Host Genetics and Gut Microbiome: Challenges and Perspectives
Open accessAbstract
The mammalian gut is colonized by trillions of microorganisms collectively called the microbiome. It is increasingly clear that this microbiome has a critical role of in many aspects of health including metabolism and immunity. While environmental factors such as diet and medications have been shown to influence the microbiome composition, the role of host genetics has only recently emerged in human studies and animal models. In this review, we summarize the current state of microbiome research with an emphasis on the effect of host genetics on the gut microbiome composition. We focus particularly on genetic determinants of the host immune system that help shape the gut microbiome and discuss avenues for future research.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Tumor microbiome alpha-diversity was significantly higher in LTS than STS patients in both the MDACC discovery cohort and the JHH validation cohort.
“alpha-diversity of the tumor microbiome, defined as the number of species present within each tumor sample (Kurilshikov et al., 2017), was significantly higher in the LTS patients compared to STS on both the MDACC discovery cohort (p < 0.0005, p < 0.0005 and p < 0.05, for each alpha-diversity indice, respectively) and the JHH validation cohort (p < 0.005, p < 0.005 and p < 0.005, for each alpha-d”
From Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes (2019) · cites this paper as Kurilshikov et al., 2017
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · see citing works
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · see citing works
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Biological insights from 108 schizophrenia-associated genetic loci
Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577 · see citing works
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762 · see citing works
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091 · see citing works
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works
Genetic studies of body mass index yield new insights for obesity biology
Study, T. L. C., Locke, A. E., The ADIPOGen Consortium, The AGEN-BMI Working Group, The CARDIOGRAMplusC4D Consortium, The CKDGen Consortium, The, G. L. G. C., The, I. C. B. P., The MAGIC Investigators, The MuTHER Consortium, et al. (2015) · Nature · doi:10.1038/nature14177 · Cited by 4,534 · see citing works
Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413 · see citing works
Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., et al. (2013) · Nature Medicine · doi:10.1038/nm.3145 · Cited by 4,386 · see citing works
Commensal <i>Bifidobacterium</i> promotes antitumor immunity and facilitates anti–PD-L1 efficacy
Sivan, A., Corrales, L., Hubert, N., Williams, J. B., Aquino-Michaels, K., Earley, Z. M., Benyamin, F. W., Man Lei, Y., Jabri, B., Alegre, M.-L., et al. (2015) · Science · doi:10.1126/science.aac4255 · Cited by 3,888 · see citing works
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works
Gut microbiota composition correlates with diet and health in the elderly
Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O’Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O’Sullivan, O., et al. (2012) · Nature · doi:10.1038/nature11319 · Cited by 3,314 · see citing works
The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220 · see citing works
Human Genetics Shape the Gut Microbiome
Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · see citing works
Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.015 · Cited by 2,915 · see citing works
Vrieze, A., Van Nood, E., Holleman, F., Salojärvi, J., Kootte, R. S., Bartelsman, J. F. W. M., Dallinga–Thie, G. M., Ackermans, M. T., Serlie, M. J., Oozeer, R., et al. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.06.031 · Cited by 2,913 · see citing works
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota
Atarashi, K., Tanoue, T., Oshima, K., Suda, W., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., et al. (2013) · Nature · doi:10.1038/nature12331 · Cited by 2,872 · see citing works
Murray, D. D., Suzuki, K., Law, M. G., Trebicka, J., Neuhaus, J., Wentworth, D. N., Johnson, M. A., Vjecha, M. J., Kelleher, A. D., Emery, S., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0139981 · Cited by 2,740 · see citing works
Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity
Henao-Mejia, J., Elinav, E., Jin, C., Hao, L., Mehal, W. Z., Strowig, T., Thaiss, C. A., Kau, A. L., Eisenbarth, S. C., Jurczak, M. J., et al. (2012) · Nature · doi:10.1038/nature10809 · Cited by 2,435 · see citing works
Population-level analysis of gut microbiome variation
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., et al. (2016) · Science · doi:10.1126/science.aad3503 · Cited by 2,400 · see citing works
Self-citationMetaPhlAn2 for enhanced metagenomic taxonomic profiling
Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116 · see citing works
Human gut microbes impact host serum metabolome and insulin sensitivity
Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., et al. (2016) · Nature · doi:10.1038/nature18646 · Cited by 2,116 · see citing works
Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5
Vijay-Kumar, M., Aitken, J. D., Carvalho, F. A., Cullender, T. C., Mwangi, S., Srinivasan, S., Sitaraman, S. V., Knight, R., Ley, R. E., & Gewirtz, A. T. (2010) · Science · doi:10.1126/science.1179721 · Cited by 2,068 · see citing works
NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis
Elinav, E., Strowig, T., Kau, A. L., Henao-Mejia, J., Thaiss, C. A., Booth, C. J., Peaper, D. R., Bertin, J., Eisenbarth, S. C., Gordon, J. I., et al. (2011) · Cell · doi:10.1016/j.cell.2011.04.022 · Cited by 2,024 · see citing works
The microbiome and innate immunity
Thaiss, C. A., Zmora, N., Levy, M., & Elinav, E. (2016) · Nature · doi:10.1038/nature18847 · Cited by 2,012 · see citing works
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., et al. (2016) · Science · doi:10.1126/science.aad3369 · Cited by 1,914 · see citing works
Self-citationThe microbiota in adaptive immune homeostasis and disease
Honda, K., & Littman, D. R. (2016) · Nature · doi:10.1038/nature18848 · Cited by 1,846 · see citing works
Nod2-Dependent Regulation of Innate and Adaptive Immunity in the Intestinal Tract
Kobayashi, K. S., Chamaillard, M., Ogura, Y., Henegariu, O., Inohara, N., Núñez, G., & Flavell, R. A. (2005) · Science · doi:10.1126/science.1104911 · Cited by 1,776 · see citing works
Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works
Zhang, X., Zhang, D., Jia, H., Feng, Q., Wang, D., Liang, D., Wu, X., Li, J., Tang, L., Li, Y., et al. (2015) · Nature Medicine · doi:10.1038/nm.3914 · Cited by 1,690 · see citing works
Systematic identification of trans eQTLs as putative drivers of known disease associations
Westra, H.-J., Peters, M. J., Esko, T., Yaghootkar, H., Schurmann, C., Kettunen, J., Christiansen, M. W., Fairfax, B. P., Schramm, K., Powell, J. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2756 · Cited by 1,658 · see citing works
Self-citationAntibiotics in early life alter the murine colonic microbiome and adiposity
Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) · Nature · doi:10.1038/nature11400 · Cited by 1,613 · see citing works
Gut-Residing Segmented Filamentous Bacteria Drive Autoimmune Arthritis via T Helper 17 Cells
Wu, H.-J., Ivanov, I. I., Darce, J., Hattori, K., Shima, T., Umesaki, Y., Littman, D. R., Benoist, C., & Mathis, D. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.001 · Cited by 1,577 · see citing works
Lamas, B., Richard, M. L., Leducq, V., Pham, H.-P., Michel, M.-L., Da Costa, G., Bridonneau, C., Jegou, S., Hoffmann, T. W., Natividad, J. M., et al. (2016) · Nature Medicine · doi:10.1038/nm.4102 · Cited by 1,482 · see citing works
The role of gut microbiota in immune homeostasis and autoimmunity
Wu, H.-J., & Wu, E. (2012) · Gut Microbes · doi:10.4161/gmic.19320 · Cited by 1,426 · see citing works
Proton pump inhibitors affect the gut microbiome
Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., Tigchelaar, E. F., Jankipersadsing, S. A., Cenit, M. C., Harmsen, H. J. M., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-310376 · Cited by 1,371 · see citing works
Self-citationRegulation of immune cell function by short‐chain fatty acids
Corrêa‐Oliveira, R., Fachi, J. L., Vieira, A., Sato, F. T., & Vinolo, M. A. R. (2016) · Clinical & Translational Immunology · doi:10.1038/cti.2016.17 · Cited by 1,346 · see citing works
Benson, A. K., Kelly, S. A., Legge, R., Ma, F., Low, S. J., Kim, J., Zhang, M., Oh, P. L., Nehrenberg, D., Hua, K., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1007028107 · Cited by 1,314 · see citing works
Alterations of the human gut microbiome in multiple sclerosis
Jangi, S., Gandhi, R., Cox, L. M., Li, N., von Glehn, F., Yan, R., Patel, B., Mazzola, M. A., Liu, S., Glanz, B. L., et al. (2016) · Nature Communications · doi:10.1038/ncomms12015 · Cited by 1,307 · see citing works
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans
Vatanen, T., Kostic, A. D., d’Hennezel, E., Siljander, H., Franzosa, E. A., Yassour, M., Kolde, R., Vlamakis, H., Arthur, T. D., Hämäläinen, A.-M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.04.007 · Cited by 1,289 · see citing works
Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease
Palm, N. W., de Zoete, M. R., Cullen, T. W., Barry, N. A., Stefanowski, J., Hao, L., Degnan, P. H., Hu, J., Peter, I., Zhang, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.006 · Cited by 1,286 · see citing works
Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor
Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173 · see citing works
Satoh‐Takayama, N., Vosshenrich, C. A. J., Lesjean‐Pottier, S., Sawa, S., Lochner, M., Rattis, F. M., Mention, J., Thiam, K., Cerf–Bensussan, N., Mandelboim, O., et al. (2008) · Immunity · doi:10.1016/j.immuni.2008.11.001 · Cited by 1,086 · see citing works
Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis
Iliev, I. D., Funari, V. A., Taylor, K. D., Nguyen, Q., Reyes, C. N., Strom, S. P., Brown, J., Becker, C. A., Fleshner, P. R., Dubinsky, M., et al. (2012) · Science · doi:10.1126/science.1221789 · Cited by 1,073 · see citing works
Genetic determinants of the gut microbiome in UK twins
Goodrich, J. K., Davenport, E. R., Beaumont, M., Jackson, M. A., Knight, R., Ober, C., Spector, T. D., Bell, J. T., Clark, A. G., & Ley, R. E. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.04.017 · Cited by 1,048 · see citing works
Characterization of the gut microbiome using 16S or shotgun metagenomics
Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., Perry, T., Kao, D., Mason, A. L., Madsen, K. L., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00459 · Cited by 942 · see citing works
Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls
Chen, J., Chia, N., Kalari, K. R., Yao, J. Z., Novotna, M., Paz Soldan, M. M., Luckey, D. H., Marietta, E. V., Jeraldo, P. R., Chen, X., et al. (2016) · Scientific Reports · doi:10.1038/srep28484 · Cited by 933 · see citing works
Sanos, S. L., Bui, V. L., Mortha, A., Oberle, K., Heners, C., Johner, C., & Diefenbach, A. (2008) · Nature Immunology · doi:10.1038/ni.1684 · Cited by 843 · see citing works
Influences of microbiota on intestinal immune system development.
Cebra, J. (1999) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/69.5.1046s · Cited by 819 · see citing works
The effect of host genetics on the gut microbiome
Bonder, M. J., Kurilshikov, A., Tigchelaar, E. F., Mujagic, Z., Imhann, F., Vila, A. V., Deelen, P., Vatanen, T., Schirmer, M., Smeekens, S. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3663 · Cited by 819 · see citing works
Self-citationImhann, F., Vich Vila, A., Bonder, M. J., Fu, J., Gevers, D., Visschedijk, M. C., Spekhorst, L. M., Alberts, R., Franke, L., van Dullemen, H. M., et al. (2018) · Gut · doi:10.1136/gutjnl-2016-312135 · Cited by 788 · see citing works
Self-citationThe Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids
Fu, J., Bonder, M. J., Cenit, M. C., Tigchelaar, E. F., Maatman, A., Dekens, J. A. M., Brandsma, E., Marczynska, J., Imhann, F., Weersma, R. K., et al. (2015) · Circulation Research · doi:10.1161/circresaha.115.306807 · Cited by 748 · see citing works
Self-citationHost genetic variation impacts microbiome composition across human body sites
Blekhman, R., Goodrich, J. K., Huang, K., Sun, Q., Bukowski, R., Bell, J. T., Spector, T. D., Keinan, A., Ley, R. E., Gevers, D., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0759-1 · Cited by 745 · see citing works
Innate Lymphoid Cells Promote Anatomical Containment of Lymphoid-Resident Commensal Bacteria
Sonnenberg, G. F., Monticelli, L. A., Alenghat, T., Fung, T. C., Hutnick, N. A., Kunisawa, J., Shibata, N., Grunberg, S., Sinha, R., Zahm, A. M., et al. (2012) · Science · doi:10.1126/science.1222551 · Cited by 738 · see citing works
Gut Microbiota Promote Hematopoiesis to Control Bacterial Infection
Khosravi, A., Yáñez, A., Price, J. G., Chow, A. T., Mérad, M., Goodridge, H. S., & Mazmanian, S. K. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.006 · Cited by 651 · see citing works
Mucus Enhances Gut Homeostasis and Oral Tolerance by Delivering Immunoregulatory Signals
Shan, M., Gentile, M., Yeiser, J. R., Walland, A. C., Bornstein, V. U., Chen, K., He, B., Cassis, L., Bigas, A., Cols, M., et al. (2013) · Science · doi:10.1126/science.1237910 · Cited by 642 · see citing works
Wang, J., Thingholm, L. B., Skiecevičienė, J., Rausch, P., Kummen, M., Hov, J. R., Degenhardt, F., Heinsen, F.-A., Rühlemann, M. C., Szymczak, S., et al. (2016) · Nature Genetics · doi:10.1038/ng.3695 · Cited by 625 · see citing works
Nod2 is required for the regulation of commensal microbiota in the intestine
Petnicki-Ocwieja, T., Hrncir, T., Liu, Y.-J., Biswas, A., Hudcovic, T., Tlaskalova-Hogenova, H., & Kobayashi, K. S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907722106 · Cited by 564 · see citing works
(2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.08.014 · Cited by 536 · see citing works
C-type lectins in immunity: recent developments
Dambuza, I. M., & Brown, G. D. (2015) · Current Opinion in Immunology · doi:10.1016/j.coi.2014.12.002 · Cited by 482 · see citing works
Association of host genome with intestinal microbial composition in a large healthy cohort
GEM Project Research Consortium, Turpin, W., Espin-Garcia, O., Xu, W., Silverberg, M. S., Kevans, D., Smith, M. I., Guttman, D. S., Griffiths, A., Panaccione, R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3693 · Cited by 460 · see citing works
Complex host genetics influence the microbiome in inflammatory bowel disease
Knights, D., Silverberg, M. S., Weersma, R. K., Gevers, D., Dijkstra, G., Huang, H., Tyler, A. D., van Sommeren, S., Imhann, F., Stempak, J. M., et al. (2014) · Genome Medicine · doi:10.1186/s13073-014-0107-1 · Cited by 418 · see citing works
Genetic and environmental control of host-gut microbiota interactions
Org, E., Parks, B. W., Joo, J. W. J., Emert, B., Schwartzman, W., Kang, E. Y., Mehrabian, M., Pan, C., Knight, R., Gunsalus, R., et al. (2015) · Genome Research · doi:10.1101/gr.194118.115 · Cited by 381 · see citing works
Xie, H., Guo, R., Zhong, H., Feng, Q., Lan, Z., Qin, B., Ward, K. J., Jackson, M. A., Xia, Y., Chen, X., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.004 · Cited by 341 · see citing works
Predominant Role of Host Genetics in Controlling the Composition of Gut Microbiota
Khachatryan, Z., Ktsoyan, Z. A., Manukyan, G. P., Kelly, D., Ghazaryan, K. A., & Aminov, R. I. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003064 · Cited by 317 · see citing works
Nod2 is essential for temporal development of intestinal microbial communities
Rehman, A., Sina, C., Gavrilova, O., Häsler, R., Ott, S. J., Baines, J. F., Schreiber, S., & Rosenstiel, P. C. (2011) · Gut · doi:10.1136/gut.2010.216259 · Cited by 316 · see citing works
Genome-Wide Association Studies of the Human Gut Microbiota
Davenport, E., Cusanovich, D. A., Michelini, K., Barreiro, L. B., Ober, C., & Gilad, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140301 · Cited by 253 · see citing works
Linking the Microbiota, Chronic Disease, and the Immune System
Hand, T. W., Vujkovic-Cvijin, I., Ridaura, V. K., & Belkaid, Y. (2016) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2016.08.003 · Cited by 247 · see citing works
Jin, D., Wu, S., Zhang, Y., Lu, R., Xia, Y., Dong, H. F., & Sun, J. (2015) · Clinical Therapeutics · doi:10.1016/j.clinthera.2015.04.004 · Cited by 236 · see citing works
Frantz, A. L., Rogier, E. W., Weber, C. R., Shen, L., Cohen, D. A., Fenton, L. A., Bruno, M. E. C., & Kaetzel, C. S. (2012) · Mucosal Immunology · doi:10.1038/mi.2012.23 · Cited by 230 · see citing works
Murine Gut Microbiota Is Defined by Host Genetics and Modulates Variation of Metabolic Traits
McKnite, A. M., Pérez-Muñoz, M. E., Lu, L., Williams, E. G., Brewer, S., Andreux, P. A., Bastiaansen, J. W. M., Wang, X., Kachman, S. D., Auwerx, J. H., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039191 · Cited by 222 · see citing works
Reprograming of gut microbiome energy metabolism by the FUT2 Crohn’s disease risk polymorphism
Tong, M., McHardy, I. H., Ruegger, P. M., Goudarzi, M., Kashyap, P., Haritunians, T., Li, X., Graeber, T. G., Schwager, E., Huttenhower, C., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.64 · Cited by 209 · see citing works
Dey, N., Wagner, V. E., Blanton, L. V., Cheng, J., Fontana, L., Haque, R., Ahmed, T., & Gordon, J. I. (2015) · Cell · doi:10.1016/j.cell.2015.08.059 · Cited by 195 · see citing works
Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data
Xu, L., Paterson, A. D., Turpin, W., & Xu, W. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129606 · Cited by 175 · see citing works
Mosquito C-type lectins maintain gut microbiome homeostasis
Pang, X., Xiao, X., Liu, Y., Zhang, R., Liu, J., Liu, Q., Wang, P., & Cheng, G. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.23 · Cited by 162 · see citing works
Wang, X., Xu, J., Zhao, X., Vasta, G. R., & Wang, J. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.552307 · Cited by 160 · see citing works
Li, D., Achkar, J., Haritunians, T., Jacobs, J. P., Hui, K. Y., D’Amato, M., Brand, S., Radford‐Smith, G. L., Halfvarson, J., Niess, J. H., et al. (2016) · Gastroenterology · doi:10.1053/j.gastro.2016.06.051 · Cited by 152 · see citing works
NLRC4 expression in intestinal epithelial cells mediates protection against an enteric pathogen
Nordlander, S., Pott, J., & Maloy, K. J. (2013) · Mucosal Immunology · doi:10.1038/mi.2013.95 · Cited by 145 · see citing works
Kellermayer, R., Dowd, S. E., Harris, R. A., Balasa, A., Schaible, T. D., Wolcott, R. D., Tatevian, N., Szigeti, R. G., Li, Z., Versalovic, J. A., et al. (2011) · The FASEB Journal · doi:10.1096/fj.10-172205 · Cited by 145 · see citing works
The Dectin-2 family of C-type lectins in immunity and homeostasis
Graham, L. M., & Brown, G. D. (2009) · Cytokine · doi:10.1016/j.cyto.2009.07.010 · Cited by 134 · see citing works
Wang, J., Kalyan, S., Steck, N., Turner, L. M., Harr, B., Künzel, S., Vallier, M., Häsler, R., Franke, A., Oberg, H., et al. (2015) · Nature Communications · doi:10.1038/ncomms7440 · Cited by 131 · see citing works
Glass, E. M., Dribinsky, Y., Yilmaz, P., et al. (2013) · The ISME Journal · doi:10.1038/ismej.2013.176 · Cited by 117 · see citing works
Singh, V., Yeoh, B. S., Xiao, X., Kumar, M., Bachman, M. A., Borregaard, N., Joe, B., & Vijay–Kumar, M. (2015) · Nature Communications · doi:10.1038/ncomms8113 · Cited by 115 · see citing works
Zhong, Y., Marungruang, N., Fåk, F., & NYMAN, M. E. (2015) · British Journal Of Nutrition · doi:10.1017/s0007114515000793 · Cited by 110 · see citing works
Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis
Hergott, C. A., Roche, A. M., Tamashiro, E., Clarke, T. B., Bailey, A., Laughlin, A. L., Bushman, F. D., & Weiser, J. N. (2016) · Blood · doi:10.1182/blood-2015-10-675173 · Cited by 110 · see citing works
Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity
Dimitriu, P. A., Boyce, G. K., Samarakoon, A., Hartmann, M., Johnson, P., & Mohn, W. W. (2012) · Environmental Microbiology Reports · doi:10.1111/j.1758-2229.2012.00393.x · Cited by 95 · see citing works
Lynch, S. V., Goldfarb, K. C., Wild, Y. K., Kong, W., De Lisle, R. C., & Brodie, E. L. (2013) · Gut Microbes · doi:10.4161/gmic.22430 · Cited by 87 · see citing works
Dysbiotic gut microbiome: A key element of Crohn's disease
Øyri, S. F., Műzes, G., & Sípos, F. (2015) · Comparative Immunology Microbiology and Infectious Diseases · doi:10.1016/j.cimid.2015.10.005 · Cited by 73 · see citing works
Caspase deficiency alters the murine gut microbiome
Brinkman, B. M., Hildebrand, F., Kubica, M., Goosens, D., Del Favero, J., Declercq, W., Raes, J., & Vandenabeele, P. (2011) · Cell Death & Disease · doi:10.1038/cddis.2011.101 · Cited by 70 · see citing works
The human microbiome in rheumatic autoimmune diseases: A comprehensive review
Coit, P., & Sawalha, A. H. (2016) · Clinical Immunology · doi:10.1016/j.clim.2016.07.026 · Cited by 42 · see citing works
MicrobiomeGWAS: a tool for identifying host genetic variants associated with microbiome compositionPreprint
Hua, X., Song, L., Yu, G., et al. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/031187 · Cited by 28 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Environment dominates over host genetics in shaping human gut microbiota
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859 · see citing works
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 · see citing works
Self-citationTumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes
Riquelme, E., Zhang, Y., Zhang, L., Montiel, M., Zoltan, M., Dong, W., Quesada, P., Sahin, I., Chandra, V., San Lucas, A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.008 · Cited by 1,577 · see citing works
Causal 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 · see citing works
Self-citationThe 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 · see citing works
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 · see citing works
Self-citationQin, 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 · see citing works
Gut reactions: Breaking down xenobiotic–microbiome interactions
Clarke, G., Sandhu, K. V., Griffin, B. T., Dinan, T. G., Cryan, J. F., & Hyland, N. P. (2019) · Pharmacological Reviews · doi:10.1124/pr.118.015768 · Cited by 319 · see citing works
Gut microbiota changes in the extreme decades of human life: a focus on centenarians
Santoro, A., Ostan, R., Candela, M., Biagi, E., Brigidi, P., Capri, M., & Franceschi, C. (2018) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2674-y · Cited by 250 · see citing works
Heterochronic faecal transplantation boosts gut germinal centres in aged mice
Stebegg, M., Silva-Cayetano, A., Innocentin, S., Jenkins, T. P., Cantacessi, C., Gilbert, C., & Linterman, M. A. (2019) · Nature Communications · doi:10.1038/s41467-019-10430-7 · Cited by 107 · see citing works
The Gut Microbiome and Individual-Specific Responses to Diet
Leshem, A., Segal, E., & Elinav, E. (2020) · mSystems · doi:10.1128/msystems.00665-20 · Cited by 109 · see citing works
Mills, S., Lane, J. A., Smith, G. J., Grimaldi, K. A., Ross, R. P., & Stanton, C. (2019) · Nutrients · doi:10.3390/nu11071468 · Cited by 88 · see citing works
Gut microbiota in ALS: possible role in pathogenesis?
McCombe, P. A., Henderson, R. D., Lee, A., Lee, J. D., Woodruff, T. M., Restuadi, R., McRae, A., Wray, N. R., Ngo, S., & Steyn, F. J. (2019) · Expert Review of Neurotherapeutics · doi:10.1080/14737175.2019.1623026 · Cited by 46 · see citing works
The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges
Tang, H. H. F., Teo, S. M., Sly, P. D., Holt, P. G., & Inouye, M. (2021) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2020.08.026 · Cited by 43 · see citing works
- Authors
- Kurilshikov, A., Wijmenga, C., Fu, J., & Zhernakova, A.
- Affiliations
- University Medical Center Groningen (NL)
- Corresponding author
- Zhernakova, Alexandra
- Venue
- Trends in Immunology
- Publisher
- Elsevier BV
- Published
- 2017-09
- Volume
- 38
- Issue
- 9
- Pages
- 633-647
- ISSN
- 1471-4906 (ISSN-L)
- OpenAlex
- W2728822570
- Cited by
- 309
- References
- 94
- Citations by year
- 2026: 15 · 2025: 38 · 2024: 34 · 2023: 29 · 2022: 31 · 2021: 47 · 2020: 42 · 2019: 42 · 2018: 25 · 2017: 6
- FWCI
- 2.95
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Trends in Immunology (publishedVersion, other-oa)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Funders
- European Research Council (FP/2007-2013/ERC, 2012-322698)
- Rosalind Franklin Fellowship (University of Groningen) (715772)
- CardioVasculair Onderzoek Nederland (2012-03)
- NWO Vidi grant (NWO-VIDI 864.13.013)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- gut microbiota, host genetics, host-microbe interactions, immune system genetics, microbiota composition, diet, host genetic factors, immunity, metabolism
- MeSH terms
- Gastrointestinal Microbiome, Animals, Diet, Humans, Immunity, Immunity, Innate, Genome, Receptors, Calcitriol, Gastrointestinal Tract, Receptors, Pattern Recognition, Host-Pathogen Interactions, Genetic Association Studies
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
