Cell Host & Microbe
Volume 26, Issue 5, 13 November 2019, Pages 666-679.e7
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Article
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

https://doi.org/10.1016/j.chom.2019.08.018Get rights and content
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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. 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 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.

Keywords

human microbiome
metagenomics
Prevotella copri
comparative microbial genomics
ancient DNA
gut microbes
metagenomic assembly
Westernization
bacterial pangenome
bacterial phylogenetics
Iceman

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Present address: Department of Agricultural Sciences, University of Naples “Federico II,” Portici, Italy

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