A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems

Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant‐rich diet consumption and diverse health states. The underlying genetic basis of these associations remains enigmatic due to the lack of genetic tools. Here, we developed a novel versatile genetic toolbox for rapid and efficient genetic insertion and allelic exchange applicable to P. copri strains from multiple clades. Enabled by the genetic platform, we systematically investigated the specificity of polysaccharide utilization loci (PULs) and identified four highly conserved PULs for utilizing arabinan, pectic galactan, arabinoxylan, and inulin, respectively. Further genetic and functional analysis of arabinan utilization systems illustrate that P. copri has evolved two distinct types of arabinan‐processing PULs (PUL Ara ) and that the type‐II PUL Ara is significantly enriched in individuals consuming a vegan diet compared to other diets. In summary, this genetic toolbox will enable functional genetic studies for P. copri in future. SYNOPSIS Genetic intractability limits functional studies of prevalent human gut commensals. Here, we establish a genetic toolbox validated by the characterization of polysaccharide utilization systems in Prevotella copri providing a roadmap for functional gene studies in human commensal bacteria. We developed a toolbox for genetic insertion and allelic exchange in P. copri . This enables functional studies of genetically diverse P. copri strains. Distinct PULs in P. copri for processing arabinan, pectic galactan, arabinoxylan and inulin were identified. Prevotella copri strains encode two types of arabinan processing PULs with distinct binding and importing modules. Graphical Abstract A novel conjugation‐based gene insertion/excision system allowing genetic manipulation of the previously intractable bacterium Prevotella copri provides insight into human diet effects on commensal bacterial metabolism.