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 journalArticle

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 languageEnglish (US)
Pages (from-to)666-679.e7
JournalCell Host and Microbe
Volume26
Issue number5
DOIs
StatePublished - 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

Fingerprint Dive into the research topics of 'The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations'. Together they form a unique fingerprint.

  • Cite this

    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