Strain identifier

BacDive ID: 141160

Type strain: Yes

Species: Massilia eburnea

Strain Designation: 10R5-21

Strain history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; 10R5-21.

NCBI tax ID(s): 1776165 (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 8.1 (current version)

General

@ref: 44081

BacDive-ID: 141160

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

description: Massilia eburnea 10R5-21 is a mesophilic, Gram-negative, motile bacterium that was isolated from lagoon sediments.

NCBI tax id

  • NCBI tax id: 1776165
  • Matching level: species

strain history

  • @ref: 67770
  • history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; 10R5-21.

doi: 10.13145/bacdive141160.20230509.8.1

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 eburnea
  • full scientific name: Massilia eburnea (Jin et al. 2017) Lu et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Pseudoduganella eburnea

@ref: 44081

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Pseudoduganella

species: Pseudoduganella eburnea

strain designation: 10R5-21

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
44081negative1.5-2.0 µm0.4-0.5 µmrod-shapedyespolar
69480yes94.722
69480negative99.995

colony morphology

  • @ref: 44081
  • colony size: 1-2 mm
  • colony color: ivory
  • incubation period: 5 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 44081
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
44081positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
44081positivegrowth5.0-9.0alkaliphile
44081positiveoptimum6.5-7.5

Physiology and metabolism

spore formation

@refspore formationconfidence
44081no
69481no100
69480no99.927

halophily

@refsaltgrowthtested relationconcentrationhalophily level
44081NaClpositivegrowth0-0.5 %(w/v)
44081non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
44081161933-hydroxybenzoate-assimilation
44081178794-hydroxybenzoate-assimilation
44081581435-dehydro-D-gluconate-assimilation
4408135391aspartate-assimilation
4408116947citrate-assimilation
4408115824D-fructose-assimilation
4408116899D-mannitol-assimilation
4408116988D-ribose-assimilation
4408117924D-sorbitol-assimilation
44081370543-hydroxybutyrate-assimilation
4408129987glutamate-assimilation
4408117240itaconate-assimilation
4408118287L-fucose-assimilation
4408117203L-proline-assimilation
4408162345L-rhamnose-assimilation
4408115792malonate-assimilation
4408117268myo-inositol-assimilation
4408117814salicin-assimilation
440819300suberic acid-assimilation
4408117057cellobiose-builds acid from
4408128757fructose-builds acid from
4408128053melibiose-builds acid from
4408130089acetate+assimilation
4408117057cellobiose+assimilation
4408117634D-glucose+assimilation
4408124996lactate+assimilation
4408128087glycogen+assimilation
4408116977L-alanine+assimilation
4408130849L-arabinose+assimilation
4408115971L-histidine+assimilation
4408117115L-serine+assimilation
4408117306maltose+assimilation
4408137684mannose+assimilation
4408128053melibiose+assimilation
4408117272propionate+assimilation
4408116634raffinose+assimilation
4408117992sucrose+assimilation
4408131011valerate+assimilation
4408116024D-mannose+builds acid from
4408117234glucose+builds acid from
4408130849L-arabinose+builds acid from
4408117306maltose+builds acid from
4408117992sucrose+builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
4408117334penicillinyesyes50 µg/mL
4408117698chloramphenicolyesyes35 µg/mL
44081100147nalidixic acidyesyes30 µg/mL
4408128077rifampicinyesyes50 µg/mL
4408128971ampicillinyesyes50 µg/mL

enzymes

@refvalueactivityec
44081catalase+1.11.1.6
44081cytochrome oxidase+1.9.3.1
44081alkaline phosphatase+3.1.3.1
44081esterase (C 4)+
44081esterase Lipase (C 8)+
44081lipase (C 14)+
44081cystine arylamidase+3.4.11.3
44081leucine arylamidase+3.4.11.1
44081trypsin+3.4.21.4
44081acid phosphatase+3.1.3.2
44081valine arylamidase+
44081naphthol-AS-BI-phosphohydrolase+
44081alpha-chymotrypsin-3.4.21.1
44081alpha-galactosidase-3.2.1.22
44081beta-galactosidase-3.2.1.23
44081beta-glucuronidase-3.2.1.31
44081beta-glucosidase-3.2.1.21
44081N-acetyl-beta-glucosaminidase-3.2.1.52
44081alpha-mannosidase-3.2.1.24
44081alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
44081lagoon sediments2015-10North Carolina Central University campus, North CarolinaUSAUSANorth AmericaR2A5 days28
67770Lagoon sediments at North Carolina Central University campusNCUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Aquatic
#Environmental#Aquatic#Marine

Sequence information

16S sequences

  • @ref: 44081
  • description: 16S rRNA gene sequence
  • accession: KU321297
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoduganella eburnea strain JCM 315871776165.3wgspatric1776165
66792Pseudoduganella eburnea JCM 315872914563247draftimg1776165
67770Massilia eburnea JCM 31587GCA_009720745contigncbi1776165

GC content

  • @ref: 44081
  • GC-content: 64.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.639yes
gram-positiveno98.556yes
anaerobicno98.932no
aerobicyes90.294no
halophileno95.181no
spore-formingno91.211no
thermophileno99.205yes
glucose-utilyes89.263no
flagellatedyes81.535no
glucose-fermentno87.241no

External links

@ref: 44081

culture collection no.: KEMB 563-061, JCM 31587

literature

  • topic: Phylogeny
  • Pubmed-ID: 32361957
  • title: Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella.
  • authors: Lu HB, Cai ZP, Yang YG, Xu MY
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-020-01422-5
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urljournalpubmed
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
44081Da-Hye Jin, Y. Subhash and Sang-Seob LeePsedoduganella eburnea sp. nov., isolated from lagoon sediments10.1099/ijsem.0.002460IJSEM 67: 5268-5272 201729087279
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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