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

Authors

Adrian Tett, University of TrentoFollow
Kun D. Huang, University of Trento
Francesco Asnicar, University of Trento
Hannah Fehlner-Peach, New York University School of Medicine
Edoardo Pasolli, University of Trento
Nicolai Karcher, University of Trento
Federica Armanini, University of Trento
Paolo Manghi, University of Trento
Kevin Bonham, The Broad Institute of MIT and Harvard
Moreno Zolfo, University of Trento
Francesca De Filippis, University of Naples Federico II
Cara Magnabosco, Flatiron Institute, New York
Richard Bonneau, New York University
John Lusingu, National Institute for Medical Research, Tanzania
John Amuasi, Kwame Nkrumah University of Science and Technology
Karl Reinhard, University of Nebraska-LincolnFollow
Thomas Rattei, University of Vienna
Fredrik Boulund, Karolinska Institutet, Stockholm
Lars Engstrand, Institute for Mummy Studies, EURAC Research, Italy
Albert Zink, Institute for Mummy Studies, EURAC Research, Italy
Maria Carmen Collado, Institute of Agrochemistry and Food Technology, National Research Council, Spain
Dan R. Littman, New York University School of Medicine
Daniel Eibach, Bernhard Nocht Institute for Tropical Medicine, Hamburg
Danilo Ercolini, University of Naples Federico II
Omar Rota-Stabelli, Fondazione Edmund Mach
Curtis Huttenhower, The Broad Institute of MIT and Harvard
Frank Maixner, Institute for Mummy Studies, EURAC Research, Italy
Nicola Segata, University of TrentoFollow

Date of this Version

2019

Document Type

Article

Citation

Cell Host & Microbe 26, 666–679, November 13, 2019

Comments

This is an open access article under the CC BY license

Abstract

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent metaanalysis 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.