Strain identifier

BacDive ID: 11335

Type strain: Yes

Species: Massilia niastensis

Strain Designation: 5516S-1

Strain history: CIP <- 2009, DSMZ <- S.-W. Kwon, KACC, Korea: strain 5516S-1

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

@ref: 15506

BacDive-ID: 11335

DSM-Number: 21313

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

description: Massilia niastensis 5516S-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from air sample.

NCBI tax id

NCBI tax idMatching level
1122215strain
544911species

strain history

@refhistory
15506<- S.-W. Kwon; 5516S-1 {2008}
121291CIP <- 2009, DSMZ <- S.-W. Kwon, KACC, Korea: strain 5516S-1

doi: 10.13145/bacdive11335.20230509.8.1

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 niastensis
  • full scientific name: Massilia niastensis Weon et al. 2009
  • synonyms

    • @ref: 20215
    • synonym: Telluria niastensis

@ref: 15506

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia niastensis

full scientific name: Massilia niastensis Weon et al. 2009

strain designation: 5516S-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29130negative2.75 µm0.7 µmrod-shapedyes
69480yes98.119
69480negative99.994
121291negativerod-shapedyes

pigmentation

  • @ref: 29130
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15506R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
33671MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
121291CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15506positivegrowth30mesophilic
29130positivegrowth05-40
29130positiveoptimum28mesophilic
33671positivegrowth30mesophilic

culture pH

@refabilitytypepH
29130positivegrowth06-08
29130positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29130
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.982

halophily

@refsaltgrowthtested relationconcentration
29130NaClpositivegrowth0-1 %
29130NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29130161933-hydroxybenzoate+carbon source
29130370543-hydroxybutyrate+carbon source
29130178794-hydroxybenzoate+carbon source
2913016449alanine+carbon source
2913022599arabinose+carbon source
2913017234glucose+carbon source
2913017240itaconate+carbon source
2913015792malonate+carbon source
2913017306maltose+carbon source
2913037684mannose+carbon source
29130506227N-acetylglucosamine+carbon source
2913026271proline+carbon source
2913026546rhamnose+carbon source
2913017814salicin+carbon source
291304853esculin+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
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12129117632nitrate-reduction
12129116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12129135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
29130acid phosphatase+3.1.3.2
29130alkaline phosphatase+3.1.3.1
29130catalase+1.11.1.6
29130cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121291oxidase+
121291catalase+1.11.1.6
121291urease-3.5.1.5
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
121291-+---+++-+----------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15506-----+++-++--+---++++
15506---------++--+---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
15506air sampleSuwon region (37°16'46" N, 126°59'10" E)Republic of KoreaKORAsia37.2794126.986
121291Environment, Air samplesSuwonRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
155061Risk group (German classification)
1212911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15506
  • description: Massilia niastensis strain 5516S-1 16S ribosomal RNA gene, partial sequence
  • accession: EU808005
  • length: 1394
  • database: ena
  • NCBI tax ID: 544911

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Massilia niastensis DSM 21313GCA_000382345scaffoldncbi1122215
66792Massilia niastensis DSM 213131122215.3wgspatric1122215
66792Massilia niastensis DSM 213132521172636draftimg1122215

GC content

@refGC-contentmethod
1550666.6high performance liquid chromatography (HPLC)
2913066.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.928no
flagellatedyes80.751no
gram-positiveno98.628yes
anaerobicno98.032yes
aerobicyes88.736yes
halophileno93.401yes
spore-formingno93.473no
thermophileno98.992yes
glucose-utilyes78.565no
glucose-fermentno90.553yes

External links

@ref: 15506

culture collection no.: DSM 21313, CIP 110038, KACC 12599

straininfo link

  • @ref: 80568
  • straininfo: 363416

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542125Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples.Weon HY, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SW, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.006908-02009*Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny22140160Massilia tieshanensis sp. nov., isolated from mining soil.Du Y, Yu X, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.034306-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysisGenetics
Phylogeny24810317Massilia kyonggiensis sp. nov., isolated from forest soil in Korea.Kim JJ Microbiol10.1007/s12275-014-4010-72014Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny26220552Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia.Singh H, Du J, Won K, Yang JE, Yin C, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0004772015Agriculture, Bacterial Typing Techniques, Base Composition, Brassica, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny26449383Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing.Feng GD, Yang SZ, Li HP, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0006702015Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Disulfides/metabolism, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tungsten, Ubiquinone/chemistryGenetics
Phylogeny27334790Massiliapinisoli sp. nov., isolated from forest soil.Altankhuu K, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0012492016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15506Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21313)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21313
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
29130Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2555628776041
33671Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7851
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
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
80568Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID363416.1StrainInfo: A central database for resolving microbial strain identifiers
121291Curators of the CIPCollection of Institut Pasteur (CIP 110038)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110038