{"id":157477,"date":"2025-06-04T12:30:10","date_gmt":"2025-06-04T12:30:10","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/157477\/"},"modified":"2025-06-04T12:30:10","modified_gmt":"2025-06-04T12:30:10","slug":"genomics-of-host-microbiome-interactions-in-humans","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/157477\/","title":{"rendered":"Genomics of host\u2013microbiome interactions in humans"},"content":{"rendered":"
  • \n

    Valdes, A. M., Walter, J., Segal, E. & Spector, T. D. Role of the gut microbiota in nutrition and health. BMJ 361<\/b>, k2179 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zheng, D., Liwinski, T. & Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Res. 30<\/b>, 492\u2013506 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tarracchini, C. et al. Exploring the vitamin biosynthesis landscape of the human gut microbiota. mSystems 9<\/b>, e0092924 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    de Vos, W. M., Tilg, H., Van Hul, M. & Cani, P. D. Gut microbiome and health: mechanistic insights. Gut 71<\/b>, 1020\u20131032 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Geng, J., Ni, Q., Sun, W., Li, L. & Feng, X. The links between gut microbiota and obesity and obesity related diseases. Biomed. Pharmacother. 147<\/b>, 112678 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Van Hul, M. & Cani, P. D. The gut microbiota in obesity and weight management: microbes as friends or foe? Nat. Rev. Endocrinol. 19<\/b>, 258\u2013271 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kandalai, S., Li, H., Zhang, N., Peng, H. & Zheng, Q. The human microbiome and cancer: a diagnostic and therapeutic perspective. Cancer Biol. Ther. 24<\/b>, 2240084 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vivarelli, S. et al. Gut microbiota and cancer: from pathogenesis to therapy. Cancers 11<\/b>, 38 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vich Vila, A. et al. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat. Commun. 11<\/b>, 362 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Amato, K. R. et al. The human gut microbiome and health inequities. Proc. Natl Acad. Sci. USA 118<\/b>, e2017947118 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Leeming, E. R., Johnson, A. J., Spector, T. D. & Le Roy, C. I. Effect of diet on the gut microbiota: rethinking intervention duration. Nutrients 11<\/b>, 2862 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Schmidt, T. S. B., Raes, J. & Bork, P. The human gut microbiome: from association to modulation. Cell 172<\/b>, 1198\u20131215 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457<\/b>, 480\u2013484 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Benson, A. K. et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl Acad. Sci. USA 107<\/b>, 18933\u201318938 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 159<\/b>, 789\u2013799 (2014). This important early study uses data from twins to estimate gut microbiome heritability.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Visscher, P. M., Hill, W. G. & Wray, N. R. Heritability in the genomics era\u2014concepts and misconceptions. Nat. Rev. Genet. 9<\/b>, 255\u2013266 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Goodrich, J. K. et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe 19<\/b>, 731\u2013743 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Davenport, E. R. et al. Genome-wide association studies of the human gut microbiota. PLoS One 10<\/b>, e0140301 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    O\u2019Callaghan, A. & van Sinderen, D. Bifidobacteria and their role as members of the human gut microbiota. Front. Microbiol. 7<\/b>, 925 (2016).<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Samuel, B. S. et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl Acad. Sci. USA 104<\/b>, 10643\u201310648 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ignatyeva, O. et al. Christensenella minuta, a new candidate next-generation probiotic: current evidence and future trajectories. Front. Microbiol. 14<\/b>, 1241259 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rothschild D et al. Environment dominates over host genetics in shaping human gut microbiota. Yearb. Pediatr. Endocrinol. https:\/\/doi.org\/10.1530\/ey.15.14.5<\/a> (2018). This key study argues that microbiome heritability is low and that environment is stronger than genetics in shaping the gut microbiome.<\/b><\/p>\n<\/li>\n

  • \n

    Hughes, D. A. et al. Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nat. Microbiol. 5<\/b>, 1079\u20131087 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, J. et al. Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative. Microbiome 6<\/b>, 101 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kurilshikov, A. et al. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat. Genet. 53<\/b>, 156\u2013165 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Boulund, U. et al. Gut microbiome associations with host genotype vary across ethnicities and potentially influence cardiometabolic traits. Cell. Host. Microbe 30<\/b>, 1464\u20131480.e6 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gacesa, R. et al. Environmental factors shaping the gut microbiome in a Dutch population. Nature 604<\/b>, 732\u2013739 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhernakova, D. V. et al. Host genetic regulation of human gut microbial structural variation. Nature 625<\/b>, 813\u2013821 (2024). This study investigates the heritability of structural variation in the gut microbiome.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Beaumont, M. et al. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol. 17<\/b>, 189 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Blekhman, R. et al. Host genetic variation impacts microbiome composition across human body sites. Genome Biol. 16<\/b>, 191 (2015). This important early study demonstrates the feasibility of testing for genome-wide host genetic associations with gut microbiome measurements as quantitative traits.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Grieneisen, L. et al. Gut microbiome heritability is nearly universal but environmentally contingent. Science 373<\/b>, 181\u2013186 (2021). This article describes a large study of microbiome heritability in wild primates.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhernakova, A. et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352<\/b>, 565\u2013569 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hejazi, J., Amiri, R., Nozarian, S., Tavasolian, R. & Rahimlou, M. Genetic determinants of food preferences: a systematic review of observational studies. BMC Nutr. 10<\/b>, 24 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vandeputte, D. et al. Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. Nat. Commun. 12<\/b>, 6740 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Org, E. et al. Genetic and environmental control of host\u2013gut microbiota interactions. Genome Res. 25<\/b>, 1558\u20131569 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chen, C. et al. Contribution of host genetics to the variation of microbial composition of cecum lumen and feces in pigs. Front. Microbiol. 9<\/b>, 2626 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Doms, S. et al. Key features of the genetic architecture and evolution of host\u2013microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice. eLife 11<\/b>, e75419 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    McKnite, A. M. et al. Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PLoS One 7<\/b>, e39191 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Leamy, L. J. et al. Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice. Genome Biol. 15<\/b>, 552 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Turpin, W. et al. Association of host genome with intestinal microbial composition in a large healthy cohort. Nat. Genet. 48<\/b>, 1413\u20131417 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bonder, M. J. et al. The effect of host genetics on the gut microbiome. Nat. Genet. 48<\/b>, 1407\u20131412 (2016). This paper describes an early study on the effects of host genetics on the gut microbiome.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, J. et al. Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nat. Genet. 48<\/b>, 1396\u20131406 (2016). This early microbiome GWAS finds associations with the gene encoding for the vitamin D receptor.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ishida, S. et al. Genome-wide association studies and heritability analysis reveal the involvement of host genetics in the Japanese gut microbiota. Commun. Biol. 3<\/b>, 686 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    R\u00fchlemann, M. C. et al. Genome-wide association study in 8956 German individuals identifies influence of ABO histo-blood groups on gut microbiome. Nat. Genet. 53<\/b>, 147\u2013155 (2021). This large GWAS identifies effects of the ABO blood group on the human gut microbiome.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, X. et al. A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases. Cell Discov. 7<\/b>, 9 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, X. et al. Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome. Nat. Genet. 54<\/b>, 52\u201361 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lopera-Maya, E. A. et al. Effect of host genetics on the gut microbiome in 7738 participants of the Dutch Microbiome Project. Nat. Genet. 54<\/b>, 143\u2013151 (2022). This large GWAS of the human gut microbiome validates the association of variants at the<\/b> LCT<\/b> locus and finds that the association is modulated by lactose intake.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Qin, Y. et al. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nat. Genet. 54<\/b>, 134\u2013142 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kolde, R. et al. Host genetic variation and its microbiome interactions within the human microbiome project. Genome Med. 10<\/b>, 6 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Scepanovic, P. et al. A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals. Microbiome 7<\/b>, 130 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tomofuji, Y. et al. Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome\u2013host interactions in the Japanese population. Cell Rep. 42<\/b>, 113324 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Moitinho-Silva, L. et al. Host genetic factors related to innate immunity, environmental sensing and cellular functions are associated with human skin microbiota. Nat. Commun. 13<\/b>, 6204 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, X. et al. A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome. Commun. Biol. 7<\/b>, 139 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fang, Z. Y. et al. Networks of human milk microbiota are associated with host genomics, childhood asthma, and allergic sensitization. Cell Host Microbe 32<\/b>, 1838\u20131852.e5 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Enattah, N. S. et al. Identification of a variant associated with adult-type hypolactasia. Nat. Genet. 30<\/b>, 233\u2013237 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rasinper\u00e4, H. et al. Transcriptional downregulation of the lactase (LCT) gene during childhood. Gut 54<\/b>, 1660\u20131661 (2005).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Garrido, D., Barile, D. & Mills, D. A. A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract. Adv. Nutr. 3<\/b>, 415S\u2013421S (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Itan, Y., Jones, B. L., Ingram, C. J. E., Swallow, D. M. & Thomas, M. G. A worldwide correlation of lactase persistence phenotype and genotypes. BMC Evol. Biol. 10<\/b>, 36 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jajosky, R. P. et al. ABO blood group antigens and differential glycan expression: perspective on the evolution of common human enzyme deficiencies. iScience 26<\/b>, 105798 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    M\u00e4kivuokko, H. et al. Association between the ABO blood group and the human intestinal microbiota composition. BMC Microbiol. 12<\/b>, 94 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rausch, P. et al. Multigenerational influences of the Fut2 gene on the dynamics of the gut microbiota in mice. Front. Microbiol. 8<\/b>, 991 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Folseraas, T. et al. Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci. J. Hepatol. 57<\/b>, 366\u2013375 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rausch, P. et al. Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proc. Natl Acad. Sci. USA 108<\/b>, 19030\u201319035 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wacklin, P. et al. Secretor genotype (FUT2 gene) is strongly associated with the composition of Bifidobacteria in the human intestine. PLoS One 6<\/b>, e20113 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tong, M. et al. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn\u2019s disease risk polymorphism. ISME J. 8<\/b>, 2193\u20132206 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang, H. et al. ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 606<\/b>, 358\u2013367 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    S\u00e9gurel, L. et al. The ABO blood group is a trans-species polymorphism in primates. Proc. Natl Acad. Sci. USA 109<\/b>, 18493\u201318498 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Burgess, S. et al. Guidelines for performing Mendelian randomization investigations: update for summer 2023. Wellcome Open. Res. 4<\/b>, 186 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Davey Smith, G. & Ebrahim, S. \u2018Mendelian randomization\u2019: can genetic epidemiology contribute to understanding environmental determinants of disease? Int. J. Epidemiol. 32<\/b>, 1\u201322 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sanderson, E. et al. Mendelian randomization. Nat. Rev. Methods Prim. 2<\/b>, 6 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sanna, S. et al. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat. Genet. 51<\/b>, 600\u2013605 (2019). Together with Liu et al. (2022), this work exemplifies the use of Mendelian randomization to identify potential causal effects of the microbiome on human health.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Arora, T. & Tremaroli, V. Therapeutic potential of butyrate for treatment of type 2 diabetes. Front. Endocrinol. 12<\/b>, 761834 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stender, S., Gellert-Kristensen, H. & Smith, G. D. Reclaiming Mendelian randomization from the deluge of papers and misleading findings. Lipids Health Dis. 23<\/b>, 286 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wade, K. H. & Hall, L. J. Improving causality in microbiome research: can human genetic epidemiology help? Wellcome Open. Res. 4<\/b>, 199 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Morgan, X. C. et al. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol. 16<\/b>, 67 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    H\u00e4sler, R. et al. Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease. Gut 66<\/b>, 2087\u20132097 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Omar Al-Hassi, H., Ng, O. & Brookes, M. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut 67<\/b>, 395 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bennet, S. M. P. et al. Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation: XXXX. Neurogastroenterol. Motil. 30<\/b>, e13468 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569<\/b>, 655\u2013662 (2019). Together with Morgan et al. (2015), this key paper describes associations between the gut microbiome and host gene regulation in IBD.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dayama, G., Priya, S., Niccum, D. E., Khoruts, A. & Blekhman, R. Interactions between the gut microbiome and host gene regulation in cystic fibrosis. Genome Med. 12<\/b>, 12 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mars, R. A. T. et al. Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome. Cell 182<\/b>, 1460\u20131473.e17 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chang, H. et al. Unveiling the links between microbial alteration and host gene disarray in Crohn\u2019s disease via TAHMC. Adv. Biol. 8<\/b>, e2400064 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mirsepasi-Lauridsen, H. C., Vallance, B. A., Krogfelt, K. A. & Petersen, A. M. Escherichia coli pathobionts associated with inflammatory bowel disease. Clin. Microbiol. Rev. 32<\/b>, e00060-18 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xu, S. et al. Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn\u2019s disease: a multi-omics Mendelian randomization study. BMC Med. 21<\/b>, 179 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Priya, S. et al. Identification of shared and disease-specific host gene\u2013microbiome associations across human diseases using multi-omic integration. Nat. Microbiol. 7<\/b>, 780\u2013795 (2022). This important study elucidates patterns of host gene\u2013microbiome interactions across diseases.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fyhrquist, N. et al. Microbe\u2013host interplay in atopic dermatitis and psoriasis. Nat. Commun. 10<\/b>, 4703 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Edfeldt, G. et al. Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers. Microbiome 11<\/b>, 67 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wang, Z. et al. Airway host\u2013microbiome interactions in chronic obstructive pulmonary disease. Respir. Res. 20<\/b>, 113 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yan, Z. et al. Multi-omics analyses of airway host\u2013microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions. Nat. Microbiol. 7<\/b>, 1361\u20131375 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Johnson, K. E. et al. Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome. Cell Genom. 4<\/b>, 100638 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang, Y. et al. Exploratory multi-omics analysis reveals host\u2013microbe interactions associated with disease severity in psoriatic skin. EBioMedicine 105<\/b>, 105222 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhu, B. et al. Characteristics of vaginal microbes and classification of the vaginal microbiome. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.08.16.553525<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Galeano Ni\u00f1o, J. L. et al. Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature 611<\/b>, 810\u2013817 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cai, L. et al. Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma. NPJ Biofilms Microbiomes 10<\/b>, 39 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Camp, J. G. et al. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 24<\/b>, 1504\u20131516 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sommer, F., Nookaew, I., Sommer, N., Fogelstrand, P. & B\u00e4ckhed, F. Site-specific programming of the host epithelial transcriptome by the gut microbiota. Genome Biol. 16<\/b>, 62 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pan, W.-H. et al. Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development. Genome Med. 10<\/b>, 27 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Davison, J. M. et al. Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor hepatocyte nuclear factor 4\u0251. Genome Res. 27<\/b>, 1195\u20131206 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Richards, A. L. et al. Gut microbiota has a widespread and modifiable effect on host gene regulation. mSystems 4<\/b>, e00323\u201318 (2019). Together with Davison et al. (2017), this key paper investigates the mechanisms of host gene\u2013microbiome cross-talk.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Semenkovich, N. P. et al. Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes. Proc. Natl Acad. Sci. USA 113<\/b>, 14805\u201314810 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Dirksen, P. et al. CeMbio\u2014the Caenorhabditis elegans microbiome resource. G3 10<\/b>, 3025\u20133039 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang, W. et al. The inducible response of the nematode Caenorhabditis elegans to members of its natural microbiota across development and adult life. Front. Microbiol. 10<\/b>, 1793 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Loomis, K. H. et al. A mixed community of skin microbiome representatives influences cutaneous processes more than individual members. Microbiome 9<\/b>, 22 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Brusilovsky, M. et al. Host\u2013microbiota interactions in the esophagus during homeostasis and allergic inflammation. Gastroenterology 162<\/b>, 521\u2013534.e8 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Meisel, J. S. et al. Commensal microbiota modulate gene expression in the skin. Microbiome 6<\/b>, 20 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ansari, I. et al. The microbiota programs DNA methylation to control intestinal homeostasis and inflammation. Nat. Microbiol. 5<\/b>, 610\u2013619 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Krautkramer, K. A. et al. Diet\u2013microbiota interactions mediate global epigenetic programming in multiple host tissues. Mol. Cell 64<\/b>, 982\u2013992 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kuang, Z. et al. The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3. Science 365<\/b>, 1428\u20131434 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ryan, F. J. et al. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. Nat. Commun. 11<\/b>, 1512 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nshanian, M. et al. Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression. Nat. Metab. 7<\/b>, 196\u2013211 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Muehlbauer, A. L. et al. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Rep. 37<\/b>, 110057 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Qin, Y. et al. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biol. 19<\/b>, 7 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Drayman, N., Patel, P., Vistain, L. & Tay, S. HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife 8<\/b>, e46339 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    L\u00f6tstedt, B., Stra\u017ear, M., Xavier, R., Regev, A. & Vickovic, S. Spatial host\u2013microbiome sequencing reveals niches in the mouse gut. Nat. Biotechnol. 42<\/b>, 1394\u20131403 (2024). Together with Galeano Ni\u00f1o et al. (2022), this notable paper describes spatial profiling of host\u2013microbiome interactions.<\/b><\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Massaquoi, M. S. et al. Cell-type-specific responses to the microbiota across all tissues of the larval zebrafish. Cell Rep. 42<\/b>, 112095 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Willms, R. J., Jones, L. O., Hocking, J. C. & Foley, E. A cell atlas of microbe-responsive processes in the zebrafish intestine. Cell Rep. 38<\/b>, 110311 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Puschhof, J. et al. Intestinal organoid cocultures with microbes. Nat. Protoc. 16<\/b>, 4633\u20134649 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Williamson, I. A. et al. A high-throughput organoid microinjection platform to study gastrointestinal microbiota and luminal physiology. Cell. Mol. Gastroenterol. Hepatol. 6<\/b>, 301\u2013319 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sanna, S., Kurilshikov, A., van der Graaf, A., Fu, J. & Zhernakova, A. Challenges and future directions for studying effects of host genetics on the gut microbiome. Nat. Genet. 54<\/b>, 100\u2013106 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xu, L., Paterson, A. D., Turpin, W. & Xu, W. Assessment and selection of competing models for zero-inflated microbiome data. PLoS One 10<\/b>, e0129606 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fisher, C. K. & Mehta, P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One 9<\/b>, e102451 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Weissbrod, O., Rothschild, D., Barkan, E. & Segal, E. Host genetics and microbiome associations through the lens of genome wide association studies. Curr. Opin. Microbiol. 44<\/b>, 9\u201319 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sham, P. C. & Purcell, S. M. Statistical power and significance testing in large-scale genetic studies. Nat. Rev. Genet. 15<\/b>, 335\u2013346 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chetty, A. & Blekhman, R. Multi-omic approaches for host\u2013microbiome data integration. Gut Microbes 16<\/b>, 2297860 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lynch, J. et al. HOMINID: a framework for identifying associations between host genetic variation and microbiome composition. Gigascience 6<\/b>, 1\u20137 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mills, R. H. et al. Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. Nat. Microbiol. 7<\/b>, 262\u2013276 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D. & Konstantinidis, K. T. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One 9<\/b>, e93827 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Durazzi, F. et al. Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Sci. Rep. 11<\/b>, 3030 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sharafutdinov, I. et al. A single-nucleotide polymorphism in Helicobacter pylori promotes gastric cancer development. Cell Host Microbe 31<\/b>, 1345\u20131358.e6 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Berthenet, E. et al. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. BMC Biol. 16<\/b>, 84 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sczyrba, A. et al. Critical assessment of metagenome interpretation\u2014a benchmark of metagenomics software. Nat. Methods 14<\/b>, 1063\u20131071 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Meisel, J. S. et al. Skin microbiome surveys are strongly influenced by experimental design. J. Invest. Dermatol. 136<\/b>, 947\u2013956 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Deissov\u00e1, T. et al. 16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling. Sci. Rep. 13<\/b>, 12577 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Elie, C. et al. Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome. Sci. Rep. 13<\/b>, 10279 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Allaband, C. et al. Time of sample collection is critical for the replicability of microbiome analyses. Nat. Metab. 6<\/b>, 1282\u20131293 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nishijima, S. et al. Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations. Cell 188<\/b>, 222\u2013236.e15 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pallister, T. et al. Food preference patterns in a UK twin cohort. Twin Res. Hum. Genet. 18<\/b>, 793\u2013805 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fildes, A. et al. Nature and nurture in children\u2019s food preferences. Am. J. Clin. Nutr. 99<\/b>, 911\u2013917 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Goodrich, J. K., Davenport, E. R., Waters, J. L., Clark, A. G. & Ley, R. E. Cross-species comparisons of host genetic associations with the microbiome. Science 352<\/b>, 532\u2013535 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Corr\u00eaa, R. O. et al. Inulin diet uncovers complex diet\u2013microbiota\u2013immune cell interactions remodeling the gut epithelium. Microbiome 11<\/b>, 90 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shinn, L. M. et al. Fecal metagenomics to identify biomarkers of food intake in healthy adults: findings from randomized, controlled, nutrition trials. J. Nutr. 154<\/b>, 271\u2013283 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Diener, C. et al. Metagenomic estimation of dietary intake from human stool. Nat. Metab. 7<\/b>, 617\u2013630 (2025).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zuppinger, C. et al. Performance of the digital dietary assessment tool MyFoodRepo. Nutrients 14<\/b>, 635 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Abdill, R. J., Adamowicz, E. M. & Blekhman, R. Public human microbiome data are dominated by highly developed countries. PLoS Biol. 20<\/b>, e3001536 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sirugo, G., Williams, S. M. & Tishkoff, S. A. The missing diversity in human genetic studies. Cell 177<\/b>, 1080 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    McCarthy, M. I. et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9<\/b>, 356\u2013369 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38<\/b>, 904\u2013909 (2006).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yang, J. et al. Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet. 43<\/b>, 519\u2013525 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Boyle, E. A., Li, Y. I. & Pritchard, J. K. An expanded view of complex traits: from polygenic to omnigenic. Cell 169<\/b>, 1177\u20131186 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Xu, F. et al. The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. Microbiome 8<\/b>, 145 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lloyd-Price, J. et al. Strains, functions and dynamics in the expanded human microbiome project. Nature 550<\/b>, 61\u201366 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Weiss, S. et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome 5<\/b>, 27 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Luca, F., Kupfer, S. S., Knights, D., Khoruts, A. & Blekhman, R. Functional genomics of host\u2013microbiome interactions in humans. Trends Genet. 34<\/b>, 30\u201340 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489<\/b>, 220\u2013230 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: and this is not optional. Front. Microbiol. 8<\/b>, 2224 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Franzosa, E. A. et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat. Methods 15<\/b>, 962\u2013968 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Valdes, A. M., Walter, J., Segal, E. & Spector, T. D. Role of the gut microbiota in nutrition…\n","protected":false},"author":2,"featured_media":157478,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3846],"tags":[3971,3973,3967,3970,3972,3968,267,7189,3900,3969,66768,66769,70,16,15],"class_list":{"0":"post-157477","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetics","8":"tag-agriculture","9":"tag-animal-genetics-and-genomics","10":"tag-biomedicine","11":"tag-cancer-research","12":"tag-gene-function","13":"tag-general","14":"tag-genetics","15":"tag-genome-wide-association-studies","16":"tag-genomics","17":"tag-human-genetics","18":"tag-metagenomics","19":"tag-microbial-genetics","20":"tag-science","21":"tag-uk","22":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/114625110922567089","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/157477","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/comments?post=157477"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/157477\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/157478"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=157477"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=157477"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=157477"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}