration
4380112936D-galactose-respiration
4380118024D-galacturonic acid-respiration
438018391D-gluconate-respiration
4380115748D-glucuronate-respiration
4380116899D-mannitol-respiration
4380116024D-mannose-respiration
4380133801D-saccharate-respiration
4380116523D-serine-respiration
4380117924D-sorbitol-respiration
4380115740formate-respiration
4380116537galactarate-respiration
4380116865gamma-aminobutyric acid-respiration
438015291gelatin-respiration
4380128066gentiobiose-respiration
4380117754glycerol-respiration
4380116977L-alanine-respiration
4380116467L-arginine-respiration
4380118287L-fucose-respiration
4380118183L-pyroglutamic acid-respiration
4380162345L-rhamnose-respiration
4380117115L-serine-respiration
4380128053melibiose-respiration
4380174611methyl (R)-lactate-respiration
4380137657methyl D-glucoside-respiration
4380117268myo-inositol-respiration
4380163154N-acetyl-beta-D-mannosamine-respiration
43801506227N-acetylglucosamine-respiration
4380135418n-acetylneuraminate-respiration
4380117309pectin-respiration
4380126490quinate-respiration
4380116634raffinose-respiration
4380117814salicin-respiration
4380117164stachyose-respiration
4380117992sucrose-respiration
4380132528turanose-respiration
4380115589L-malate+assimilation
4380117634D-glucose+assimilation
4380153426tween 80+hydrolysis
4380116651(S)-lactate+respiration
43801309162-oxoglutarate+respiration
438018295beta-hydroxybutyrate+respiration
4380173706bromosuccinate+respiration
4380117057cellobiose+respiration
4380129990D-aspartate+respiration
4380178697D-fructose 6-phosphate+respiration
4380114314D-glucose 6-phosphate+respiration
4380123652dextrin+respiration
4380170744glycine-proline+respiration
4380129991L-aspartate+respiration
4380129985L-glutamate+respiration
4380115971L-histidine+respiration
4380117306maltose+respiration
4380151850methyl pyruvate+respiration
4380128037N-acetylgalactosamine+respiration
4380127082trehalose+respiration
4380153423tween 40+respiration
4380130089acetate+/-respiration
4380116947citrate+/-respiration
4380132323glucuronamide+/-respiration
4380117596inosine+/-respiration
4380117272propionate+/-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4380171321fusidateyesyes
4380145735troleandomycinyesyes
4380150694minocyclineyesyes
438016472lincomycinyesyes
4380128001vancomycinyesyes
43801100147nalidixic acidyesyes
4380128077rifampicinyesyes
43801161680aztreonamyesyes

enzymes

@refvalueactivityec
43801cytochrome oxidase+1.9.3.1
43801catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43801C10:0 3OH3.6
    43801C12:03.6
    43801C12:0 2OH2.1
    43801C16:032.3
    43801C16:1ω7c / C16:1ω6c42.9
    43801C17:0cyclo2.7
    43801C18:1ω7c / C18:1ω6c7.7
    43801C17:0 iso 3OH1.1
    43801C17:1 iso ω5c1.5
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar plates
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 1
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6.21
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43801
  • sample type: A soil sample collected from the riverbank of Zahuapan River at Las Cascadas de Atlihuetzia
  • geographic location: Tlaxcala
  • country: Mexico
  • origin.country: MEX
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 43801
  • description: 16S rRNA gene sequence
  • accession: KT003718
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella violacea CECT 8897GCA_014191875contigncbi1715466
66792Massilia violacea strain CECT 88971715466.3wgspatric1715466
66792Massilia violacea CECT 88972824303488draftimg1715466

GC content

  • @ref: 43801
  • GC-content: 65
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes90.351no
gram-positiveno98.295yes
anaerobicno98.008no
aerobicyes87.485yes
halophileno95.875no
spore-formingno92.515yes
glucose-utilyes81.705yes
flagellatedyes78.355no
thermophileno99.317yes
glucose-fermentno89.777no

External links

@ref: 43801

culture collection no.: CECT 8897, LMG 28941

straininfo link

  • @ref: 96814
  • straininfo: 396407

literature

  • topic: Phylogeny
  • Pubmed-ID: 26611862
  • title: Massilia violacea sp. nov., isolated from riverbank soil.
  • authors: Embarcadero-Jimenez S, Peix A, Igual JM, Rivera-Orduna FN, Tao Wang E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000776
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Mexico, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • 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
43801Salvador Embarcadero-Jiménez, Álvaro Peix, José Mariano Igual, Flor N. Rivera-Orduna, En Tao WangMassilia violacea sp. nov., isolated from riverbank soil10.1099/ijsem.0.000776IJSEM 66: 707-711 201626611862
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
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
96814Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID396407.1