Strain identifier

BacDive ID: 132571

Type strain: Yes

Species: Microvirga massiliensis

Strain Designation: JC119

Strain history: <- J.-C. Lagier, Timone Hospital, Marseille, France; JC119

NCBI tax ID(s): 1033741 (species)

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General

@ref: 24360

BacDive-ID: 132571

DSM-Number: 26813

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Microvirga massiliensis JC119 is a mesophilic, motile bacterium that was isolated from human feces, 16-year-old Senegalese man.

NCBI tax id

  • NCBI tax id: 1033741
  • Matching level: species

strain history

  • @ref: 24360
  • history: <- J.-C. Lagier, Timone Hospital, Marseille, France; JC119

doi: 10.13145/bacdive132571.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Microvirga
  • species: Microvirga massiliensis
  • full scientific name: Microvirga massiliensis Caputo et al. 2016

@ref: 24360

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Microvirga

species: Microvirga massiliensis

full scientific name: Microvirga massiliensis Caputo et al. 2016

strain designation: JC119

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes94.478
6948099.996negative

Culture and growth conditions

culture medium

  • @ref: 24360
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf

culture temp

  • @ref: 24360
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no91
69480no99.928

Isolation, sampling and environmental information

isolation

  • @ref: 24360
  • sample type: human feces, 16-year-old Senegalese man
  • geographic location: Sine Saloum, Dielmo
  • country: Senegal
  • origin.country: SEN
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Host#Human#Male
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8035.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_3711;97_4563;98_5856;99_8035&stattab=map
  • Last taxonomy: Microvirga massiliensis subclade
  • 16S sequence: JF824802
  • Sequence Identity:
  • Total samples: 10331
  • soil counts: 7646
  • aquatic counts: 694
  • animal counts: 1033
  • plant counts: 958

Safety information

risk assessment

  • @ref: 24360
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24360
  • description: Microvirga massiliensis strain JC119 16S ribosomal RNA gene, partial sequence
  • accession: JF824802
  • length: 1475
  • database: ena
  • NCBI tax ID: 1033741

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microvirga massiliensis JC119GCA_001006805scaffoldncbi1033741
66792Microvirga massiliensis JC119GCA_001050495contigncbi1033741
66792Microvirga massiliensis JC1192802429303draftimg1033741
66792Microvirga massiliensis JC1192634166464draftimg1033741

GC content

  • @ref: 24360
  • GC-content: 63.28
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno91no
motileyes74.335no
flagellatedno84.313no
gram-positiveno97.465no
anaerobicno96.073no
aerobicyes87.094no
halophileno93.5no
spore-formingno93.395no
thermophileno97.671yes
glucose-utilyes88.544no
glucose-fermentno90.731no

External links

@ref: 24360

culture collection no.: DSM 26813, CSUR P153

straininfo link

  • @ref: 90888
  • straininfo: 402135

literature

  • topic: Genetics
  • Pubmed-ID: 26749561
  • title: Microvirga massiliensis sp. nov., the human commensal with the largest genome.
  • authors: Caputo A, Lagier JC, Azza S, Robert C, Mouelhi D, Fournier PE, Raoult D
  • journal: Microbiologyopen
  • DOI: 10.1002/mbo3.329
  • year: 2016
  • mesh: Adolescent, Alphaproteobacteria/classification/*genetics, Bacterial Typing Techniques, Computational Biology/methods, France, Gastrointestinal Microbiome/genetics, *Genome, Bacterial, *Genomics/methods, Humans, Male, Metagenome, Metagenomics/methods, Molecular Sequence Annotation, Phenotype, Phylogeny, Sequence Analysis, DNA
  • topic2: Phylogeny

Reference

@idauthorstitledoi/urlcatalogue
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
24360Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26813Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26813)
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
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
90888Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402135.1