Strain identifier

BacDive ID: 133930

Type strain: Yes

Species: Massilia lurida

Strain Designation: D5

NCBI tax ID(s): 1036180 (species)

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

@ref: 30901

BacDive-ID: 133930

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

description: Massilia lurida D5 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1036180
  • Matching level: species

doi: 10.13145/bacdive133930.20230509.8.1

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 lurida
  • full scientific name: Massilia lurida Luo et al. 2013
  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella lurida

@ref: 30901

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Massilia

species: Massilia lurida

strain designation: D5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30901negative2.1 µm0.75 µmrod-shapedyes
69480yes95.022
69480negative99.994

pigmentation

  • @ref: 30901
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30901positivegrowth10-37
30901positiveoptimum29mesophilic

culture pH

@refabilitytypepHPH range
30901positivegrowth6.0-9.0alkaliphile
30901positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30901
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30901no
69481no100
69480no99.998

halophily

  • @ref: 30901
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %

observation

  • @ref: 30901
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3090122599arabinose+carbon source
3090117057cellobiose+carbon source
3090128757fructose+carbon source
3090117234glucose+carbon source
3090117754glycerol+carbon source
3090117716lactose+carbon source
3090125115malate+carbon source
3090117306maltose+carbon source
3090137684mannose+carbon source
3090128053melibiose+carbon source
30901506227N-acetylglucosamine+carbon source
3090126546rhamnose+carbon source
3090117814salicin+carbon source
3090127082trehalose+carbon source
3090118222xylose+carbon source
309014853esculin+hydrolysis

enzymes

@refvalueactivityec
30901acid phosphatase+3.1.3.2
30901alkaline phosphatase+3.1.3.1
30901catalase+1.11.1.6
30901gelatinase+
30901cytochrome oxidase+1.9.3.1
30901urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 30901
  • sample type: soil

isolation source categories

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

Sequence information

16S sequences

  • @ref: 30901
  • description: Massilia lurida strain D5 16S ribosomal RNA gene, partial sequence
  • accession: HQ839786
  • length: 1486
  • database: nuccore
  • NCBI tax ID: 1036180

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella lurida CGMCC 1.10822GCA_007830455contigncbi1036180
66792Massilia lurida strain CGMCC 1.108221036180.3wgspatric1036180
66792Massilia lurida CGMCC 1.108222596583599draftimg1036180

GC content

  • @ref: 30901
  • GC-content: 65.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.265no
flagellatedyes63.995no
gram-positiveno98.332yes
anaerobicno99.327yes
aerobicyes94.32yes
halophileno92.189yes
spore-formingno92.902no
thermophileno99.153yes
glucose-utilyes87.963no
glucose-fermentno90.798no

External links

@ref: 30901

culture collection no.: CGMCC 1.10822, KCTC 23880

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny28933315Massilia buxea sp. nov., isolated from a rock surface.Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WYInt J Syst Evol Microbiol10.1099/ijsem.0.0023012017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
30901Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172723128776041
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