Strain identifier
BacDive ID: 132494
Type strain: 
Species: Virgibacillus massiliensis
Strain Designation: Vm-5
Strain history: <- S. Khelaifia, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Marseille, France; Vm-5
NCBI tax ID(s): 1462526 (species)
version 8.1 (current version)
General
@ref: 24283
BacDive-ID: 132494
DSM-Number: 28587
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, motile
description: Virgibacillus massiliensis Vm-5 is a spore-forming, mesophilic, motile bacterium that was isolated from human stool, 10-year old healthy Amazonian boy.
NCBI tax id
- NCBI tax id: 1462526
- Matching level: species
strain history
- @ref: 24283
- history: <- S. Khelaifia, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Marseille, France; Vm-5
doi: 10.13145/bacdive132494.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Virgibacillus
- species: Virgibacillus massiliensis
- full scientific name: Virgibacillus massiliensis Khelaifia et al. 2023
@ref: 24283
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Virgibacillus
species: Virgibacillus massiliensis
full scientific name: Virgibacillus massiliensis
strain designation: Vm-5
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 98.23 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 24283
- name: BHI MEDIUM (DSMZ Medium 215)
- growth: yes
- link: https://mediadive.dsmz.de/medium/215
- composition: Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
culture temp
- @ref: 24283
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.621 |
Isolation, sampling and environmental information
isolation
- @ref: 24283
- sample type: human stool, 10-year old healthy Amazonian boy
- country: Brazil
- origin.country: BRA
- continent: Middle and South America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | #Child |
| #Host | #Human | #Male |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_4297.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1861;97_2610;98_3234;99_4297&stattab=map
- Last taxonomy: Virgibacillus
- 16S sequence: HG931931
- Sequence Identity:
- Total samples: 11
- soil counts: 3
- aquatic counts: 2
- animal counts: 6
Sequence information
16S sequences
- @ref: 24283
- description: Virgibacillus sp. Vm-5 partial 16S rRNA gene, isolate Vm-5
- accession: HG931931
- length: 1530
- database: ena
- NCBI tax ID: 1462526
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Virgibacillus massiliensis Vm-5 | GCA_000723585 | contig | ncbi | 1462526 |
| 66792 | Virgibacillus massiliensis Vm-5 | GCA_014905475 | scaffold | ncbi | 1462526 |
| 66792 | Virgibacillus massiliensis Vm-5 | 2617271113 | draft | img | 1462526 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 90.964 | no |
| flagellated | yes | 89.26 | no |
| gram-positive | yes | 92.094 | no |
| anaerobic | no | 99.355 | no |
| aerobic | yes | 93.44 | no |
| halophile | yes | 93.74 | no |
| spore-forming | yes | 96.276 | no |
| glucose-util | yes | 87.816 | no |
| thermophile | no | 96.401 | yes |
| glucose-ferment | no | 88.42 | no |
External links
@ref: 24283
culture collection no.: DSM 28587, CSUR P971
straininfo link
- @ref: 90823
- straininfo: 406295
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | topic2 | mesh |
|---|---|---|---|---|---|---|---|---|
| Genetics | 26649181 | Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut. | Khelaifia S, Croce O, Lagier JC, Robert C, Couderc C, Di Pinto F, Davoust B, Djossou F, Raoult D, Fournier PE | New Microbes New Infect | 10.1016/j.nmni.2015.09.012 | 2015 | Phylogeny | |
| Metabolism | 31886235 | Identification of a New Serine Alkaline Peptidase from the Moderately Halophilic Virgibacillus natechei sp. nov., Strain FarD(T) and its Application as Bioadditive for Peptide Synthesis and Laundry Detergent Formulations. | Mechri S, Bouacem K, Amziane M, Dab A, Nateche F, Jaouadi B | Biomed Res Int | 10.1155/2019/6470897 | 2019 | Transcriptome | *Bacterial Proteins/chemistry/genetics/metabolism, Detergents, Escherichia coli/genetics, Hydrogen-Ion Concentration, Recombinant Proteins/chemistry/genetics/metabolism, Sequence Analysis, Protein, *Serine Proteases/chemistry/genetics/metabolism, *Virgibacillus/enzymology/genetics |
| Metabolism | 34143291 | Distribution of class IId bacteriocin-producing Virgibacillus salexigens in various environments. | Omachi H, Terahara T, Futami K, Kawato S, Imada C, Kamei K, Waku T, Kondo A, Naganuma T, Agustini TW, Kobayashi T | World J Microbiol Biotechnol | 10.1007/s11274-021-03085-4 | 2021 | Phylogeny | Amino Acid Sequence, Anti-Bacterial Agents/metabolism, Bacterial Proteins/genetics/metabolism, Bacteriocins/*genetics/metabolism, Environmental Microbiology, Humans, RNA, Ribosomal, 16S, Seawater/microbiology, Sequence Analysis, DNA, Virgibacillus/*classification/*genetics/metabolism, Whole Genome Sequencing |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
| 24283 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28587 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28587) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 69479 | João 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 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 90823 | Reimer, 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 identifiers | 10.60712/SI-ID406295.1 |