Strain identifier

BacDive ID: 11342

Type strain: Yes

Species: Massilia namucuonensis

Strain Designation: 333-1-0411

Strain history: <- Y. Li, Capital Normal University, College of Life Science, Beijing, China <- Y. Li and B. Kong

NCBI tax ID(s): 1035707 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 17922

BacDive-ID: 11342

DSM-Number: 25159

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

description: Massilia namucuonensis 333-1-0411 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1035707
  • Matching level: species

strain history

  • @ref: 17922
  • history: <- Y. Li, Capital Normal University, College of Life Science, Beijing, China <- Y. Li and B. Kong

doi: 10.13145/bacdive11342.20230509.8.1

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 namucuonensis
  • full scientific name: Massilia namucuonensis Kong et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella namucuonensis

@ref: 17922

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia namucuonensis

full scientific name: Massilia namucuonensis Kong et al. 2013

strain designation: 333-1-0411

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30584negative1 µm0.4 µmrod-shapedyes
69480yes95.371
69480negative99.998

colony morphology

  • @ref: 17922
  • incubation period: 2-3 days

pigmentation

  • @ref: 30584
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17922
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
17922positivegrowth30mesophilic
30584positivegrowth04-37
30584positiveoptimum29mesophilic

culture pH

@refabilitytypepHPH range
30584positivegrowth5.5-9.5alkaliphile
30584positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30584
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30584no
69481no100
69480no99.985

halophily

  • @ref: 30584
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3058422599arabinose+carbon source
3058424265gluconate+carbon source
3058417234glucose+carbon source
3058425115malate+carbon source
3058417306maltose+carbon source
3058429864mannitol+carbon source
3058437684mannose+carbon source
3058418401phenylacetate+carbon source
3058453258sodium citrate+carbon source
3058453424tween 20+carbon source
3058453426tween 80+carbon source
305844853esculin+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
17922catalase+1.11.1.6
17922cytochrome-c oxidase+1.9.3.1
30584acid phosphatase+3.1.3.2
30584alkaline phosphatase+3.1.3.1
30584catalase+1.11.1.6
30584gelatinase+
30584cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
17922-----+++------------

Isolation, sampling and environmental information

isolation

  • @ref: 17922
  • sample type: soil
  • geographic location: Tibet Autonomous Region, 25 m from the Namucuo Saltwater Lake (30° 46' 27'' N, 90° 52' 00'' E) at an altitude of 4598 m)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 30.7742
  • longitude: 90.8667

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 17922
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17922
  • description: Massilia namucuonensis strain 333-1-0411 16S ribosomal RNA gene, partial sequence
  • accession: JF799985
  • length: 1490
  • database: ena
  • NCBI tax ID: 1035707

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella namucuonensis CGMCC 1.11014GCA_900116645scaffoldncbi1035707
66792Massilia namucuonensis strain CGMCC 1.110141035707.5wgspatric1035707
66792Massilia namucuonensis CGMCC 1.110142671180040draftimg1035707

GC content

@refGC-contentmethod
1792266.7thermal denaturation, midpoint method (Tm)
3058466.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.053yes
flagellatedyes59.518no
gram-positiveno98.554yes
anaerobicno99.252yes
aerobicyes91.814yes
halophileno95.201yes
spore-formingno93.277no
glucose-fermentno89.617no
thermophileno98.735yes
glucose-utilyes90.348no

External links

@ref: 17922

culture collection no.: DSM 25159, CGMCC 1.11014

straininfo link

  • @ref: 80575
  • straininfo: 406384

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22447703Massilia namucuonensis sp. nov., isolated from a soil sample.Kong BH, Li YH, Liu M, Liu Y, Li CL, Liu L, Yang ZW, Yu RInt J Syst Evol Microbiol10.1099/ijs.0.039255-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Tibet, Ubiquinone/analysisGenetics
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
Phylogeny32601835Massilia aquatica sp. nov., Isolated from a Subtropical Stream in China.Lu HB, Deng TC, Xu MYCurr Microbiol10.1007/s00284-020-02104-12020Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, Nucleic Acid Hybridization, Oxalobacteraceae, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rivers, Sequence Analysis, DNA, *UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17922Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25159)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25159
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
30584Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2691528776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
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
80575Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406384.1StrainInfo: A central database for resolving microbial strain identifiers