References
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). The effect of host genetics on the gut microbiome. Nat Genet 48, 1407–1412.
Camp, J.G., Frank, C.L., Lickwar, C.R., Guturu, H., Rube, T., Wenger, A. M., Chen, J., Bejerano, G., Crawford, G.E., and Rawls, J.F. (2014). Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res 24, 1504–1516.
Fan, P., Bian, B., Teng, L., Nelson, C.D., Driver, J., Elzo, M.A., and Jeong, K.C. (2020). Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation. ISME J 14, 302–317.
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). Human genetics shape the gut microbiome. Cell 159, 789–799.
Kemis, J.H., Linke, V., Barrett, K.L., Boehm, F.J., Traeger, L.L., Keller, M. P., Rabaglia, M.E., Schueler, K.L., Stapleton, D.S., Gatti, D.M., et al. (2019). Genetic determinants of gut microbiota composition and bile acid profiles in mice. PLoS Genet 15, e1008073.
Khan, A.A., Yurkovetskiy, L., O’Grady, K., Pickard, J.M., de Pooter, R., Antonopoulos, D.A., Golovkina, T., and Chervonsky, A. (2019). Polymorphic immune mechanisms regulate commensal repertoire. Cell Rep 29, 541–550.e4.
Krautkramer, K.A., Kreznar, J.H., Romano, K.A., Vivas, E.I., Barrett-Wilt, G.A., Rabaglia, M.E., Keller, M.P., Attie, A.D., Rey, F.E., and Denu, J. M. (2016). Diet-microbiota interactions mediate global epigenetic programming in multiple host tissues. Mol Cell 64, 982–992.
Li, J., and Wei, H. (2019). Establishment of an efficient germ-free animal system to support functional microbiome research. Sci China Life Sci 62, 1400–1403.
Liu, S., and Weiner, H.L. (2016). Control of the gut microbiome by fecal microRNA. Microb Cell 3, 176–177.
Plichta, D.R., Graham, D.B., Subramanian, S., and Xavier, R.J. (2019). Therapeutic opportunities in inflammatory bowel disease: Mechanistic dissection of host-microbiome relationships. Cell 178, 1041–1056.
Poole, A.C., Goodrich, J.K., Youngblut, N.D., Luque, G.G., Ruaud, A., Sutter, J.L., Waters, J.L., Shi, Q., El-Hadidi, M., Johnson, L.M., et al. (2019). Human salivary amylase gene copy number impacts oral and gut microbiomes. Cell Host Microbe 25, 553–564.e7.
Power, R.A., Parkhill, J., and de Oliveira, T. (2017). Microbial genomewide association studies: lessons from human GWAS. Nat Rev Genet 18, 41–50.
Qin, N., Dong, X., and Zhao, L. (2018). Microbiome: From community metabolism to host diseases. Sci China Life Sci 61, 741–743.
Richards, A.L., Muehlbauer, A.L., Alazizi, A., Burns, M.B., Findley, A., Messina, F., Gould, T.J., Cascardo, C., Pique-Regi, R., Blekhman, R., et al. (2019). Gut microbiota has a widespread and modifiable effect on host gene regulation. mSystems 4, e00323–18.
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). Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215.
Suzuki, T.A., Phifer-Rixey, M., Mack, K.L., Sheehan, M.J., Lin, D., Bi, K., and Nachman, M.W. (2019). Host genetic determinants of the gut microbiota of wild mice. Mol Ecol 28, 3197–3207.
Wang, J., Kalyan, S., Steck, N., Turner, L.M., Harr, B., Künzel, S., Vallier, M., Häsler, R., Franke, A., Oberg, H.H., et al. (2015). Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome. Nat Commun 6, 6440.
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). Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nat Genet 48, 1396–1406.
Wang, J., Chen, L., Zhao, N., Xu, X., Xu, Y., and Zhu, B. (2018). Of genes and microbes: Solving the intricacies in host genomes. Protein Cell 9, 446–461.
Zhang, Q., Pan, Y., Zeng, B., Zheng, X., Wang, H., Shen, X., Li, H., Jiang, Q., Zhao, J., Meng, Z.X., et al. (2019). Intestinal lysozyme liberates Nod1 ligands from microbes to direct insulin trafficking in pancreatic beta cells. Cell Res 29, 516–532.
Acknowledgements
This work was supported by the National Key Research and Development Program of China (2018YFC2000504, 2017YFD0500503 and 2017YFD0501000), the National Natural Science Foundation of China (81770434 and 81370906) and the National Program on Key Basic Research Project of China (973 Program) (2007CB513007 and 2013CB531406).
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Li, J., Wang, J. & Wei, H. Strengthening the functional research on the interaction between host genes and microbiota. Sci. China Life Sci. 63, 929–932 (2020). https://doi.org/10.1007/s11427-020-1650-4
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DOI: https://doi.org/10.1007/s11427-020-1650-4