This research aimed to explore the pathobiome to enhance the understanding of the roles played by disease-associated microbes. A comparative analysis of microbiomes in rice samples was conducted to shed light on the potential impact of the rice yellow mottle virus on microbiome composition. Forty samples were collected from rice fields of the Office du Niger in Mali. Bacterial DNA was extracted at the LaboREM-Biotech and the RT-PCR was conducted to confirm the presence of the virus. The next-generation sequencing of extracted bacterial DNA was employed to examine bacterial communities in both infected and uninfected plants. The Minnesota Supercomputing Institute, R-studio, Dada2, and Quiime were utilized to compare bacterial communities and identify bacteria present in healthy and infected rice plants. The results support the notion that plant infection by pathogenic viruses significantly influences microbial communities. The overall microbial diversity in infected and uninfected rice plants did not show a significant difference. Viral invasion led to alterations in microbiome members, potentially fostering colonization through mutualistic relationships or aiding in plant defense against pathogens during infection. The study highlighted the differential enrichment of bacteria from various families in plants, indicating a significant change in the rice bacterial community composition with infection.

Keywords: Metagenomic analysis, microbiome, bacterial community, rice yellow mottle virus, viral infection, rice, Mali