Strain identifier

BacDive ID: 11328

Type strain: Yes

Species: Massilia dura

Strain Designation: 16

Strain history: CIP <- 2006, KCTC

NCBI tax ID(s): 321982 (species)

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General

@ref: 7033

BacDive-ID: 11328

DSM-Number: 17513

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

description: Massilia dura 16 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 321982
  • Matching level: species

strain history

@refhistory
7033<- W.-J. Li, Yunnan University, China
374742006, KCTC
67771<- W-J Li, Yunnan Int. Microbiol., China
118978CIP <- 2006, KCTC

doi: 10.13145/bacdive11328.20230509.8.1

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 dura
  • full scientific name: Massilia dura Zhang et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella dura

@ref: 7033

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia dura

full scientific name: Massilia dura Zhang et al. 2006

strain designation: 16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31701negative1.8-2.2 µm0.6-0.8 µmrod-shapedyes
67771negative
69480yes95.079
69480negative99.996
118978negativerod-shapedno

pigmentation

  • @ref: 31701
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7033R2A 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
37474MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
118978CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7033positivegrowth30mesophilic
31701positivegrowth10-45
31701positiveoptimum28-30mesophilic
37474positivegrowth30mesophilic
59466positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31701positivegrowth6.5-8.5alkaliphile
31701positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31701aerobe
59466aerobe
67771aerobe
118978facultative anaerobe

spore formation

@refspore formationconfidence
31701no
69481no100
69480no99.973

halophily

@refsaltgrowthtested relationconcentration
31701NaClpositivegrowth0-1 %
31701NaClpositiveoptimum0-1 %

observation

@refobservation
31701aggregates in chains
67771quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170117234glucose+carbon source
3170117992sucrose+carbon source
3170117632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11897817632nitrate-reduction
11897816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11897835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31701catalase+1.11.1.6
31701cytochrome oxidase+1.9.3.1
31701urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118978oxidase+
118978catalase+1.11.1.6
118978urease+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
118978-+++-++---+++-------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7033-----+/-+-+++--+------+
7033-----+/-+-+-+--+------+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7033----+-+---++++-+--------++-++---+---+--+-------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7033soilJiangsu provinceChinaCHNAsia
67771From soilJiangsu ProvinceChinaCHNAsia
118978Environment, Heavy metal, polluted farm soilNanjing, JiangsuChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70331Risk group (German classification)
1189781Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31701
  • description: Massilia dura strain 16 16S ribosomal RNA gene, partial sequence
  • accession: AY965998
  • length: 1478
  • database: nuccore
  • NCBI tax ID: 321982

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella dura DSM 17513GCA_009727155contigncbi321982
66792Pseudoduganella dura KCTC 12342GCA_014651395scaffoldncbi321982
66792Massilia dura strain DSM 17513321982.3wgspatric321982
66792Massilia dura strain KCTC 12342321982.4wgspatric321982

GC content

  • @ref: 31701
  • GC-content: 65.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes83.76no
gram-positiveno98.707no
anaerobicno98.558yes
aerobicyes92.202yes
halophileno94.743no
spore-formingno94.017no
thermophileno99.329yes
glucose-utilyes88.545no
motileyes88.67yes
glucose-fermentno90.024yes

External links

@ref: 7033

culture collection no.: DSM 17513, CCTCC AB 204070, KCTC 12342, CCUG 52213, CIP 109188

straininfo link

  • @ref: 80561
  • straininfo: 232829

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449458Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China.Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y, Xu LH, Jiang CL, Lai RInt J Syst Evol Microbiol10.1099/ijs.0.64083-02006Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/*genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny23087170Massilia lurida sp. nov., isolated from soil.Luo X, Xie Q, Wang J, Pang H, Fan J, Zhang JInt J Syst Evol Microbiol10.1099/ijs.0.047068-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7033Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17513)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17513
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
31701Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797828776041
37474Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6901
59466Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52213)https://www.ccug.se/strain?id=52213
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
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
80561Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232829.1StrainInfo: A central database for resolving microbial strain identifiers
118978Curators of the CIPCollection of Institut Pasteur (CIP 109188)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109188