The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Adrian Tett; Kun D. Huang; Francesco Asnicar; Hannah Fehlner-Peach; Edoardo Pasolli; Nicolai Karcher; Federica Armanini; Paolo Manghi; Kevin Bonham; Moreno Zolfo; Francesca De Filippis; Cara Magnabosco; Richard Bonneau; John Lusingu; John Amuasi; Karl Reinhard; Thomas Rattei; Fredrik Boulund; Lars Engstrand; Albert Zink; Maria Carmen Collado; Dan R. Littman; Daniel Eibach; Danilo Ercolini; Omar Rota-Stabelli; Curtis Huttenhower; Frank Maixner; Nicola Segata

doi:10.1016/j.chom.2019.08.018

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Adrian Tett, Kun D. Huang, Francesco Asnicar, Hannah Fehlner-Peach, Edoardo Pasolli, Nicolai Karcher, Federica Armanini, Paolo Manghi, Kevin Bonham, Moreno Zolfo, Francesca De Filippis, Cara Magnabosco, Richard Bonneau, John Lusingu, John Amuasi, Karl Reinhard, Thomas Rattei, Fredrik Boulund, Lars Engstrand, Albert ZinkMaria Carmen Collado, Dan R. Littman, Daniel Eibach, Danilo Ercolini, Omar Rota-Stabelli, Curtis Huttenhower, Frank Maixner, Nicola Segata

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Pages (from-to)	666-679.e7
Journal	Cell Host and Microbe
Volume	26
Issue number	5
DOIs	https://doi.org/10.1016/j.chom.2019.08.018
State	Published - Nov 13 2019

Keywords

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

ASJC Scopus subject areas

Parasitology
Microbiology
Virology

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10.1016/j.chom.2019.08.018

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Tett, A., Huang, K. D., 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., ... Segata, N. (2019). The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host and Microbe, 26(5), 666-679.e7. https://doi.org/10.1016/j.chom.2019.08.018

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, Littman, DR, 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 and Microbe, vol. 26, no. 5, pp. 666-679.e7. https://doi.org/10.1016/j.chom.2019.08.018

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title = "The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations",

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.",

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AU - Huang, Kun D.

AU - Asnicar, Francesco

AU - Fehlner-Peach, Hannah

AU - Pasolli, Edoardo

AU - Karcher, Nicolai

AU - Armanini, Federica

AU - Manghi, Paolo

AU - Bonham, Kevin

AU - Zolfo, Moreno

AU - De Filippis, Francesca

AU - Magnabosco, Cara

AU - Bonneau, Richard

AU - Lusingu, John

AU - Amuasi, John

AU - Reinhard, Karl

AU - Rattei, Thomas

AU - Boulund, Fredrik

AU - Engstrand, Lars

AU - Zink, Albert

AU - Collado, Maria Carmen

AU - Littman, Dan R.

AU - Eibach, Daniel

AU - Ercolini, Danilo

AU - Rota-Stabelli, Omar

AU - Huttenhower, Curtis

AU - Maixner, Frank

AU - Segata, Nicola

PY - 2019/11/13

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N2 - 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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KW - ancient DNA

KW - bacterial pangenome

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KW - gut microbes

KW - human microbiome

KW - metagenomic assembly

KW - metagenomics

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JO - Cell Host and Microbe

JF - Cell Host and Microbe

IS - 5

ER -

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Abstract

Keywords

ASJC Scopus subject areas

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