Challenges and future directions for studying effects of host genetics on the gut microbiome

被引：70

作者：

Sanna, Serena ^{[1
,2
,3
]}

Kurilshikov, Alexander ^{[2
,3
]}

van der Graaf, Adriaan ^{[2
,3
,4
]}

Fu, Jingyuan ^{[2
,3
,5
]}

Zhernakova, Alexandra ^{[2
,3
]}

机构：

[1] Natl Res Council CNR, Inst Genet & Biomed Res IRGB, Cagliari, Italy

[2] Univ Groningen, Dept Genet, Groningen, Netherlands

[3] Univ Med Ctr Groningen, Groningen, Netherlands

[4] Univ Lausanne, Dept Computat Biol, Lausanne, Switzerland

[5] Univ Groningen, Dept Pediat, Groningen, Netherlands

来源：

NATURE GENETICS | 2022年 / 54卷 / 02期

基金：

欧洲研究理事会;

关键词：

GENOME-WIDE ASSOCIATION; FETAL-HEMOGLOBIN; DETECTS MULTIPLE; METAGENOMICS; INSIGHTS; DISEASE; ADULT; TWINS; LOCI;

D O I：

10.1038/s41588-021-00983-z

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

This Perspective discusses the analytical issues concerning heterogeneity and power encountered in microbial genome-wide association studies and highlights potential future directions for genetic analysis of the microbiome. The human gut microbiome is a complex ecosystem that is involved in its host's metabolism, immunity and health. Although interindividual variations in gut microbial composition are mainly driven by environmental factors, some gut microorganisms are heritable and thus can be influenced by host genetics. In the past 5 years, 12 microbial genome-wide association studies (mbGWAS) with >1,000 participants have been published, yet only a few genetic loci have been consistently confirmed across multiple studies. Here we discuss the state of the art for mbGWAS, focusing on current challenges such as the heterogeneity of microbiome measurements and power issues, and we elaborate on potential future directions for genetic analysis of the microbiome.

引用

页码：100 / 106

页数：7

共 68 条

[1] A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing [J].

Andreu-Sanchez, Sergio ;

Chen, Lianmin ;

Wang, Daoming ;

Augustijn, Hannah E. ;

Zhernakova, Alexandra ;

Fu, Jingyuan .

FRONTIERS IN GENETICS, 2021, 12

[2] A reference map of potential determinants for the human serum metabolome [J].

Bar, Noam ;

Korem, Tal ;

Weissbrod, Omer ;

Zeevi, David ;

Rothschild, Daphna ;

Leviatan, Sigal ;

Kosower, Noa ;

Lotan-Pompan, Maya ;

Weinberger, Adina ;

Le Roy, Caroline I. ;

Menni, Cristina ;

Visconti, Alessia ;

Falchi, Mario ;

Spector, Tim D. ;

Adamski, Jerzy ;

Franks, Paul W. ;

Pedersen, Oluf ;

Segal, Eran .

NATURE, 2020, 588 (7836) :135-140

[3] Host genetic variation impacts microbiome composition across human body sites [J].

Blekhman, Ran ;

Goodrich, Julia K. ;

Huang, Katherine ;

Sun, Qi ;

Bukowski, Robert ;

Bell, Jordana T. ;

Spector, Timothy D. ;

Keinan, Alon ;

Ley, Ruth E. ;

Gevers, Dirk ;

Clark, Andrew G. .

GENOME BIOLOGY, 2015, 16

[4] The effect of host genetics on the gut microbiome [J].

Bonder, Marc Jan ;

Kurilshikov, Alexander ;

Tigchelaar, Ettje F. ;

Mujagic, Zlatan ;

Imhann, Floris ;

Vila, Arnau Vich ;

Deelen, Patrick ;

Vatanen, Tommi ;

Schirmer, Melanie ;

Smeekens, Sanne P. ;

Zhernakova, Dania V. ;

Jankipersadsing, Soesma A. ;

Jaeger, Martin ;

Oosting, Marije ;

Cenit, Maria Carmen ;

Masclee, Ad A. M. ;

Swertz, Morris A. ;

Li, Yang ;

Kumar, Vinod ;

Joosten, Leo ;

Harmsen, Hermie ;

Weersma, Rinse K. ;

Franke, Lude ;

Hofker, Marten H. ;

Xavier, Ramnik J. ;

Jonkers, Daisy ;

Netea, Mihai G. ;

Wijmenga, Cisca ;

Fu, Jingyuan ;

Zhernakova, Alexandra .

NATURE GENETICS, 2016, 48 (11) :1407-1412

[5] The multiple faces of CD5 [J].

Burgueno-Bucio, Erica ;

Mier-Aguilar, Carlos A. ;

Soldevila, Gloria .

JOURNAL OF LEUKOCYTE BIOLOGY, 2019, 105 (05) :891-904

[6] Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls [J].

Burton, Paul R. ;

Clayton, David G. ;

Cardon, Lon R. ;

Craddock, Nick ;

Deloukas, Panos ;

Duncanson, Audrey ;

Kwiatkowski, Dominic P. ;

McCarthy, Mark I. ;

Ouwehand, Willem H. ;

Samani, Nilesh J. ;

Todd, John A. ;

Donnelly, Peter ;

Barrett, Jeffrey C. ;

Davison, Dan ;

Easton, Doug ;

Evans, David ;

Leung, Hin-Tak ;

Marchini, Jonathan L. ;

Morris, Andrew P. ;

Spencer, Chris C. A. ;

Tobin, Martin D. ;

Attwood, Antony P. ;

Boorman, James P. ;

Cant, Barbara ;

Everson, Ursula ;

Hussey, Judith M. ;

Jolley, Jennifer D. ;

Knight, Alexandra S. ;

Koch, Kerstin ;

Meech, Elizabeth ;

Nutland, Sarah ;

Prowse, Christopher V. ;

Stevens, Helen E. ;

Taylor, Niall C. ;

Walters, Graham R. ;

Walker, Neil M. ;

Watkins, Nicholas A. ;

Winzer, Thilo ;

Jones, Richard W. ;

McArdle, Wendy L. ;

Ring, Susan M. ;

Strachan, David P. ;

Pembrey, Marcus ;

Breen, Gerome ;

St Clair, David ;

Caesar, Sian ;

Gordon-Smith, Katherine ;

Jones, Lisa ;

Fraser, Christine ;

Green, Elain K. .

NATURE, 2007, 447 (7145) :661-678

[7] The long-term genetic stability and individual specificity of the human gut microbiome [J].

Chen, Lianmin ;

Wang, Daoming ;

Garmaeva, Sanzhima ;

Kurilshikov, Alexander ;

Vila, Arnau Vich ;

Gacesa, Ranko ;

Sinha, Trishla ;

Segal, Eran ;

Weersma, Rinse K. ;

Wijmenga, Cisca ;

Zhernakova, Alexandra ;

Fu, Jingyuan .

CELL, 2021, 184 (09) :2302-+

[8] Runx2+Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling [J].

Chen, Shuo ;

Jing, Junjun ;

Yuan, Yuan ;

Feng, Jifan ;

Han, Xia ;

Wen, Quan ;

Thach-Vu Ho ;

Lee, Chelsea ;

Chai, Yang .

CELL REPORTS, 2020, 32 (06)

[9] metaSNV: A tool for metagenomic strain level analysis [J].

Costea, Paul Igor ;

Munch, Robin ;

Coelho, Luis Pedro ;

Paoli, Lucas ;

Sunagawa, Shinichi ;

Bork, Peer .

PLOS ONE, 2017, 12 (07)

[10] Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels [J].

Danjou, Fabrice ;

Zoledziewska, Magdalena ;

Sidore, Carlo ;

Steri, Maristella ;

Busonero, Fabio ;

Maschio, Andrea ;

Mulas, Antonella ;

Perseu, Lucia ;

Barella, Susanna ;

Porcu, Eleonora ;

Pistis, Giorgio ;

Pitzalis, Maristella ;

Pala, Mauro ;

Menzel, Stephan ;

Metrustry, Sarah ;

Spector, Timothy D. ;

Leoni, Lidia ;

Angius, Andrea ;

Uda, Manuela ;

Moi, Paolo ;

Thein, Swee Lay ;

Galanello, Renzo ;

Abecasis, Gonaalo R. ;

Schlessinger, David ;

Sanna, Serena ;

Cucca, Francesco .

NATURE GENETICS, 2015, 47 (11) :1264-+

← 1 2 3 4 5 6 7 →