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

被引：255

作者：

Tett, Adrian ^{[1
]}

Huang, Kun D. ^{[1
,2
]}

Asnicar, Francesco ^{[1
]}

Fehlner-Peach, Hannah ^{[3
]}

Pasolli, Edoardo ^{[1
,20
]}

Karcher, Nicolai ^{[1
]}

Armanini, Federica ^{[1
]}

Manghi, Paolo ^{[1
]}

Bonham, Kevin ^{[4
,6
]}

Zolfo, Moreno ^{[1
]}

De Filippis, Francesca ^{[6
,7
]}

Magnabosco, Cara ^{[8
]}

Bonneau, Richard ^{[8
,9
,10
]}

Lusingu, John ^{[11
]}

Amuasi, John ^{[12
]}

Reinhard, Karl ^{[13
]}

Rattei, Thomas ^{[14
]}

Boulund, Fredrik ^{[15
]}

Engstrand, Lars ^{[16
]}

Zink, Albert ^{[16
]}

Carmen Collado, Maria ^{[17
]}

Littman, Dan R. ^{[3
]}

Eibach, Daniel ^{[18
,19
]}

Ercolini, Danilo ^{[6
,7
]}

Rota-Stabelli, Omar ^{[2
]}

Huttenhower, Curtis ^{[4
,5
]}

Maixner, Frank ^{[16
]}

Segata, Nicola ^{[1
]}

机构：

[1] Univ Trento, CIBIO Dept, I-38123 Trento, Italy

[2] Fdn Edmund Mach, Dept Sustainable Agroecosyst & Bioresources, 1 38010 S, San Michele All Adige, Italy

[3] NYU, Sch Med, Skirball Inst, Kimmel Ctr Biol & Med, New York, NY 10016 USA

[4] Broad Inst MIT & Harvard, Cambridge, MA 02115 USA

[5] Harvard TH Chan Sch Publ Hlth, Biostat Dept, Boston, MA 02115 USA

[6] Univ Naples Federico II, Dept Agr Sci, Portici, Italy

[7] Univ Naples Federico II, Task Force Microbiome Studies, Portici, Italy

[8] Flatiron Inst, Ctr Computat Biol, New York, NY 10010 USA

[9] NYU, Dept Biol, New York, NY 10003 USA

[10] NYU, Dept Comp Sci, New York, NY 10003 USA

[11] Natl Inst Med Res, Tanga Ctr, Dar Es Salaam, Tanzania

[12] Kwame Nkrumah Univ Sci & Technol, Kumasi Ctr Collaborat Res Trop Med, Kumasi, Ghana

[13] Univ Nebraska, Sch Nat Resources, Hardin Hall, Lincoln, NE 68583 USA

[14] Univ Vienna, Dept Microbiol & Ecosyst Sci, CUBE Div Computat Syst Biol, Althanstr 14, A-1090 Vienna, Austria

[15] Karolinska Inst, Dept Microbiol Tumor & Cell Biol, Ctr Translat Microbiome Res, S-17165 Stockholm, Sweden

[16] EURAC Res, Inst Mummy Studies, Viale Druso 1, I-39100 Bolzano, Italy

[17] Natl Res Council IATA CSIC, Inst Agrochem & Food Technol, Valencia 46980, Spain

[18] Bernhard Nocht Inst Trop Med, Dept Infect Dis Epidemiol, D-20359 Hamburg, Germany

[19] German Ctr Infect Res, D-20359 Hamburg, Germany

[20] Univ Naples Federico II, Dept Agr Sci, Portici, Italy

来源：

CELL HOST & MICROBE | 2019年 / 26卷 / 05期

基金：

欧洲研究理事会; 欧盟地平线“2020”;

关键词：

HUMAN GUT MICROBIOME; LOS MUERTOS CHIQUITOS; RIO ZAPE VALLEY; GENOMIC INSIGHTS; READ ALIGNMENT; SEQUENCE; METAGENOME; DNA; IDENTIFICATION; DURANGO;

D O I：

10.1016/j.chom.2019.08.018

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

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.

引用

页码：666 / +

页数：21

共 2 条

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