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: Iceman; Prevotella copri; Westernization; ancient DNA; bacterial pangenome; bacterial phylogenetics; comparative microbial genomics; gut microbes; human microbiome; metagenomic assembly; metagenomics.
Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.
Conflict of interest statement
The authors declare no competing interests.
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Gut Microbiota in 2015: Prevotella in the Gut: Choose CarefullyRE Ley. Nat Rev Gastroenterol Hepatol 13 (2), 69-70. PMID 26828918. - ReviewGut microbial communities often contain many Bacteroides or their close relatives, Prevotella, but not both. Prevotella strains are associated with plant-rich diets but a …
Application of Metagenomics in the Human Gut MicrobiomeWL Wang et al. World J Gastroenterol 21 (3), 803-14. PMID 25624713. - ReviewThere are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against patho …
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- Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. - PubMed
- Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 1999;23:147. - PubMed
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