Plants host complex microbial communities, collectively known as the plant microbiome, which play a central role in plant health and productivity. Microbiome composition is shaped by plant genotype, soil physicochemical properties, microbial interactions, and environmental stressors. Through the secretion of diverse root exudates, plants actively modulate microbial recruitment, enhancing adaptation to fluctuating environments and facilitating the acquisition of essential nutrients such as nitrogen (N) and phosphorus (P). However, crop domestication and modern breeding have unintentionally reduced the capacity of cultivated wheat to establish beneficial associations with soil microbes, potentially limiting nutrient acquisition efficiency. To investigate this, we analyse the functional potential of the ancestral wheat microbiome with a specific focus on bacterial genes and metabolic pathways related to N acquisition and P solubilisation. We are constructing a genomically characterized culture collection of wheat-associated bacterial isolates and performing whole-genome sequencing followed by comprehensive functional annotation. Comparative genomic analyses will identify key taxa, metabolic traits, and nutrient-mobilising pathways enriched in ancestral wheat–associated bacteria under nutrient-depleted conditions. This genome-based approach enables the systematic dissection of domestication-driven shifts in microbial functional capacity and the identification of candidate bacterial traits associated with improved nutrient mobilisation. By exploring bacterial functional genomics, this work establishes a mechanistic framework to uncover microbial traits that can inform sustainable nutrient management and enhance climate resilience in modern wheat production systems.