MichBarbier/Rice_field_microbiota_associated_with_blast_disease_from_Burkina_Faso

Here are the scripts used to analyse the microbiota data in Sanga et al., 202X : "The root microbiome of local rice in Burkina Faso hosts Bacillus and Priestia strains conferring protection against Blast disease (Pyricularia oryzae)." Here are the scripts used to analyse the microbiota data in **Sanga et al., 202X : "The root microbiome of local rice in Burkina Faso hosts *Bacillus* and *Priestia* strains conferring protection against Blast disease (*Pyricularia oryzae*)."** **Abstract :** Rice blast disease, caused by *Pyricularia oryzae*, is a major constraint on rice production in Burkina Faso. This study evaluated the antagonistic and biocontrol capacities of 44 bacterial strains isolated from rice roots across different agro-ecological zones in Burkina Faso. *In vitro* assays revealed that several *Bacillus* and *Burkholderia* isolates significantly inhibited *Py. oryzae* mycelial growth, with three *Bacillus* strains achieving over 50% inhibition. These strains also showed moderate antagonistic activity against other rice fungal pathogens, including *Bipolaris oryzae* and *Curvularia lunata*. In planta experiments using the susceptible rice cultivar FKR64 showed that root inoculation with selected *Bacillus* and *Priestia* isolates significantly reduced rice blast severity, achieving up to 25% reduction in disease progression. Phylogenetic analyses based on 16S rRNA sequences placed the most effective antagonistic isolates within the *Bacillus* subtilis clade, with some strains closely related to *B. aerius*, *B. velezensis*, and those harbouring the biocontrol capacity within the *Priestia* genus as closely related to *Pr. zantholi*. To explore the relevance of these bacteria in the field, previously generated rice root microbiome datasets were reanalysed in relation to blast disease incidence in their respective fields. Differential abundance and indicator taxon analyses revealed that several *Priestia* and *Kosakonia* ASVs, and to a lesser extent *Bacillus* ASVs, were significantly enriched in rice roots from fields with no detectable blast incidence. Notably, some enriched ASVs showed high sequence similarity to isolates identified here as protective bacteria. Together, these results …