Literature DB >> 27126034

Cross-species comparisons of host genetic associations with the microbiome.

Julia K Goodrich1, Emily R Davenport1, Jillian L Waters2, Andrew G Clark1, Ruth E Ley3.   

Abstract

Recent studies in human populations and mouse models reveal notable congruences in gut microbial taxa whose abundances are partly regulated by host genotype. Host genes associating with these taxa are related to diet sensing, metabolism, and immunity. These broad patterns are further validated in similar studies of nonmammalian microbiomes. The next generation of genome-wide association studies will expand the size of the data sets and refine the microbial phenotypes to fully capture these intriguing signatures of host-microbiome coevolution.
Copyright © 2016, American Association for the Advancement of Science.

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Year:  2016        PMID: 27126034      PMCID: PMC5116907          DOI: 10.1126/science.aad9379

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  37 in total

1.  Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors.

Authors:  Andrew K Benson; Scott A Kelly; Ryan Legge; Fangrui Ma; Soo Jen Low; Jaehyoung Kim; Min Zhang; Phaik Lyn Oh; Derrick Nehrenberg; Kunjie Hua; Stephen D Kachman; Etsuko N Moriyama; Jens Walter; Daniel A Peterson; Daniel Pomp
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-11       Impact factor: 11.205

2.  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

3.  Richness of human gut microbiome correlates with metabolic markers.

Authors:  Emmanuelle Le Chatelier; Trine Nielsen; Junjie Qin; Edi Prifti; Falk Hildebrand; Gwen Falony; Mathieu Almeida; Manimozhiyan Arumugam; Jean-Michel Batto; Sean Kennedy; Pierre Leonard; Junhua Li; Kristoffer Burgdorf; Niels Grarup; Torben Jørgensen; Ivan Brandslund; Henrik Bjørn Nielsen; Agnieszka S Juncker; Marcelo Bertalan; Florence Levenez; Nicolas Pons; Simon Rasmussen; Shinichi Sunagawa; Julien Tap; Sebastian Tims; Erwin G Zoetendal; Søren Brunak; Karine Clément; Joël Doré; Michiel Kleerebezem; Karsten Kristiansen; Pierre Renault; Thomas Sicheritz-Ponten; Willem M de Vos; Jean-Daniel Zucker; Jeroen Raes; Torben Hansen; Peer Bork; Jun Wang; S Dusko Ehrlich; Oluf Pedersen
Journal:  Nature       Date:  2013-08-29       Impact factor: 49.962

4.  Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins.

Authors:  Elizabeth E Hansen; Catherine A Lozupone; Federico E Rey; Meng Wu; Janaki L Guruge; Aneesha Narra; Jonathan Goodfellow; Jesse R Zaneveld; Daniel T McDonald; Julia A Goodrich; Andrew C Heath; Rob Knight; Jeffrey I Gordon
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-11       Impact factor: 11.205

5.  Structure, function and diversity of the healthy human microbiome.

Authors: 
Journal:  Nature       Date:  2012-06-13       Impact factor: 49.962

6.  Human gut microbiome viewed across age and geography.

Authors:  Tanya Yatsunenko; Federico E Rey; Mark J Manary; Indi Trehan; Maria Gloria Dominguez-Bello; Monica Contreras; Magda Magris; Glida Hidalgo; Robert N Baldassano; Andrey P Anokhin; Andrew C Heath; Barbara Warner; Jens Reeder; Justin Kuczynski; J Gregory Caporaso; Catherine A Lozupone; Christian Lauber; Jose Carlos Clemente; Dan Knights; Rob Knight; Jeffrey I Gordon
Journal:  Nature       Date:  2012-05-09       Impact factor: 49.962

7.  Directional dominance on stature and cognition in diverse human populations.

Authors:  Peter K Joshi; Tonu Esko; Ozren Polašek; James F Wilson; Hannele Mattsson; Niina Eklund; Ilaria Gandin; Teresa Nutile; Anne U Jackson; Claudia Schurmann; Albert V Smith; Weihua Zhang; Yukinori Okada; Alena Stančáková; Jessica D Faul; Wei Zhao; Traci M Bartz; Maria Pina Concas; Nora Franceschini; Stefan Enroth; Veronique Vitart; Stella Trompet; Xiuqing Guo; Daniel I Chasman; Jeffery R O'Connel; Tanguy Corre; Suraj S Nongmaithem; Yuning Chen; Massimo Mangino; Daniela Ruggiero; Michela Traglia; Aliki-Eleni Farmaki; Tim Kacprowski; Andrew Bjonnes; Ashley van der Spek; Ying Wu; Anil K Giri; Lisa R Yanek; Lihua Wang; Edith Hofer; Cornelius A Rietveld; Olga McLeod; Marilyn C Cornelis; Cristian Pattaro; Niek Verweij; Clemens Baumbach; Abdel Abdellaoui; Helen R Warren; Dragana Vuckovic; Hao Mei; Claude Bouchard; John R B Perry; Stefania Cappellani; Saira S Mirza; Miles C Benton; Ulrich Broeckel; Sarah E Medland; Penelope A Lind; Giovanni Malerba; Alexander Drong; Loic Yengo; Lawrence F Bielak; Degui Zhi; Peter J van der Most; Daniel Shriner; Reedik Mägi; Gibran Hemani; Tugce Karaderi; Zhaoming Wang; Tian Liu; Ilja Demuth; Jing Hua Zhao; Weihua Meng; Lazaros Lataniotis; Sander W van der Laan; Jonathan P Bradfield; Andrew R Wood; Amelie Bonnefond; Tarunveer S Ahluwalia; Leanne M Hall; Erika Salvi; Seyhan Yazar; Lisbeth Carstensen; Hugoline G de Haan; Mark Abney; Uzma Afzal; Matthew A Allison; Najaf Amin; Folkert W Asselbergs; Stephan J L Bakker; R Graham Barr; Sebastian E Baumeister; Daniel J Benjamin; Sven Bergmann; Eric Boerwinkle; Erwin P Bottinger; Archie Campbell; Aravinda Chakravarti; Yingleong Chan; Stephen J Chanock; Constance Chen; Y-D Ida Chen; Francis S Collins; John Connell; Adolfo Correa; L Adrienne Cupples; George Davey Smith; Gail Davies; Marcus Dörr; Georg Ehret; Stephen B Ellis; Bjarke Feenstra; Mary F Feitosa; Ian Ford; Caroline S Fox; Timothy M Frayling; Nele Friedrich; Frank Geller; Generation Scotland; Irina Gillham-Nasenya; Omri Gottesman; Misa Graff; Francine Grodstein; Charles Gu; Chris Haley; Christopher J Hammond; Sarah E Harris; Tamara B Harris; Nicholas D Hastie; Nancy L Heard-Costa; Kauko Heikkilä; Lynne J Hocking; Georg Homuth; Jouke-Jan Hottenga; Jinyan Huang; Jennifer E Huffman; Pirro G Hysi; M Arfan Ikram; Erik Ingelsson; Anni Joensuu; Åsa Johansson; Pekka Jousilahti; J Wouter Jukema; Mika Kähönen; Yoichiro Kamatani; Stavroula Kanoni; Shona M Kerr; Nazir M Khan; Philipp Koellinger; Heikki A Koistinen; Manraj K Kooner; Michiaki Kubo; Johanna Kuusisto; Jari Lahti; Lenore J Launer; Rodney A Lea; Benjamin Lehne; Terho Lehtimäki; David C M Liewald; Lars Lind; Marie Loh; Marja-Liisa Lokki; Stephanie J London; Stephanie J Loomis; Anu Loukola; Yingchang Lu; Thomas Lumley; Annamari Lundqvist; Satu Männistö; Pedro Marques-Vidal; Corrado Masciullo; Angela Matchan; Rasika A Mathias; Koichi Matsuda; James B Meigs; Christa Meisinger; Thomas Meitinger; Cristina Menni; Frank D Mentch; Evelin Mihailov; Lili Milani; May E Montasser; Grant W Montgomery; Alanna Morrison; Richard H Myers; Rajiv Nadukuru; Pau Navarro; Mari Nelis; Markku S Nieminen; Ilja M Nolte; George T O'Connor; Adesola Ogunniyi; Sandosh Padmanabhan; Walter R Palmas; James S Pankow; Inga Patarcic; Francesca Pavani; Patricia A Peyser; Kirsi Pietilainen; Neil Poulter; Inga Prokopenko; Sarju Ralhan; Paul Redmond; Stephen S Rich; Harri Rissanen; Antonietta Robino; Lynda M Rose; Richard Rose; Cinzia Sala; Babatunde Salako; Veikko Salomaa; Antti-Pekka Sarin; Richa Saxena; Helena Schmidt; Laura J Scott; William R Scott; Bengt Sennblad; Sudha Seshadri; Peter Sever; Smeeta Shrestha; Blair H Smith; Jennifer A Smith; Nicole Soranzo; Nona Sotoodehnia; Lorraine Southam; Alice V Stanton; Maria G Stathopoulou; Konstantin Strauch; Rona J Strawbridge; Matthew J Suderman; Nikhil Tandon; Sian-Tsun Tang; Kent D Taylor; Bamidele O Tayo; Anna Maria Töglhofer; Maciej Tomaszewski; Natalia Tšernikova; Jaakko Tuomilehto; Andre G Uitterlinden; Dhananjay Vaidya; Astrid van Hylckama Vlieg; Jessica van Setten; Tuula Vasankari; Sailaja Vedantam; Efthymia Vlachopoulou; Diego Vozzi; Eero Vuoksimaa; Melanie Waldenberger; Erin B Ware; William Wentworth-Shields; John B Whitfield; Sarah Wild; Gonneke Willemsen; Chittaranjan S Yajnik; Jie Yao; Gianluigi Zaza; Xiaofeng Zhu; The BioBank Japan Project; Rany M Salem; Mads Melbye; Hans Bisgaard; Nilesh J Samani; Daniele Cusi; David A Mackey; Richard S Cooper; Philippe Froguel; Gerard Pasterkamp; Struan F A Grant; Hakon Hakonarson; Luigi Ferrucci; Robert A Scott; Andrew D Morris; Colin N A Palmer; George Dedoussis; Panos Deloukas; Lars Bertram; Ulman Lindenberger; Sonja I Berndt; Cecilia M Lindgren; Nicholas J Timpson; Anke Tönjes; Patricia B Munroe; Thorkild I A Sørensen; Charles N Rotimi; Donna K Arnett; Albertine J Oldehinkel; Sharon L R Kardia; Beverley Balkau; Giovanni Gambaro; Andrew P Morris; Johan G Eriksson; Margie J Wright; Nicholas G Martin; Steven C Hunt; John M Starr; Ian J Deary; Lyn R Griffiths; Henning Tiemeier; Nicola Pirastu; Jaakko Kaprio; Nicholas J Wareham; Louis Pérusse; James G Wilson; Giorgia Girotto; Mark J Caulfield; Olli Raitakari; Dorret I Boomsma; Christian Gieger; Pim van der Harst; Andrew A Hicks; Peter Kraft; Juha Sinisalo; Paul Knekt; Magnus Johannesson; Patrik K E Magnusson; Anders Hamsten; Reinhold Schmidt; Ingrid B Borecki; Erkki Vartiainen; Diane M Becker; Dwaipayan Bharadwaj; Karen L Mohlke; Michael Boehnke; Cornelia M van Duijn; Dharambir K Sanghera; Alexander Teumer; Eleftheria Zeggini; Andres Metspalu; Paolo Gasparini; Sheila Ulivi; Carole Ober; Daniela Toniolo; Igor Rudan; David J Porteous; Marina Ciullo; Tim D Spector; Caroline Hayward; Josée Dupuis; Ruth J F Loos; Alan F Wright; Giriraj R Chandak; Peter Vollenweider; Alan Shuldiner; Paul M Ridker; Jerome I Rotter; Naveed Sattar; Ulf Gyllensten; Kari E North; Mario Pirastu; Bruce M Psaty; David R Weir; Markku Laakso; Vilmundur Gudnason; Atsushi Takahashi; John C Chambers; Jaspal S Kooner; David P Strachan; Harry Campbell; Joel N Hirschhorn; Markus Perola
Journal:  Nature       Date:  2015-07-01       Impact factor: 49.962

8.  Defining the core Arabidopsis thaliana root microbiome.

Authors:  Derek S Lundberg; Sarah L Lebeis; Sur Herrera Paredes; Scott Yourstone; Jase Gehring; Stephanie Malfatti; Julien Tremblay; Anna Engelbrektson; Victor Kunin; Tijana Glavina Del Rio; Robert C Edgar; Thilo Eickhorst; Ruth E Ley; Philip Hugenholtz; Susannah Green Tringe; Jeffery L Dangl
Journal:  Nature       Date:  2012-08-02       Impact factor: 49.962

9.  The gut microbiome modulates colon tumorigenesis.

Authors:  Joseph P Zackular; Nielson T Baxter; Kathryn D Iverson; William D Sadler; Joseph F Petrosino; Grace Y Chen; Patrick D Schloss
Journal:  MBio       Date:  2013-11-05       Impact factor: 7.867

10.  mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities.

Authors:  Jun Ma; Cristian Coarfa; Xiang Qin; Penelope E Bonnen; Aleksandar Milosavljevic; James Versalovic; Kjersti Aagaard
Journal:  BMC Genomics       Date:  2014-04-03       Impact factor: 3.969

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  97 in total

Review 1.  The Role of the Gut Microbiome in Predicting Response to Diet and the Development of Precision Nutrition Models. Part II: Results.

Authors:  Riley L Hughes; Mary E Kable; Maria Marco; Nancy L Keim
Journal:  Adv Nutr       Date:  2019-11-01       Impact factor: 8.701

Review 2.  The Central Nervous System and the Gut Microbiome.

Authors:  Gil Sharon; Timothy R Sampson; Daniel H Geschwind; Sarkis K Mazmanian
Journal:  Cell       Date:  2016-11-03       Impact factor: 41.582

3.  The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish.

Authors:  Keaton Stagaman; Adam R Burns; Karen Guillemin; Brendan Jm Bohannan
Journal:  ISME J       Date:  2017-03-17       Impact factor: 10.302

4.  The gut microbiota response to helminth infection depends on host sex and genotype.

Authors:  Fei Ling; Natalie Steinel; Jesse Weber; Lei Ma; Chris Smith; Decio Correa; Bin Zhu; Daniel Bolnick; Gaoxue Wang
Journal:  ISME J       Date:  2020-01-31       Impact factor: 10.302

5.  Interactions of commensal and pathogenic microorganisms with the mucus layer in the colon.

Authors:  Rui Cai; Chen Cheng; Jianwei Chen; Xiaoqiang Xu; Chao Ding; Bing Gu
Journal:  Gut Microbes       Date:  2020-03-29

Review 6.  Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities.

Authors:  Kevin D Kohl
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-03-23       Impact factor: 6.237

Review 7.  Gut dysbiosis and age-related neurological diseases; an innovative approach for therapeutic interventions.

Authors:  Aleah Holmes; Carson Finger; Diego Morales-Scheihing; Juneyoung Lee; Louise D McCullough
Journal:  Transl Res       Date:  2020-08-02       Impact factor: 7.012

8.  HOMINID: a framework for identifying associations between host genetic variation and microbiome composition.

Authors:  Joshua Lynch; Karen Tang; Sambhawa Priya; Joanna Sands; Margaret Sands; Evan Tang; Sayan Mukherjee; Dan Knights; Ran Blekhman
Journal:  Gigascience       Date:  2017-12-01       Impact factor: 6.524

Review 9.  Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology.

Authors:  Manuel Ferrer; David Rojo; Celia Méndez-García; Coral Barbas
Journal:  J Bacteriol       Date:  2018-01-10       Impact factor: 3.490

Review 10.  Determinants of IBD Heritability: Genes, Bugs, and More.

Authors:  Williams Turpin; Ashleigh Goethel; Larbi Bedrani; Kenneth Croitoru Mdcm
Journal:  Inflamm Bowel Dis       Date:  2018-05-18       Impact factor: 5.325

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