Literature DB >> 35115688

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

Serena Sanna1,2, Alexander Kurilshikov3, Adriaan van der Graaf3,4, Jingyuan Fu3,5, Alexandra Zhernakova6.   

Abstract

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.
© 2022. Springer Nature America, Inc.

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Year:  2022        PMID： 35115688     DOI： 10.1038/s41588-021-00983-z

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   41.307


  58 in total

1.  Association of host genome with intestinal microbial composition in a large healthy cohort.

Authors:  Williams Turpin; Osvaldo Espin-Garcia; Wei Xu; Mark S Silverberg; David Kevans; Michelle I Smith; David S Guttman; Anne Griffiths; Remo Panaccione; Anthony Otley; Lizhen Xu; Konstantin Shestopaloff; Gabriel Moreno-Hagelsieb; Andrew D Paterson; Kenneth Croitoru
Journal:  Nat Genet       Date:  2016-10-03       Impact factor: 38.330

2.  Population-level analysis of gut microbiome variation.

Authors:  Gwen Falony; Marie Joossens; Sara Vieira-Silva; Jun Wang; Youssef Darzi; Karoline Faust; Alexander Kurilshikov; Marc Jan Bonder; Mireia Valles-Colomer; Doris Vandeputte; Raul Y Tito; Samuel Chaffron; Leen Rymenans; Chloë Verspecht; Lise De Sutter; Gipsi Lima-Mendez; Kevin D'hoe; Karl Jonckheere; Daniel Homola; Roberto Garcia; Ettje F Tigchelaar; Linda Eeckhaudt; Jingyuan Fu; Liesbet Henckaerts; Alexandra Zhernakova; Cisca Wijmenga; Jeroen Raes
Journal:  Science       Date:  2016-04-28       Impact factor: 47.728

3.  Human genetics shape the gut microbiome.

Authors:  Julia K Goodrich; Jillian L Waters; Angela C Poole; Jessica L Sutter; Omry Koren; Ran Blekhman; Michelle Beaumont; William Van Treuren; Rob Knight; Jordana T Bell; Timothy D Spector; Andrew G Clark; Ruth E Ley
Journal:  Cell       Date:  2014-11-06       Impact factor: 41.582

4.  Environment dominates over host genetics in shaping human gut microbiota.

Authors:  Daphna Rothschild; Omer Weissbrod; Elad Barkan; Alexander Kurilshikov; Tal Korem; David Zeevi; Paul I Costea; Anastasia Godneva; Iris N Kalka; Noam Bar; Smadar Shilo; Dar Lador; Arnau Vich Vila; Niv Zmora; Meirav Pevsner-Fischer; David Israeli; Noa Kosower; Gal Malka; Bat Chen Wolf; Tali Avnit-Sagi; Maya Lotan-Pompan; Adina Weinberger; Zamir Halpern; Shai Carmi; Jingyuan Fu; Cisca Wijmenga; Alexandra Zhernakova; Eran Elinav; Eran Segal
Journal:  Nature       Date:  2018-02-28       Impact factor: 49.962

5.  Genetic Determinants of the Gut Microbiome in UK Twins.

Authors:  Julia K Goodrich; Emily R Davenport; Michelle Beaumont; Matthew A Jackson; Rob Knight; Carole Ober; Tim D Spector; Jordana T Bell; Andrew G Clark; Ruth E Ley
Journal:  Cell Host Microbe       Date:  2016-05-11       Impact factor: 21.023

6.  Large-scale association analyses identify host factors influencing human gut microbiome composition.

Authors:  Alexander Kurilshikov; Carolina Medina-Gomez; Rodrigo Bacigalupe; Djawad Radjabzadeh; Jun Wang; Ayse Demirkan; Caroline I Le Roy; Juan Antonio Raygoza Garay; Casey T Finnicum; Xingrong Liu; Daria V Zhernakova; Marc Jan Bonder; Tue H Hansen; Fabian Frost; Malte C Rühlemann; Williams Turpin; Jee-Young Moon; Han-Na Kim; Kreete Lüll; Elad Barkan; Shiraz A Shah; Myriam Fornage; Joanna Szopinska-Tokov; Zachary D Wallen; Dmitrii Borisevich; Lars Agreus; Anna Andreasson; Corinna Bang; Larbi Bedrani; Jordana T Bell; Hans Bisgaard; Michael Boehnke; Dorret I Boomsma; Robert D Burk; Annique Claringbould; Kenneth Croitoru; Gareth E Davies; Cornelia M van Duijn; Liesbeth Duijts; Gwen Falony; Jingyuan Fu; Adriaan van der Graaf; Torben Hansen; Georg Homuth; David A Hughes; Richard G Ijzerman; Matthew A Jackson; Vincent W V Jaddoe; Marie Joossens; Torben Jørgensen; Daniel Keszthelyi; Rob Knight; Markku Laakso; Matthias Laudes; Lenore J Launer; Wolfgang Lieb; Aldons J Lusis; Ad A M Masclee; Henriette A Moll; Zlatan Mujagic; Qi Qibin; Daphna Rothschild; Hocheol Shin; Søren J Sørensen; Claire J Steves; Jonathan Thorsen; Nicholas J Timpson; Raul Y Tito; Sara Vieira-Silva; Uwe Völker; Henry Völzke; Urmo Võsa; Kaitlin H Wade; Susanna Walter; Kyoko Watanabe; Stefan Weiss; Frank U Weiss; Omer Weissbrod; Harm-Jan Westra; Gonneke Willemsen; Haydeh Payami; Daisy M A E Jonkers; Alejandro Arias Vasquez; Eco J C de Geus; Katie A Meyer; Jakob Stokholm; Eran Segal; Elin Org; Cisca Wijmenga; Hyung-Lae Kim; Robert C Kaplan; Tim D Spector; Andre G Uitterlinden; Fernando Rivadeneira; Andre Franke; Markus M Lerch; Lude Franke; Serena Sanna; Mauro D'Amato; Oluf Pedersen; Andrew D Paterson; Robert Kraaij; Jeroen Raes; Alexandra Zhernakova
Journal:  Nat Genet       Date:  2021-01-18       Impact factor: 41.307

7.  Genome-wide associations of human gut microbiome variation and implications for causal inference analyses.

Authors:  David A Hughes; Rodrigo Bacigalupe; Jun Wang; Malte C Rühlemann; Raul Y Tito; Gwen Falony; Marie Joossens; Sara Vieira-Silva; Liesbet Henckaerts; Leen Rymenans; Chloë Verspecht; Susan Ring; Andre Franke; Kaitlin H Wade; Nicholas J Timpson; Jeroen Raes
Journal:  Nat Microbiol       Date:  2020-06-22       Impact factor: 17.745

8.  Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Authors:  Alexandra Zhernakova; Alexander Kurilshikov; Marc Jan Bonder; Ettje F Tigchelaar; Melanie Schirmer; Tommi Vatanen; Zlatan Mujagic; Arnau Vich Vila; Gwen Falony; Sara Vieira-Silva; Jun Wang; Floris Imhann; Eelke Brandsma; Soesma A Jankipersadsing; Marie Joossens; Maria Carmen Cenit; Patrick Deelen; Morris A Swertz; Rinse K Weersma; Edith J M Feskens; Mihai G Netea; Dirk Gevers; Daisy Jonkers; Lude Franke; Yurii S Aulchenko; Curtis Huttenhower; Jeroen Raes; Marten H Hofker; Ramnik J Xavier; Cisca Wijmenga; Jingyuan Fu
Journal:  Science       Date:  2016-04-28       Impact factor: 47.728

9.  Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

Authors:  Edoardo Pasolli; Francesco Asnicar; Serena Manara; Moreno Zolfo; Nicolai Karcher; Federica Armanini; Francesco Beghini; Paolo Manghi; Adrian Tett; Paolo Ghensi; Maria Carmen Collado; Benjamin L Rice; Casey DuLong; Xochitl C Morgan; Christopher D Golden; Christopher Quince; Curtis Huttenhower; Nicola Segata
Journal:  Cell       Date:  2019-01-17       Impact factor: 41.582
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  6 in total

Review 1.  Genetics of irritable bowel syndrome: shifting gear via biobank-scale studies.

Authors:  Michael Camilleri; Alexandra Zhernakova; Isotta Bozzarelli; Mauro D'Amato
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2022-08-10       Impact factor: 73.082

Review 2.  Atherosclerosis: Recent developments.

Authors:  Johan L M Björkegren; Aldons J Lusis
Journal:  Cell       Date:  2022-05-02       Impact factor: 66.850

Review 3.  First 1000 Days and Beyond After Birth: Gut Microbiota and Necrotizing Enterocolitis in Preterm Infants.

Authors:  Shuqin Zeng; Junjie Ying; Shiping Li; Yi Qu; Dezhi Mu; Shaopu Wang
Journal:  Front Microbiol       Date:  2022-06-21       Impact factor: 6.064

Review 4.  Individual Genetic Heterogeneity.

Authors:  Mauno Vihinen
Journal:  Genes (Basel)       Date:  2022-09-10       Impact factor: 4.141

Review 5.  Effects of Green Tea Catechins on Prostate Cancer Chemoprevention: The Role of the Gut Microbiome.

Authors:  Nagi B Kumar; Stephanie Hogue; Julio Pow-Sang; Michael Poch; Brandon J Manley; Roger Li; Jasreman Dhillon; Alice Yu; Doratha A Byrd
Journal:  Cancers (Basel)       Date:  2022-08-18       Impact factor: 6.575

6.  C-phycocyanin alleviated cisplatin-induced oxidative stress and inflammation via gut microbiota-metabolites axis in mice.

Authors:  Yubing Zhang; Lili Li; Song Qin; Jingyi Yuan; Xiaonan Xie; Fan Wang; Shanliang Hu; Yuetao Yi; Min Chen
Journal:  Front Nutr       Date:  2022-09-20
  6 in total

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