Highlights

  • P. copri is not a monotypic species but composed of four distinct clades
  • The P. copri complex is more prevalent in populations with non-Westernized lifestyles
  • P. copri clades are frequently co-present within non-Westernized individuals
  • Ancient stool samples suggest Westernization leads to P. copri underrepresentation

Summary

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. copriP. 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 modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

Credit CDC

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Citation:  Cell Host & Microbe 26, 666–679, November 13, 2019 ª 2019 The Author(s). Published by Elsevier Inc.   This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).