Host Genetics and Gut Microbiome: Challenges and Perspectives

Trends in Immunology

Volumn 38, Issue 9, 2017, Pages 633-647

  Kurilshikov, Alexander ^a   Wijmenga, Cisca ^a,b   Fu, Jingyuan ^a   Zhernakova, Alexandra ^a  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ENVIRONMENTAL FACTOR; GENETICS; HERITABILITY; HOST; HUMAN; IMMUNE SYSTEM; INTESTINE FLORA; NONHUMAN; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW; ANIMAL; DIET; GASTROINTESTINAL TRACT; GENETIC ASSOCIATION STUDY; GENOME; HOST PATHOGEN INTERACTION; IMMUNITY; INNATE IMMUNITY; MICROBIOLOGY; PHYSIOLOGY;

CALCITRIOL RECEPTOR; PATTERN RECOGNITION RECEPTOR;

ANIMALS; DIET; GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRACT; GENETIC ASSOCIATION STUDIES; GENOME; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNITY; IMMUNITY, INNATE; RECEPTORS, CALCITRIOL; RECEPTORS, PATTERN RECOGNITION;

EID: 85021322151     PISSN: 14714906     EISSN: 14714981     Source Type: Journal    
DOI: 10.1016/j.it.2017.06.003     Document Type: Review

References (92)

1. Wu, H.J., Wu, E., The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes 3 (2012), 4–14.
2. Turnbaugh, P.J., et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 (2006), 1027–1131.
3. Zhernakova, A., et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352 (2016), 565–569.
4. Falony, G., et al. Population-level analysis of gut microbiome variation. Science 352 (2016), 560–564.
5. Honda, K., Littman, D.R., The microbiota in adaptive immune homeostasis and disease. Nature 535 (2016), 75–84.
6. Thaiss, C.A., et al. The microbiome and innate immunity. Nature 535 (2016), 65–74.
7. Hergott, C.B., et al. Peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis. Blood 127 (2016), 2460–2471.
8. Turnbaugh, P.J., et al. A core gut microbiome in obese and lean twins. Nature 457 (2009), 480–484.
9. Goodrich, J.K., et al. Human genetics shape the gut microbiome. Cell 159 (2014), 789–799.
10. Goodrich, J.K., et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe 19 (2016), 731–743.
11. Xie, H., et al. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Syst. 3 (2016), 572–584.e3.
12. Turpin, W., et al. Association of host genome with intestinal microbial composition in a large healthy cohort. Nat. Genet. 48 (2016), 1413–1417.
13. Integrative HMP (iHMP) Research Network Consortium, The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 16 (2014), 276–289.
14. Turnbaugh, P.J., et al. The human microbiome project. Nature 449 (2007), 804–810.
15. Claesson, M.J., et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488 (2016), 178–184.
16. Smith, M.I., et al. Gut microbiomes of Malawian twin pairs discordant for Kwashiorkor. Science 339 (2013), 548–554.
17. Gevers, D., et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15 (2014), 382–392.
18. Qin, J., et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490 (2012), 55–60.
19. 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 (2016), 1396–1406.
20. Lozupone, C.A., et al. Diversity, stability and resilience of the human gut microbiota. Nature 489 (2012), 220–230.
21. Dey, N., et al. Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel. Cell 163 (2015), 95–107.
22. Turnbaugh, P.J., et al. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3 (2008), 213–223.
23. David, L.A., et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505 (2014), 559–563.
24. Ridaura, V.K., et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science, 341, 2013, 1241214.
25. Koeth, R.A., et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19 (2013), 576–585.
26. Imhann, F., et al. Proton pump inhibitors affect the gut microbiome. Gut 65 (2016), 740–748.
27. Cho, I., et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 488 (2012), 621–626.
28. Locke, A.E., et al. Genetic studies of body mass index yield new insights for obesity biology. Nature 518 (2015), 197–206.
29. Forslund, K., et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528 (2015), 262–266.
30. Vatanen, T., et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165 (2015), 842–853.
31. Fu, J., et al. The gut microbiome contributes to a substantial proportion of the variation in blood lipids. Circ. Res. 117 (2015), 817–824.
32. Zhong, Y., et al. Effects of two whole-grain barley varieties on caecal SCFA, gut microbiota and plasma inflammatory markers in rats consuming low- and high-fat diets. Br. J. Nutr. 113 (2015), 1558–1570.
33. Pedersen, H.K., et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 535 (2016), 376–381.
34. Vrieze, A., et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143 (2012), 913–916.e7.
35. Ivanov, I.I., et al. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4 (2008), 337–349.
36. Westra, H.J., et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 45 (2013), 1238–1243.
37. Cebra, J.J., Influences of microbiota on intestinal immune system development. Am. J. Clin. Nutr. 69 (1999), 1046S–1051S.
38. Hand, T.W., et al. Linking the microbiota, chronic disease, and the immune system. Trends Endocrinol. Metab. 27 (2016), 831–843.
39. Corrêa-Oliveira, R., et al. Regulation of immune cell function by short-chain fatty acids. Clin. Transl. Immunol., 5, 2016, e73.
40. Elinav, E., et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145 (2011), 745–757.
41. Frantz, A.L., et al. Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides. Mucosal Immunol. 5 (2012), 501–512.
42. Vijay-Kumar, M., et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328 (2010), 228–231.
43. Sonnenberg, G.F., et al. Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science 336 (2012), 1321–1325.
44. Jovel, J., et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol., 7, 2016, 459.
45. Truong, D.T., et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12 (2015), 902–903.
46. Yatsunenko, T., et al. Human gut microbiome viewed across age and geography. Nature 486 (2012), 222–227.
47. Davenport, E.R., et al. Genome-wide association studies of the human gut microbiota. PLoS One 10 (2015), 1–22.
48. 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. U. S. A. 107 (2010), 18933–18938.
49. McKnite, A.M., et al. Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PLoS One, 7, 2012, e39191.
50. Org, E., et al. Genetic and environmental control of host-gut microbiota interactions. Genome Res. 25 (2015), 1558–1569.
51. Wang, J., et al. Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome. Nat. Commun., 6, 2015, 6440.
52. Tong, M., et al. Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. 8 (2014), 1–14.
53. Khachatryan, Z.A., et al. Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One, 3, 2008, e3064.
54. Knights, D., et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med., 6, 2014, 107.
55. Blekhman, R., et al. Host genetic variation impacts microbiome composition across human body sites. Genome Biol., 16, 2015, 191.
56. Bonder, M.J., et al. The effect of host genetics on the gut microbiome. Nat. Genet. 48 (2016), 1407–1412.
57. Jin, D., et al. Lack of vitamin D receptor causes dysbiosis and changes the functions of the murine intestinal microbiome. Clin. Ther. 37 (2015), 996–1009.e7.
58. Li, D., et al. A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology 151 (2016), 724–732.
59. Imhann, F., et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut, 2016, 10.1136/gutjnl-2016-312135 Published online October 8, 2016.
60. Khosravi, A., et al. Gut microbiota promote hematopoiesis to control bacterial infection. Cell Host Microbe 15 (2014), 374–381.
61. Satoh-Takayama, N., et al. Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense. Immunity 29 (2008), 958–970.
62. Sanos, S.L., et al. RORγt and commensal microflora are required for the differentiation of mucosal interleukin 22–producing NKp46+ cells. Nat. Immunol. 10 (2009), 83–91.
63. Kellermayer, R., et al. Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. FASEB J. 25 (2011), 1449–1460.
64. Lynch, S.V., et al. Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota. Gut Microbes 4 (2013), 41–47.
65. Brinkman, B.M., et al. Caspase deficiency alters the murine gut microbiome. Cell Death Dis., 2, 2011, e220.
66. Øyri, S.F., et al. Dysbiotic gut microbiome: a key element of Crohn's disease. Comp. Immunol. Microbiol. Infect. Dis. 43 (2015), 36–49.
67. Coit, P., Sawalha, A.H., The human microbiome in rheumatic autoimmune diseases: a comprehensive review. Clin. Immunol. 170 (2016), 70–79.
68. Jangi, S., et al. Alterations of the human gut microbiome in multiple sclerosis. Nat. Commun., 7, 2016, 12015.
69. Petnicki-Ocwieja, T., et al. Nod2 is required for the regulation of commensal microbiota in the intestine. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 15813–15818.
70. Rehman, A., et al. Nod2 is essential for temporal development of intestinal microbial communities. Gut 60 (2011), 1354–1362.
71. Kobayashi, K.S., Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract. Science 307 (2005), 731–734.
72. Nordlander, S., et al. NLRC4 expression in intestinal epithelial cells mediates protection against an enteric pathogen. Mucosal Immunol. 7 (2014), 775–785.
73. Henao-Mejia, J., et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482 (2012), 179–185.
74. Lamas, B., et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat. Med. 22 (2016), 598–605.
75. Sokol, H., et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. U. S. A. 105 (2008), 16731–16736.
76. Singh, V., et al. Interplay between enterobactin, myeloperoxidase and lipocalin 2 regulates E. coli survival in the inflamed gut. Nat. Commun., 6, 2015, 7113.
77. Graham, L.M., Brown, G.D., The dectin-2 family of C-type lectins in immunity and homeostasis. Cytokine 48 (2009), 148–155.
78. Dambuza, I.M., Brown, G.D., C-type lectins in immunity: recent developments. Curr. Opin. Immunol. 32 (2015), 21–27.
79. Shan, M., et al. Mucus enhances gut homeostasis and oral tolerance by delivering immunoregulatory signals. Science 342 (2013), 447–453.
80. Wang, X.W., et al. A shrimp C-type lectin inhibits proliferation of the hemolymph microbiota by maintaining the expression of antimicrobial peptides. J. Biol. Chem. 289 (2014), 11779–11790.
81. Pang, X., et al. Mosquito C-type lectins maintain gut microbiome homeostasis. Nat. Microbiol., 1, 2016, 16023.
82. Iliev, I.D., et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 336 (2012), 1314–1317.
83. Dimitriu, P.A., et al. Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity. Environ. Microbiol. Rep. 5 (2013), 200–210.
84. Wu, H.J., et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 32 (2010), 815–827.
85. Sivan, A., et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350 (2015), 1084–1089.
86. Atarashi, K., et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500 (2013), 232–236.
87. Chen, J., et al. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci. Rep., 6, 2016, 28484.
88. Zhang, X., et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat. Med. 21 (2015), 895–905.
89. Palm, N.W., et al. Immunoglobulin a coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158 (2014), 1000–1010.
90. Hua, X., et al. MicrobiomeGWAS: a tool for identifying host genetic variants associated with microbiome composition. bioRxiv, 2015, 10.1101/031187.
91. Xu, L., et al. Assessment and selection of competing models for zero-inflated microbiome data. PLoS One, 10, 2015, e0129606.
92. Ripke, S., et al. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511 (2014), 421–427.