Strain identifier

BacDive ID: 11326

Type strain: Yes

Species: Massilia lutea

Strain Designation: 101

Strain history: CIP <- 2006, KCTC

NCBI tax ID(s): 321985 (species)

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General

@ref: 7008

BacDive-ID: 11326

DSM-Number: 17473

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

description: Massilia lutea 101 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from heavy-metal-polluted farm soil.

NCBI tax id

  • NCBI tax id: 321985
  • Matching level: species

strain history

@refhistory
7008<- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China
332802006, KCTC
120683CIP <- 2006, KCTC

doi: 10.13145/bacdive11326.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella lutea

@ref: 7008

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia lutea

full scientific name: Massilia lutea Zhang et al. 2006

strain designation: 101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31701negative3-3.5 µm1.8-2 µmrod-shapedyes
69480yes97.087
69480negative99.998
120683negativerod-shapedno

colony morphology

  • @ref: 59468
  • incubation period: 3 days

pigmentation

  • @ref: 31701
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7008R2A 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
33280MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120683CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7008positivegrowth30mesophilic
31701positivegrowth10-45
31701positiveoptimum28-30mesophilic
33280positivegrowth30mesophilic
59468positivegrowth30mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31701aerobe
59468aerobe
120683facultative anaerobe

spore formation

@refspore formationconfidence
31701no
69481no100
69480no99.987

halophily

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

observation

  • @ref: 31701
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3170117234glucose+carbon source
3170117992sucrose+carbon source
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
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12068317632nitrate-reduction
12068316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12068335581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31701catalase+1.11.1.6
31701cytochrome 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
120683oxidase+
120683alcohol dehydrogenase-1.1.1.1
120683catalase+1.11.1.6
120683lysine decarboxylase-4.1.1.18
120683ornithine decarboxylase-4.1.1.17
120683urease+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
120683-+++-++---+++---+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7008-----++++-+--+-----++

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7008----+-+---++++-+-------+++-++--+++--++-+-------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7008heavy-metal-polluted farm soilNanjing, Jiangsu provinceChinaCHNAsia
120683Environment, Heavy metal, polluted farm soilNanjing, JiangsuChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Engineered#Contamination#Heavy metal
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70081Risk group (German classification)
1206831Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7008
  • description: Massilia lutea strain 101 16S ribosomal RNA gene, partial sequence
  • accession: AY966001
  • length: 1464
  • database: ena
  • NCBI tax ID: 321985

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella lutea DSM 17473GCA_004209755chromosomencbi321985
66792Massilia lutea strain DSM 17473321985.3completepatric321985
66792Massilia lutea DSM 174732843750665completeimg321985

GC content

  • @ref: 7008
  • GC-content: 63.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.41no
anaerobicno98.914yes
halophileno93.893yes
spore-formingno93.031yes
glucose-utilyes88.825no
motileyes85.53yes
flagellatedyes83.292no
aerobicyes91.916yes
thermophileno99.5yes
glucose-fermentno90.308yes

External links

@ref: 7008

culture collection no.: DSM 17473, CCTCC AB 204073, KCTC 12345, CCUG 52216, CIP 109190

straininfo link

  • @ref: 80559
  • straininfo: 232832

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
Phylogeny19783608Massilia jejuensis sp. nov. and Naxibacter suwonensis sp. nov., isolated from air samples.Weon HY, Yoo SH, Kim SJ, Kim YS, Anandham R, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.015479-02009*Air Microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny21515701Massilia flava sp. nov., isolated from soil.Wang J, Zhang J, Pang H, Zhang Y, Li Y, Fan JInt J Syst Evol Microbiol10.1099/ijs.0.031344-02011Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7008Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17473)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17473
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
33280Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6903
59468Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52216)https://www.ccug.se/strain?id=52216
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
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
80559Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232832.1StrainInfo: A central database for resolving microbial strain identifiers
120683Curators of the CIPCollection of Institut Pasteur (CIP 109190)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109190