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

EMBO J. 2021 Dec 1;40(23):e108287. doi: 10.15252/embj.2021108287. Epub 2021 Oct 21.


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 (PULAra ) and that the type-II PULAra 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.

Keywords: Prevotella copri; genetic manipulation; human diet; hybrid two-component system; polysaccharide utilization locus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Diet, Vegetarian*
  • Feces / microbiology
  • Gastrointestinal Microbiome*
  • Genetic Loci*
  • Genome, Bacterial*
  • Humans
  • Polysaccharides / metabolism*
  • Prevotella / classification
  • Prevotella / genetics*
  • Prevotella / isolation & purification
  • Prevotella / metabolism*


  • Polysaccharides
  • araban

Supplementary concepts

  • Prevotella copri