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Environment dominates over host genetics in shaping human gut microbiota
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Abstract
Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements. We further demonstrate that microbiome data significantly improve the prediction accuracy for many human traits, such as glucose and obesity measures, compared to models that use only host genetic and environmental data. These results suggest that microbiome alterations aimed at improving clinical outcomes may be carried out across diverse genetic backgrounds.
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In the citing paper
“This can be attributed to the highly individual-specificity of the human microbiome,10,11 shaped by genetics, diet, age, geography, disease status, and intrinsic host factors.12”
From Gut microbiota drives structural variation of exogenous probiotics to enhance colonization (2025) · cites this paper as [12]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“adult microbial communities seem to be predominantly shaped by prior stochastic environmental exposures, as well as multiple other factors such as diet, antibiotic therapy and host genetics, with direct 'inheritance' from the mother at birth playing a lesser role.”
From Human microbiome myths and misconceptions (2023) · cites this paper as [16]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“proportionally few microbiota species are truly 'heritable' and persist through from birth to adulthood in the offspring 15,16 .”
From Human microbiome myths and misconceptions (2023) · cites this paper as [16]
Experimental — accuracy not yet measuredIn the citing paper
“Diet has emerged as a driving factor in microbiota composition and function (Flint et al., 2017; Muegge et al., 2011; Rothschild et al., 2018; Zhernakova et al., 2016).”
From Gut-microbiota-targeted diets modulate human immune status (2021) · cites this paper as Rothschild et al., 2018
In the citing paper
“However, the effect size is likely small given recent microbial-genetic association studies showing environmental factors to have substantially greater impact on the gut microbiome than genetics22.”
From The gut Microbiome in adult and pediatric functional gastrointestinal disorders (2019) · cites this paper as [22]
In the citing paper
“Genome-wide analyses estimate that host variants account for roughly 2%–8% of interindividual compositional variation,58,59”
From Gut dysbiosis in oncology: a risk factor for immunoresistance (2026) · cites this paper as [59]
In the citing paper
“Together, they explain nearly 20% of interindividual variation in microbial composition, with drugs often exerting the stronger influence.59,70”
From Gut dysbiosis in oncology: a risk factor for immunoresistance (2026) · cites this paper as [59]
In the citing paper
“with host genetics accounting for <10% of variation (14).”
From Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response (2021) · cites this paper as [14]
In the citing paper
“Despite the low number of samples, these results suggest that the environment has more influence on the gut microbiome than the pathological condition, which is in accordance with recent findings 22,23 .”
From Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice (2019) · cites this paper as [22]
In the citing paper
“Diet is a key modifiable factor influencing the composition of the gut microbiota, indicating the potential for therapeutic dietary strategies to manipulate microbial diversity, composition, and stability.”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [4]
In the citing paper
“Besides diet, the gut microbiota is shaped by a combination of extrinsic (e.g., lifestyle and medication) and intrinsic (e.g., host genetics, immune and metabolic regulations) factors. It is generally acknowledged that the extrinsic factors elicit the predominant effect, with diet the most widely studied [4].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [4]
In the citing paper
“Diet is thought to explain over 50% of these microbial structural variations in mice and 20% in humans signalling the potential for dietary strategies in disease management through gut microbiota modulation [3,4].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [4]
In the citing paper
“The gut microbiome is shaped by a wealth of environmental factors whose impacts dominate over host genetics.126”
From Interaction between microbiota and immunity in health and disease (2020) · cites this paper as [126]
In the citing paper
“host-genetic influences on gut microbiome composition (Goodrich et al., 2016;Rothschild et al., 2018) are also likely to play a role in influencing the rate and extent of microbial xenobiotic metabolism.”
From Gut reactions: Breaking down xenobiotic–microbiome interactions (2019) · cites this paper as Rothschild et al., 2018
In the citing paper
“and alternately, estimating that host genetics explain only a minor percentage of microbiome variation [69].”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [69]
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Citations
Cites
A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
XGBoost: A Scalable Tree Boosting System
Chen, T., & Guestrin, C. (2016) · Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · doi:10.1145/2939672.2939785 · Cited by 54,569
A Mathematical Theory of Communication
Shannon, C. E. (1948) · The MIT Press eBooks · doi:10.1002/j.1538-7305.1948.tb00917.x · Cited by 50,201
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Flagged first, then by citations
Research works printed but not linked: 1
- Legendre P. & Legendre. L. Numerical Ecology Vol. 24, 3rd edn (Elsevier, 2012)
Cited by
Sorted by citations
Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
Gut microbiota in human metabolic health and disease
Fan, Y., & Pedersen, O. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0433-9 · Cited by 4,724
Interaction between microbiota and immunity in health and disease
Zheng, D., Liwinski, T., & Elinav, E. (2020) · Cell Research · doi:10.1038/s41422-020-0332-7 · Cited by 3,947
Self-citationRole of the gut microbiota in nutrition and health
Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018) · BMJ · doi:10.1136/bmj.k2179 · Cited by 2,375
Self-citationYou are what you eat: Diet, health and the gut microbiota
Zmora, N., Suez, J., & Elinav, E. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0061-2 · Cited by 1,792
Self-citationLarge-scale association analyses identify host factors influencing human gut microbiome composition
Kurilshikov, A., Medina-Gomez, C., Bacigalupe, R., Radjabzadeh, D., Wang, J., Demirkan, A., Le Roy, C. I., Raygoza Garay, J. A., Finnicum, C. T., Liu, X., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00763-1 · Cited by 1,786
Self-citationCausal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases
Sanna, S., van Zuydam, N. R., Mahajan, A., Kurilshikov, A., Vich Vila, A., Võsa, U., Mujagic, Z., Masclee, A. A. M., Jonkers, D. M. A. E., Oosting, M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0350-x · Cited by 1,539
Self-citationAn insight into gut microbiota and its functionalities
Adak, A., & Khan, M. R. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-018-2943-4 · Cited by 1,485
Gut-microbiota-targeted diets modulate human immune status
Wastyk, H. C., Fragiadakis, G. K., Perelman, D., Dahan, D., Merrill, B. D., Yu, F. B., Topf, M., Gonzalez, C. G., Van Treuren, W., Han, S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.019 · Cited by 1,385
Gut microbiota in colorectal cancer: mechanisms of action and clinical applications
Wong, S. H., & Yu, J. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0209-8 · Cited by 1,392
Human gut microbiota/microbiome in health and diseases: a review
Gomaa, E. Z. (2020) · Antonie van Leeuwenhoek · doi:10.1007/s10482-020-01474-7 · Cited by 1,294
Gut Microbiome: Profound Implications for Diet and Disease
Hills, R. D., Pontefract, B., Mishcon, H. R., Black, C. A., Sutton, S. C., & Theberge, C. R. (2019) · Nutrients · doi:10.3390/nu11071613 · Cited by 1,143
Gut Microbiota and Short Chain Fatty Acids: Implications in Glucose Homeostasis
Portincasa, P., Bonfrate, L., Vacca, M., Angelis, M. D., Farella, I., Lanza, E., Khalil, M., Wang, D. Q. ‐., Sperandio, M., & Ciaula, A. D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031105 · Cited by 1,053
Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response
Spencer, C. N., McQuade, J. L., Gopalakrishnan, V., McCulloch, J. A., Vetizou, M., Cogdill, A. P., Khan, M. A. W., Zhang, X., White, M. G., Peterson, C. B., et al. (2021) · Science · doi:10.1126/science.aaz7015 · Cited by 966
Microbial genes and pathways in inflammatory bowel disease
Schirmer, M., Garner, A., Vlamakis, H. C., & Xavier, R. J. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0213-6 · Cited by 979
The gut microbiome: Relationships with disease and opportunities for therapy
Durack, J., & Lynch, S. V. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20180448 · Cited by 979
Scheiman, J., Luber, J. M., Chavkin, T. A., MacDonald, T., Tung, A., Pham, L.-D., Wibowo, M. C., Wurth, R. C., Punthambaker, S., Tierney, B. T., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0485-4 · Cited by 892
Diet-microbiota interactions and personalized nutrition
Kolodziejczyk, A. A., Zheng, D., & Elinav, E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0256-8 · Cited by 879
Self-citationA practical guide to amplicon and metagenomic analysis of microbiome data
Liu, Y., Qin, Y., Chen, T., Lu, M., Qian, X., Guo, X., & Bai, Y. (2020) · Protein & Cell · doi:10.1007/s13238-020-00724-8 · Cited by 931
The Human Gut Microbiome: From Association to Modulation
Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845
Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration
Leeming, E. R., Johnson, A. J., Spector, T. D., & Le Roy, C. I. (2019) · Nutrients · doi:10.3390/nu11122862 · Cited by 817
US immigration westernizes the human gut microbiome
Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.029 · Cited by 794
Dietary metabolism, the gut microbiome, and heart failure
Tang, W. H. W., Li, D. Y., & Hazen, S. L. (2019) · Nature Reviews Cardiology · doi:10.1038/s41569-018-0108-7 · Cited by 789
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752
The Gut Microbiota and Inflammation: An Overview
Bander, Z. A., Nitert, M. D., Mousa, A., & Naderpoor, N. (2020) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph17207618 · Cited by 804
Factors affecting the composition of the gut microbiota, and its modulation
Hasan, N., & Yang, H. (2019) · PeerJ · doi:10.7717/peerj.7502 · Cited by 807
Daily sampling reveals personalized diet-microbiome associations in humans
Johnson, A. J., Vangay, P., Al-Ghalith, G. A., Hillmann, B. M., Ward, T. L., Shields-Cutler, R. R., Kim, A. D., Shmagel, A. K., Syed, A. N., Walter, J., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.05.005 · Cited by 742
Environmental factors shaping the gut microbiome in a Dutch population
Gacesa, R., Kurilshikov, A., Vich Vila, A., Sinha, T., Klaassen, M. A. Y., Bolte, L. A., Andreu-Sánchez, S., Chen, L., Collij, V., Hu, S., et al. (2022) · Nature · doi:10.1038/s41586-022-04567-7 · Cited by 735
Self-citationGut microbiota in colorectal cancer development and therapy
Wong, C. C., & Yu, J. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00766-x · Cited by 779
Alcohol, liver disease and the gut microbiota
Bajaj, J. S. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0099-1 · Cited by 724
Deschasaux, M., Bouter, K. E., Prodan, A., Levin, E., Groen, A. K., Herrema, H., Tremaroli, V., Bakker, G. J., Attaye, I., Pinto-Sietsma, S.-J., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0160-1 · Cited by 695
Gut Microbiota as a Trigger for Metabolic Inflammation in Obesity and Type 2 Diabetes
Scheithauer, T. P. M., Rampanelli, E., Nieuwdorp, M., Vallance, B. A., Verchere, C. B., van Raalte, D. H., & Herrema, H. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.571731 · Cited by 715
Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice
Bárcena, C., Valdés-Mas, R., Mayoral, P., Garabaya, C., Durand, S., Rodríguez, F., Fernández-García, M. T., Salazar, N., Nogacka, A. M., Garatachea, N., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0504-5 · Cited by 661
The Gut Microbiota in the First Decade of Life
Derrien, M., Alvarez, A., & de Vos, W. M. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2019.08.001 · Cited by 682
The human virome: assembly, composition and host interactions
Liang, G., & Bushman, F. D. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00536-5 · Cited by 652
Jackson, M. A., Verdi, S., Maxan, M.-E., Shin, C. M., Zierer, J., Bowyer, R. C. E., Martin, T., Williams, F. M. K., Menni, C., Bell, J. T., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05184-7 · Cited by 616
Liu, B., Liu, X., Liang, Z., & Wang, J. (2021) · World Journal of Gastroenterology · doi:10.3748/wjg.v27.i25.3837 · Cited by 662
The influence of the microbiome on respiratory health
Wypych, T. P., Wickramasinghe, L. C., & Marsland, B. J. (2019) · Nature Immunology · doi:10.1038/s41590-019-0451-9 · Cited by 611
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project
Lopera-Maya, E. A., Kurilshikov, A., van der Graaf, A., Hu, S., Andreu-Sánchez, S., Chen, L., Vila, A. V., Gacesa, R., Sinha, T., Collij, V., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00992-y · Cited by 553
Self-citationWalter, J., Armet, A. M., Finlay, B. B., & Shanahan, F. (2020) · Cell · doi:10.1016/j.cell.2019.12.025 · Cited by 596
Gut Microbiota and Cancer: From Pathogenesis to Therapy
Vivarelli, S., Salemi, R., Candido, S., Falzone, L., Santagati, M., Stefani, S., Torino, F., Banna, G. L., Tonini, G., & Libra, M. (2019) · Cancers · doi:10.3390/cancers11010038 · Cited by 586
Qin, Y., Havulinna, A. S., Liu, Y., Jousilahti, P., Ritchie, S. C., Tokolyi, A., Sanders, J. G., Valsta, L., Brożyńska, M., Zhu, Q., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00991-z · Cited by 586
Emerging Targets in Type 2 Diabetes and Diabetic Complications
Demir, S., Nawroth, P. P., Herzig, S., & Üstünel, B. E. (2021) · Advanced Science · doi:10.1002/advs.202100275 · Cited by 582
Lazăr, V., Diţu, L.-M., Pîrcălăbioru, G. G., Gheorghe, I., Curuțiu, C., Holban, A. M., Picu, A. A., Petcu, L. M., & Chifiriuc, M. C. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01830 · Cited by 552
Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies
Aggarwal, N., Kitano, S., Puah, G. R. Y., Kittelmann, S., Hwang, I. Y., & Chang, M. W. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00431 · Cited by 571
Xue, M., Sun, H., Wu, X., Liu, J., & Guan, L. L. (2020) · Microbiome · doi:10.1186/s40168-020-00819-8 · Cited by 526
Probiotic Gastrointestinal Transit and Colonization After Oral Administration: A Long Journey
Han, S., Lu, Y., Xie, J., Fei, Y., Zheng, G., Wang, Z., Liu, J., Lv, L., Ling, Z., Berglund, B., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.609722 · Cited by 525
Gut microbiota derived metabolites in cardiovascular health and disease
Wang, Z., & Zhao, Y. (2018) · Protein & Cell · doi:10.1007/s13238-018-0549-0 · Cited by 491
Microbiota-derived metabolites as drivers of gut–brain communication
Ahmed, H., Leyrolle, Q., Koistinen, V., Kärkkäinen, O., Layé, S., Delzenne, N., & Hanhineva, K. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2102878 · Cited by 462
Microbiota and the social brain
Sherwin, E., Bordenstein, S. R., Quinn, J. L., Dinan, T. G., & Cryan, J. F. (2019) · Science · doi:10.1126/science.aar2016 · Cited by 462
Next-generation sequencing: insights to advance clinical investigations of the microbiome
Wensel, C. R., Pluznick, J. L., Salzberg, S. L., & Sears, C. L. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154944 · Cited by 437
Aron-Wisnewsky, J., Warmbrunn, M. V., Nieuwdorp, M., & Clément, K. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.10.057 · Cited by 452
A reference map of potential determinants for the human serum metabolome
Bar, N., Korem, T., Weissbrod, O., Zeevi, D., Rothschild, D., Leviatan, S., Kosower, N., Lotan‐Pompan, M., Weinberger, A., Roy, C. I. L., et al. (2020) · Nature · doi:10.1038/s41586-020-2896-2 · Cited by 440
Self-citationThe person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449
Major microbiota dysbiosis in severe obesity: fate after bariatric surgery
Aron-Wisnewsky, J., Prifti, E., Belda, E., Ichou, F., Kayser, B. D., Dao, M. C., Verger, E. O., Hedjazi, L., Bouillot, J.-L., Chevallier, J.-M., et al. (2019) · Gut · doi:10.1136/gutjnl-2018-316103 · Cited by 418
The microbiome and gut homeostasis
Lee, J., Tsolis, R. M., & Bäumler, A. J. (2022) · Science · doi:10.1126/science.abp9960 · Cited by 452
The progress of gut microbiome research related to brain disorders
Zhu, S., Jiang, Y., Xu, K., Cui, M., Ye, W., Zhao, G., Jin, L., & Chen, X. (2020) · Journal of Neuroinflammation · doi:10.1186/s12974-020-1705-z · Cited by 419
Haran, J. P., Bhattarai, S. K., Foley, S. E., Dutta, P., Ward, D. V., Bucci, V., & McCormick, B. A. (2019) · mBio · doi:10.1128/mbio.00632-19 · Cited by 412
Trøseid, M., Andersen, G. Ø., Broch, K., & Hov, J. R. (2020) · EBioMedicine · doi:10.1016/j.ebiom.2020.102649 · Cited by 412
Haahtela, T. (2019) · Allergy · doi:10.1111/all.13763 · Cited by 407
Unravelling the collateral damage of antibiotics on gut bacteria
Maier, L., Goemans, C., Wirbel, J., Kuhn, M., Eberl, C., Pruteanu, M., Müller, P., García‐Santamarina, S., Cacace, E., Zhang, B., et al. (2021) · Nature · doi:10.1038/s41586-021-03986-2 · Cited by 405
Gut microbiota and cardiovascular disease: opportunities and challenges
Kazemian, N., Mahmoudi, M., Halperin, F. A., Wu, J. C., & Pakpour, S. (2020) · Microbiome · doi:10.1186/s40168-020-00821-0 · Cited by 404
Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows
Difford, G. F., Plichta, D. R., Løvendahl, P., Lassen, J., Noel, S. J., Højberg, O., Wright, A. G., Zhu, Z., Kristensen, L., Nielsen, H. B., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007580 · Cited by 404
The Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?
Shanahan, F., Ghosh, T. S., & O’Toole, P. W. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.09.057 · Cited by 383
What defines a healthy gut microbiome?
Hul, M. V., Cani, P. D., Petitfils, C., de Vos, W. M., Tilg, H., & El-Omar, E. M. (2024) · Gut · doi:10.1136/gutjnl-2024-333378 · Cited by 448
Modulating the microbiome to improve therapeutic response in cancer
McQuade, J. L., Daniel, C. R., Helmink, B. A., & Wargo, J. A. (2019) · The Lancet Oncology · doi:10.1016/s1470-2045(18)30952-5 · Cited by 376
Liu, X., Tong, X., Zou, Y., Lin, X., Zhao, H., Tian, L., Jie, Z., Wang, Q., Zhang, Z., Lu, H., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00968-y · Cited by 383
Axes of a revolution: challenges and promises of big data in healthcare
Shilo, S., Rossman, H., & Segal, E. (2020) · Nature Medicine · doi:10.1038/s41591-019-0727-5 · Cited by 370
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Song, M., & Chan, A. T. (2019) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2018.07.012 · Cited by 355
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Korpela, K., Costea, P. I., Coelho, L. P., Kandels-Lewis, S. E., Willemsen, G. A. H. M., Boomsma, D. I., Segata, N., & Bork, P. (2018) · Genome Research · doi:10.1101/gr.233940.117 · Cited by 328
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Chong, P. P., Chin, V. K., Looi, C. Y., Wong, W. F., Madhavan, P., & Yong, P. V. C. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01136 · Cited by 353
Zhou, X., Baumann, R., Gao, X., Mendoza, M., Singh, S., Sand, I. K., Xia, Z., Cox, L. M., Chitnis, T., Yoon, H., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.021 · Cited by 326
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Overacre-Delgoffe, A. E., Bumgarner, H. J., Cillo, A. R., Burr, A. H. P., Tometich, J. T., Bhattacharjee, A., Bruno, T. C., Vignali, D. A. A., & Hand, T. W. (2021) · Immunity · doi:10.1016/j.immuni.2021.11.003 · Cited by 318
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Plichta, D. R., Graham, D. B., Subramanian, S., & Xavier, R. J. (2019) · Cell · doi:10.1016/j.cell.2019.07.045 · Cited by 316
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West, A. G., Waite, D. W., Deines, P., Bourne, D. G., Digby, A., McKenzie, V. J., & Taylor, M. W. (2018) · Biological Conservation · doi:10.1016/j.biocon.2018.11.016 · Cited by 324
Koh, A., & Bäckhed, F. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.005 · Cited by 322
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Heiss, C. N., & Olofsson, L. E. (2019) · Journal of Neuroendocrinology · doi:10.1111/jne.12684 · Cited by 304
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McBurney, M. I., Davis, C. D., Fraser, C. M., Schneeman, B. O., Huttenhower, C., Verbeke, K., Walter, J., & Latulippe, M. E. (2019) · Journal of Nutrition · doi:10.1093/jn/nxz154 · Cited by 296
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O’Donnell, J. A., Zheng, T., Méric, G., & Marques, F. Z. (2023) · Nature Reviews Nephrology · doi:10.1038/s41581-022-00654-0 · Cited by 302
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Pham, V. T., Dold, S., Rehman, A., Bird, J. K., & Steinert, R. E. (2021) · Nutrition Research · doi:10.1016/j.nutres.2021.09.001 · Cited by 300
Metadata
- Authors
- Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., Shilo, S., Lador, D., Vila, A. V., Zmora, N., Pevsner-Fischer, M., Israeli, D., Kosower, N., Malka, G., Wolf, B. C., Avnit-Sagi, T., Lotan-Pompan, M., Weinberger, A., Halpern, Z., Carmi, S., Fu, J., Wijmenga, C., Zhernakova, A., Elinav, E., & Segal, E.
- Affiliations
- Weizmann Institute of Science (IL)
- University Medical Center Groningen (NL)
- Tel Aviv University (IL)
- Jerusalem Mental Health Center (IL)
- Hebrew University of Jerusalem (IL)
- ORCID
- Venue
- Nature
- Published
- 2018-02-28
- Volume
- 555
- Issue
- 7695
- Pages
- 210-215
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2787902098
- Cited by
- 2,859
- References
- 111
- Citations by year
- 2026: 227 · 2025: 295 · 2024: 367 · 2023: 349 · 2022: 390 · 2021: 411 · 2020: 390 · 2019: 286 · 2018: 135
- FWCI
- 110.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- Howard Hughes Medical Institute
- Bill and Melinda Gates Foundation
- Leona M. and Harry B. Helmsley Charitable Trust
- Canadian Institute for Advanced Research
- Stiftelsen Kristian Gerhard Jebsen
- Wellcome Trust (085475, 076113)
- Rijksuniversiteit Groningen
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO SPI 92–266, NWO-VIDI 864.13.013, 864.13.013, 016.Vidi.178.056, SPI 92-266)
- Israel Science Foundation
- Abisch-Frenkel-Stiftung
- H2020 European Research Council (715772)
- FP7 Ideas: European Research Council (322698)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Keywords
- gut microbiota, host genetics, genetic ancestry, environmental factors, diet, drugs, anthropometry, glucose, obesity
- MeSH terms
- Gastrointestinal Microbiome, Adolescent, Adult, Aged, Aged, 80 and over, Diet, Environment, Family Characteristics, Female, Glucose, Humans, Israel, Life Style, Male, Middle Aged, Obesity, Phenotype, RNA, Bacterial, RNA, Ribosomal, 16S, Twins, Reproducibility of Results, Cohort Studies, Twin Studies as Topic, Polymorphism, Single Nucleotide, Heredity, Young Adult, Gene-Environment Interaction, Healthy Volunteers
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