The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations
Tett, A; Huang, KD; Asnicar, F; Fehlner-Peach, H; Pasolli, E; Karcher, N; Armanini, F; Manghi, P; Bonham, K; Zolfo, M; De Filippis, F; Magnabosco, C; Bonneau, R; Lusingu, J; Amuasi, J; Reinhard, K; Rattei, T; Boulund, F; Engstrand, L; Zink, A; Collado, MC
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.
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