Recent depiction of the tree of life has revealed the dominance of Bacteria diversification compared to the two other domains of life, Archaea and Eukarya (Hug et al., 2016). Hence, a large fraction of this diversity is currently only accessible via cultivation-independent approaches. Bacteria colonize all ecosystems, participate to biogeochemical cycles and play a crucial role in eucaryotic interactions (symbiosis, commensalism, pathogenicity). Bacteria brought both usefulness and dangerosity to mankind. Exploration of bacterial diversity is a corner stone in many disciplines such as environment (bioremediation, biomonitoring), agriculture (plant health, biocontrol), agro-food (transformation, food quality and security), industry (biotechnology), and clinical research (disease diagnostic, antibioresistance, vaccine development…).

Access the database:

 R-Syst::Bacteria

Database content:

The database is under implementation. Currently, plant pathogenic bacteria are the most represented strains in R-Syst::Bacteria.

• Taxonomy:
  • Species and pathovar names of the strains are given with the highest precision by specialist. Valid names according to the International Code of Nomenclature of Bacteria (Lapage et al., 1992) and to the International Standards for naming pathovars of Phytopathogenic Bacteria (Dye et al., 1980) are used (Bull et al. 2008). Whenever possible, the most update classification is adopted. For instance, for Ralstonia genus, the classification proposed by Safni et al. (2014) is used for plant pathogenic species.
• Genetic:
  • Barcodes: gyrB, rpoD, rpoB, leuS, mutS (implementation in progress)
  • Simplified MultiLocus Sequence Analysis (MLSA) schemes and protocols are accessible here
• Phenotype:
  • Pictures of cultures coming soon.

• Data have severals origins:
  • > barcoded strains from the CIRM-CFBP  (CIRM-Plant associated Bacteria)
  • > barcoded strains from NCBI (Nucleotide database) might be included after careful check when the data is missing in our own database.

References:

• Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, Saddler GS, Scortichini M, Stead DE, Takikawa Y. 2008.DEMYSTIFYING THE NOMENCLATURE OF BACTERIAL PLANT PATHOGENS.J. Plant Pathol. 90:403-417.
• Dye DW, Bradbury JF, Goto M, Hayward AC, Lelliott RA, Schroth MN. 1980. International standards for naming pathovars of phytopathogenic bacteria and a list of pathovar names and pathotype strains. Review of Plant Pathology 59:153-168. The revision of the Standards is available from : http://www.isppweb.org/about_tppb_naming.asp
• Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF.2016. A new view of the tree of life. Nature Microbiology 1:16048.
• Lapage SP, Sneath PHA, Lessel EF, et al., editors. International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. Washington (DC): ASM Press; 1992. Available from: https://www.ncbi.nlm.nih.gov/books/NBK8817/
• Sfni I, Cleenwerck I, De Vos P, Fegan M, Sly L, Kappler U. 2014.Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov. Int J Syst Evol Microbiol 64:3087-3103.