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.

Tett, A.; Huang, K.; 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, M.C.; Littman, D.R.; Eibach, D.; Ercolini, D.; Rota-Stabelli, O.; Huttenhower, C.; Maixner, F.; Segata, N. (2019). The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations. CELL HOST & MICROBE, 26 (5): 666-679. doi: 10.1016/j.chom.2019.08.018 handle: http://hdl.handle.net/10449/58315

The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations

Huang, Kun;Rota-Stabelli, Omar;
2019-01-01

Abstract

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.
Human microbiome
Metagenomics
Prevotella copri
Comparative microbial genomics
Ancient DNA
Gut microbes
Metagenomic assembly
Westernization
Bacterial pangenome
Bacterial phylogenetics
Iceman
Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA
2019
Tett, A.; Huang, K.; 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, M.C.; Littman, D.R.; Eibach, D.; Ercolini, D.; Rota-Stabelli, O.; Huttenhower, C.; Maixner, F.; Segata, N. (2019). The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations. CELL HOST & MICROBE, 26 (5): 666-679. doi: 10.1016/j.chom.2019.08.018 handle: http://hdl.handle.net/10449/58315
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