@article{a6b02d6e9cba4f27bc3643dff5390b6d,
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.",
keywords = "Iceman, Prevotella copri, Westernization, ancient DNA, bacterial pangenome, bacterial phylogenetics, comparative microbial genomics, gut microbes, human microbiome, metagenomic assembly, metagenomics",
author = "Adrian Tett and Huang, {Kun D.} and Francesco Asnicar and Hannah Fehlner-Peach and Edoardo Pasolli and Nicolai Karcher and Federica Armanini and Paolo Manghi and Kevin Bonham and Moreno Zolfo and {De Filippis}, Francesca and Cara Magnabosco and Richard Bonneau and John Lusingu and John Amuasi and Karl Reinhard and Thomas Rattei and Fredrik Boulund and Lars Engstrand and Albert Zink and Collado, {Maria Carmen} and Littman, {Dan R.} and Daniel Eibach and Danilo Ercolini and Omar Rota-Stabelli and Curtis Huttenhower and Frank Maixner and Nicola Segata",
note = "Funding Information: We thank Levi Waldron and the members of his laboratory for the effort in developing and supporting curatedMetagenomicData (Pasolli et al. 2017) and all the members of the Segata laboratory for fruitful discussions and support. We also thank Eleonora Nigro for her illustration of the visual abstract. We thank the team of the NGS Core Facility at CIBIO (Veronica De Sanctis, Roberto Bertorelli, and Paola Fassan) for support in sample preparation and for metagenomic sequencing and the high-performance computing team at the University of Trento. We thank the GeNaPi Project, a collaborative study between Emalaikat Foundation, University of Valencia, and IATA-CSIC, for data and sample collection from the Ethiopia cohort, particularly Mari Olcina and Lourdes Larruy. We thank all field workers and laboratory technicians involved in the sample collection in Ghana and Tanzania. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716575) to N.S. This work was also supported by the NIH NHGRI grant R01HG005220, the NIDDK grant R24DK110499, the NIDDK grant U54DE023798, and the CMIT grant 6935956 to C.H.; the NYU-HHC CTSI grant (1TL1TR001447) to H.F.P.; the US National Institute of Health grant R01-DK103358-01 to R.B. and D.R.L.; the Howard Hughes Medical Institute to D.R.L.; and the MIUR ?Futuro in Ricerca? RBFR13EWWI_001, the European Union (H2020-SFS-2018-1 project MASTER-818368 and H2020-SC1-BHC project ONCOBIOME-825410) to N.S. Further support was provided by the Programma Ricerca Budget Eurac 2017 of the Province of Bolzano, Italy to F.M. and by the EU-H2020 (DiMeTrack-707345) to E.P. and N.S. Conception and Design, A.T. and N.S.; Sample Collection, Processing, and Data generation, H.F.P. F. Armanini, K.B. C.M. R.B. J.L. J.A. K.R. T.R. F.B. L.E. A.Z. M.C.C. D.R.L. D.E. and F.M.; Public Data Collection and Curation, A.T. E.P. N.K. and P.M.; Data Analysis; A.T. E.P. K.D.H, F. Asnicar, N.K. M.Z. F.D.F. D.E. O.R.S. and F.M.; Data Interpretation, A.T. K.D.H. F.D.F. D.E. O.R.S. C.H. F.M. and N.S.; Writing ? Original Draft, A.T. and N.S.; Writing ? Review & Editing, A.T. N.S. C.H. O.R.S. D.E. and F.M. All authors read and approved the final manuscript. The authors declare no competing interests. Funding Information: We thank Levi Waldron and the members of his laboratory for the effort in developing and supporting curatedMetagenomicData ( Pasolli et al., 2017 ) and all the members of the Segata laboratory for fruitful discussions and support. We also thank Eleonora Nigro for her illustration of the visual abstract. We thank the team of the NGS Core Facility at CIBIO (Veronica De Sanctis, Roberto Bertorelli, and Paola Fassan) for support in sample preparation and for metagenomic sequencing and the high-performance computing team at the University of Trento. We thank the GeNaPi Project, a collaborative study between Emalaikat Foundation, University of Valencia, and IATA-CSIC, for data and sample collection from the Ethiopia cohort, particularly Mari Olcina and Lourdes Larruy. We thank all field workers and laboratory technicians involved in the sample collection in Ghana and Tanzania. This project has received funding from the European Research Council (ERC) under the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant agreement No 716575 ) to N.S. This work was also supported by the NIH NHGRI grant R01HG005220 , the NIDDK grant R24DK110499 , the NIDDK grant U54DE023798 , and the CMIT grant 6935956 to C.H.; the NYU-HHC CTSI grant ( 1TL1TR001447 ) to H.F.P.; the US National Institute of Health grant R01-DK103358-01 to R.B. and D.R.L.; the Howard Hughes Medical Institute to D.R.L.; and the MIUR “Futuro in Ricerca” RBFR13EWWI_001 , the European Union (H2020-SFS-2018-1 project MASTER-818368 and H2020-SC1-BHC project ONCOBIOME-825410) to N.S. Further support was provided by the Programma Ricerca Budget Eurac 2017 of the Province of Bolzano, Italy to F.M., and by the EU-H2020 (DiMeTrack-707345) to E.P. and N.S. Publisher Copyright: {\textcopyright} 2019 The Authors",
year = "2019",
month = nov,
day = "13",
doi = "10.1016/j.chom.2019.08.018",
language = "English (US)",
volume = "26",
pages = "666--679.e7",
journal = "Cell Host and Microbe",
issn = "1931-3128",
publisher = "Cell Press",
number = "5",
}