The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary…

• HH
  Howard Hughes Medical Institute
• CA
  Clinical and Translational Science Institute, New York University

  Award: 1TL1TR001447
• EC
  European Commission

  Awards: 716575, 707345, 825410, EU-H2020, 818368, H2020, MASTER-818368, ONCOBIOME-825410, H2020-SC1-BHC, H2020-SC1
• MD
  Ministero dell’Istruzione, dell’Università e della Ricerca

  Awards: H2020, RBFR13EWWI_001
• UD
  Universitat de València
• UD
  Università degli Studi di Trento
• PA
  Provincia autonoma di Bolzano - Alto Adige
• NI
  National Institutes of Health

  Awards: U54DE023798, R24DK110499, EU-H2020, H2020, R01HG005220, R01-DK103358-01
• H2
  Horizon 2020 Framework Programme

  Awards: 818368, SC1-BHC, H2020-SC1, ONCOBIOME-825410, 825410
• ER
  European Research Council
• H2
  Horizon 2020

  Award: 716575
• NH
  National Human Genome Research Institute

  Award: R01HG005220
• NI
  National Institute of Diabetes and Digestive and Kidney Diseases

  Awards: R24DK110499, U54DE023798
• HE
  H2020 European Research Council

  Award: 716575