Elevated rates of horizontal gene transfer in the industrialized human microbiome

被引：200

作者：

Groussin, Mathieu ^{[1
,2
,3
,4
]}

Poyet, Mathilde ^{[1
,2
,3
,4
]}

Sistiaga, Ainara ^{[4
,5
,6
]}

Kearney, Sean M. ^{[1
,2
]}

Moniz, Katya ^{[1
,2
,4
]}

Noel, Mary ^{[4
,7
]}

Hooker, Jeff ^{[4
,7
]}

Gibbons, Sean M. ^{[7
,8
,9
]}

Segurel, Laure ^{[4
,10
]}

Froment, Alain ^{[4
,11
]}

Mohamed, Rihlat Said ^{[12
]}

Fezeu, Alain ^{[4
,13
]}

Juimo, Vanessa A. ^{[4
,13
]}

Lafosse, Sophie ^{[10
]}

Tabe, Francis E. ^{[14
]}

Girard, Catherine ^{[4
,15
,16
]}

Iqaluk, Deborah ^{[4
]}

Nguyen, Le Thanh Tu ^{[1
,2
,3
,4
]}

Shapiro, B. Jesse ^{[4
,15
,17
,18
]}

Lehtimaki, Jenni ^{[4
,19
,20
]}

Ruokolainen, Lasse ^{[4
,19
]}

Kettunen, Pinja P. ^{[4
,19
]}

Vatanen, Tommi ^{[3
,4
,21
]}

Sigwazi, Shani ^{[4
,22
]}

Mabulla, Audax ^{[4
,23
]}

Dominguez-Rodrigo, Manuel ^{[4
,24
,25
]}

Nartey, Yvonne A. ^{[4
,26
]}

Agyei-Nkansah, Adwoa ^{[4
,27
,28
]}

Duah, Amoako ^{[4
,29
]}

Awuku, Yaw A. ^{[4
,30
]}

Valles, Kenneth A. ^{[4
,31
]}

Asibey, Shadrack O. ^{[4
,32
]}

Afihene, Mary Y. ^{[4
,33
]}

Roberts, Lewis R. ^{[4
,34
]}

Plymoth, Amelie ^{[4
,26
]}

Onyekwere, Charles A. ^{[4
,35
]}

Summons, Roger E. ^{[4
,5
]}

Xavier, Ramnik J. ^{[3
,4
,36
,37
,38
]}

Alm, Eric J. ^{[1
,2
,3
,4
]}

机构：

[1] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[2] MIT, Ctr Microbiome Informat & Therapeut, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[3] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[4] MIT, Global Microbiome Conservancy, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[5] MIT, Dept Earth Atmospher & Planetary Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[6] Univ Copenhagen, GLOBE Inst, Copenhagen, Denmark

[7] Chief Dull Knife Coll, Lame Deer, MT USA

[8] Inst Syst Biol, Seattle, WA USA

[9] Univ Washington, Dept Bioengn, Seattle, WA 98195 USA

[10] Univ Paris Diderot Sorbonne, UMR7206 Ecoanthropol, CNRS, MNHN, Paris, France

[11] Museum Natl Hist Nat, Inst Rech Dev, UMR 208, Paris, France

[12] Univ Witwatersrand, Fac Hlth Sci, Sch Clin Med, Dept Paediat, Johannesburg, South Africa

[13] Inst Rech Dev, Yaounde, Cameroon

[14] Univ Yaounde I, Fac Med & Sci Biomed, Yaounde, Cameroon

[15] Univ Montreal, Dept Sci Biol, CP 6128,Succursale Ctr Ville, Montreal, PQ, Canada

[16] Univ Laval, Ctr Detud Nordiques, Dept Biochim, 1030 Rue Med, Quebec City, PQ, Canada

[17] McGill Univ, Dept Microbiol & Immunol, Montreal, PQ, Canada

[18] McGill Univ, McGill Genome Ctr, Montreal, PQ, Canada

[19] Univ Helsinki, Fac Biol & Environm Sci, Organismal & Evolutionary Biol Res Programme, Helsinki, Finland

[20] Finnish Environm Inst SYKE, Environm Policy Ctr, Helsinki, Finland

[21] Univ Auckland, Liggins Inst, Auckland 1023, New Zealand

[22] Tumaini Univ Makumira, Arusha, Tanzania

[23] Univ Dar Salaam, Dept Archaeol & Heritage Studies, Dar Es Salaam, Tanzania

[24] Univ Alcala, Dept Hist & Philosophy, Prehist Unit, Madrid, Spain

[25] Univ Alcala Henares, Inst Evolut Africa, Madrid, Spain

[26] Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden

[27] Univ Ghana, Dept Med & Therapeut, Med Sch, Accra, Ghana

[28] Korle Bu Teaching Hosp, Accra, Ghana

[29] St Domin Hosp, Dept Med, Akwatia, Ghana

[30] Sch Med Sci Univ Cape Coast, Dept Internal Med & Therapeut, Cape Coast, Ghana

[31] Mayo Clin, Med Scientist Training Program, Rochester, NY 55905 USA

[32] Catholic Univ Coll, Sunyani, Ghana

[33] Kwame Nkrumah Univ Sci & Technol, Dept Med, Kumasi, Ghana

[34] Mayo Clin, Div Gastroenterol & Hepatol, 200 First St SW, Rochester, MN USA

[35] Lagos State Univ Coll Med, Dept Med, Lagos, Nigeria

[36] Massachusetts Gen Hosp, Ctr Computat & Integrat Biol, Boston, MA 02114 USA

[37] Harvard Med Sch, Boston, MA 02115 USA

[38] Massachusetts Gen Hosp, Dept Mol Biol, Boston, MA 02114 USA

来源：

CELL | 2021年 / 184卷 / 08期

基金：

欧盟地平线“2020”;

关键词：

GUT MICROBIOTA; GENOME; EVOLUTION; BACTERIA; INFLAMMATION; ANNOTATION; MECHANISMS; ALIGNMENT; RESOURCE; REVEALS;

D O I：

10.1016/j.cell.2021.02.052

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

引用

页码：2053 / +

页数：33

共 85 条

[1]

Agarwala R, 2018, NUCLEIC ACIDS RES, V46, pD8, DOI [10.1093/nar/gkx1095, 10.1093/nar/gks1189, 10.1093/nar/gkq1172]

[2] A unified catalog of 204,938 reference genomes from the human gut microbiome [J].

Almeida, Alexandre ;

Nayfach, Stephen ;

Boland, Miguel ;

Strozzi, Francesco ;

Beracochea, Martin ;

Shi, Zhou Jason ;

Pollard, Katherine S. ;

Sakharova, Ekaterina ;

Parks, Donovan H. ;

Hugenholtz, Philip ;

Segata, Nicola ;

Kyrpides, Nikos C. ;

Finn, Robert D. .

NATURE BIOTECHNOLOGY, 2021, 39 (01) :105-114

[3] SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].

Bankevich, Anton ;

Nurk, Sergey ;

Antipov, Dmitry ;

Gurevich, Alexey A. ;

Dvorkin, Mikhail ;

Kulikov, Alexander S. ;

Lesin, Valery M. ;

Nikolenko, Sergey I. ;

Son Pham ;

Prjibelski, Andrey D. ;

Pyshkin, Alexey V. ;

Sirotkin, Alexander V. ;

Vyahhi, Nikolay ;

Tesler, Glenn ;

Alekseyev, Max A. ;

Pevzner, Pavel A. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477

[4] Fitting Linear Mixed-Effects Models Using lme4 [J].

Bates, Douglas ;

Maechler, Martin ;

Bolker, Benjamin M. ;

Walker, Steven C. .

JOURNAL OF STATISTICAL SOFTWARE, 2015, 67 (01) :1-48

[5] Scaffolding pre-assembled contigs using SSPACE [J].

Boetzer, Marten ;

Henkel, Christiaan V. ;

Jansen, Hans J. ;

Butler, Derek ;

Pirovano, Walter .

BIOINFORMATICS, 2011, 27 (04) :578-579

[6] Trimmomatic: a flexible trimmer for Illumina sequence data [J].

Bolger, Anthony M. ;

Lohse, Marc ;

Usadel, Bjoern .

BIOINFORMATICS, 2014, 30 (15) :2114-2120

[7] Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation [J].

Brewster, Ryan ;

Tamburini, Fiona B. ;

Asiimwe, Edgar ;

Oduaran, Ovokeraye ;

Hazelhurst, Scott ;

Bhatt, Ami S. .

TRENDS IN MICROBIOLOGY, 2019, 27 (10) :824-835

[8] Mobile genes in the human microbiome are structured from global to individual scales [J].

Brito, I. L. ;

Yilmaz, S. ;

Huang, K. ;

Xu, L. ;

Jupiter, S. D. ;

Jenkins, A. P. ;

Naisilisili, W. ;

Tamminen, M. ;

Smillie, C. S. ;

Wortman, J. R. ;

Birren, B. W. ;

Xavier, R. J. ;

Blainey, P. C. ;

Singh, A. K. ;

Gevers, D. ;

Alm, E. J. .

NATURE, 2016, 535 (7612) :435-+

[9] Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation [J].

Browne, Hilary P. ;

Forster, Samuel C. ;

Anonye, Blessing O. ;

Kumar, Nitin ;

Neville, B. Anne ;

Stares, Mark D. ;

Goulding, David ;

Lawley, Trevor D. .

NATURE, 2016, 533 (7604) :543-+

[10] Fast and sensitive protein alignment using DIAMOND [J].

Buchfink, Benjamin ;

Xie, Chao ;

Huson, Daniel H. .

NATURE METHODS, 2015, 12 (01) :59-60

← 1 2 3 4 5 6 7 8 9 →