Data supporting the publication: Plant species and field site shape root endosphere microbiomes of wild inoculum plants used in traditional cereal-based fermentation

Munkoyo is a traditional, non-alcoholic fermented cereal drink central to Zambian diets, rural livelihoods, and cultural identity. Its production empowers women, who predominantly oversee its preparation and trade. However, sustaining Munkoyo production is challenging because the plants used as fermentation starters are collected from the wild, risking overharvesting, and little is known about the root microbiomes driving fermentation. This study examined three wild plant species used as inoculum for producing Munkoyo. Root endosphere, rhizosphere, and bulk soil samples were collected from five districts in Zambia, and bacterial communities were characterized using 16S rRNA gene amplicon sequencing. Bulk soil bacterial communities varied strongly across field sites and were structured by soil physicochemical properties, whereas root endosphere microbiomes were more distinct and differed among plant species and locations. The findings contribute to a better understanding of the bacterial communities involved in traditional fermented beverage production. They highlight the importance of plant species and soil environment in structuring root microbiomes, with implications for fermentation quality, sustainable cultivation of fermentation plants, and cultural heritage preservation.