Кишечный микробиом - основной фактор поддержания здоровья и развития болезней человека
Аннотация
Цель обзора. Отразить современные представления о роли микробиома в поддержании здоровья человека и развитии различных заболеваний. Краткое содержание. Благодаря современным достижениям молекулярной и клеточной биологии существенно расширились наши представления о патогенезе многих заболеваний человека и разработаны новые подходы к их диагностике, лечению и профилактике. На основе результатов современных молекулярных, генетических, эпигенетических, микробиологических и биохимических исследований стало возможным, с одной стороны, изучать точечные мутации и варианты полиморфизма отдельных нуклеотидов в рамках полногеномного анализа, с другой - с помощью высокоточного анализа и других методик проводить одновременное исследование тысяч генов (анализ ДНК) или их производных (РНК и белки) с созданием индивидуального профиля самих генов или их экспрессии («генетическая подпись»), а также осуществлять анализ индивидуального микробиома пациента с оценкой его патогенного потенциала. Подобные исследования позволяют все чаще проводить оценку индивидуальной предрасположенности к заболеваниям, прогноза болезни и эффективности выбранной стратегии лечения («персонализированная медицина»). Заключение. Исследование микробиома человека, а также полногеномные исследования способствуют достижению новых успехов в диагностике, лечении и профилактике заболеваний человека.
Список литературы
1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, et al. The sequence of the human genome. Science 2001;291:1304-1351.
3. Manolio TA, Brooks LD, Collins FS. A HapMap harvest of insights into the genetics of common disease. J Clin Invest 2008;118:1590-1605.
4. Manolio TA, Collins FS. The HapMap and genome-wide association studies in diagnosis and therapy. Annu Rev Med 2009;60:443-456.
5. Hou L, Heilbronner U, Degenhardt F, Adli M, Akiyama K, Akula N, Ardau R, et al. Genetic variants associated with response to lithium treatment in bipolar disorder: a genome-wide association study. Lancet 2016.
6. Proctor LM. The Human Microbiome Project in 2011 and beyond. Cell Host Microbe 2011;10:287-291.
7. Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 2011;9:279-290.
8. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-214.
9. Human Microbiome Project C. A framework for human microbiome research. Nature 2012;486:215-221.
10. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, et al. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol 2012;10: e1001377.
11. Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends Genet 2013;29:51-58.
12. Rossen NG, Fuentes S, van der Spek MJ, Tijssen JG, Hartman JH, Duflou A, Lowenberg M, et al. Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis. Gastroenterology 2015;149:110-118 e114.
13. Lynch SV, Pedersen O. The Human Intestinal Microbiome in Health and Disease. N Engl J Med 2016;375:2369-2379.
14. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014;32:834-841.
15. Yatsunenko T, Rey FE, Manary MJ, Trehan I, DominguezBello MG, Contreras M, Magris M, et al. Human gut microbiome viewed across age and geography. Nature 2012;486:222-227.
16. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 2016;352:565-569.
17. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, et al. Population-level analysis of gut microbiome variation. Science 2016;352:560-564.
18. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 2010;107:14691-14696.
19. Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2014;20:159166.
20. Cho I, Yamanishi S, Cox L, Methe BA, Zavadil J, Li K, Gao Z, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012;488:621626.
21. Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 2013;152:39-50.
22. Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, et al. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A 2014;111:805-810.
23. Fujimura KE, Sitarik AR, Havstad S, Lin DL, Levan S, Fadrosh D, Panzer AR, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med 2016;22:1187-1191.
24. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, et al. Human genetics shape the gut microbiome. Cell 2014;159:789-799.
25. Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature 2007;448:427-434.
26. Hall LJ, Walshaw J, Watson AJ. Gut microbiome in newonset Crohn’s disease. Gastroenterology 2014;147:932934.
27. Sha S, Xu B, Wang X, Zhang Y, Wang H, Kong X, Zhu H, et al. The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease. Diagn Microbiol Infect Dis 2013;75:245251.
28. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007;104:13780-13785.
29. Peterson DA, Frank DN, Pace NR, Gordon JI. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 2008;3:417-427.
30. Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, et al. Helminth infection promotes colonization resistance via type 2 immunity. Science 2016;352:608-612.
31. Moschen AR, Gerner RR, Wang J, Klepsch V, Adolph TE, Reider SJ, Hackl H, et al. Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations. Cell Host Microbe 2016;19:455469.
32. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell 2014;157:121-141.
33. Weinstock JV, Elliott DE. Helminths and the IBD hygiene hypothesis. Inflamm Bowel Dis 2009;15:128-133.
34. Cleynen I, Boucher G, Jostins L, Schumm LP, Zeissig S, Ahmad T, Andersen V, et al. Inherited determinants of Crohn’s disease and ulcerative colitis phenotypes: a genetic association study. Lancet 2016;387:156-167.
35. Ramanan D, Tang MS, Bowcutt R, Loke P, Cadwell K. Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus. Immunity 2014;41:311324.
36. Konishi H, Fujiya M, Tanaka H, Ueno N, Moriichi K, Sasajima J, Ikuta K, et al. Probiotic-derived ferrichrome inhibits colon cancer progression via JNK-mediated apoptosis. Nat Commun 2016;7:12365.
37. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013;341:1241214.
38. Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 2016;535:376-381.
39. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 2013;339:548-554.
40. Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, Alam MA, Benezra A, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature 2014;510:417-421.
41. Vrieze A, Van Nood E, Holleman F, Salojarvi J, Kootte RS, Bartelsman JF, Dallinga-Thie GM, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012;143:913-916 e917.
42. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 2013;19:576-585.
43. Zhu W, Gregory JC, Org E, Buffa JA, Gupta N, Wang Z, Li L, et al. Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk. Cell 2016;165:111-124.
44. Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E, Gu X, et al. Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis. Cell 2015;163:1585-1595.
45. Fung TC, Olson CA, Hsiao EY. Interactions between the microbiota, immune and nervous systems in health and disease. Nat Neurosci 2017;20:145-155.
46. Sampson TR, Mazmanian SK. Control of brain development, function, and behavior by the microbiome. Cell Host Microbe 2015;17:565-576.
47. Fasano A, Visanji NP, Liu LW, Lang AE, Pfeiffer RF. Gastrointestinal dysfunction in Parkinson’s disease. Lancet Neurol 2015;14:625-639.
48. Shannon KM, Keshavarzian A, Mutlu E, Dodiya HB, Daian D, Jaglin JA, Kordower JH. Alpha-synuclein in colonic submucosa in early untreated Parkinson’s disease. Mov Disord 2012;27:709-715.
49. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, et al. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease. Cell 2016;167:1469-1480 e1412.
50. Erny D, Hrabe de Angelis AL, Jaitin D, Wieghofer P, Staszewski O, David E, Keren-Shaul H, et al. Host microbiota constantly control maturation and function of microglia in the CNS. Nat Neurosci 2015;18:965-977.
51. Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature 2016;535:75-84.
52. Vatanen T, Kostic AD, d’Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, et al. Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell 2016;165:842-853.
53. Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature 2016;535:65-74.
54. Ijssennagger N, Belzer C, Hooiveld GJ, Dekker J, van Mil SW, Muller M, Kleerebezem M, et al. Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon. Proc Natl Acad Sci U S A 2015;112:10038-10043.
55. Reinhardt C, Bergentall M, Greiner TU, Schaffner F, Ostergren-Lunden G, Petersen LC, Ruf W, et al. Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling. Nature 2012;483:627-631.
56. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 2015;161:264-276.
57. Ege MJ, Mayer M, Normand AC, Genuneit J, Cookson WO, Braun-Fahrlander C, Heederik D, et al. Exposure to environmental microorganisms and childhood asthma. N Engl J Med 2011;364:701-709.
58. Lynch SV, Wood RA, Boushey H, Bacharier LB, Bloomberg GR, Kattan M, O’Connor GT, et al. Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children. J Allergy Clin Immunol 2014;134:593-601 e512.
59. Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, et al. Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. N Engl J Med 2016;375:411-421.
60. Jonsson AL, Backhed F. Drug the Bug! Cell 2015;163:15651566.
61. Tilg H. A Gut Feeling about Thrombosis. N Engl J Med 2016;374:2494-2496.
62. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, Feldstein AE, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011;472:57-63.
63. Tang WH, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu Y, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013;368:1575-1584.
64. Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, Zhang D, et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat Commun 2015;6:6528.
65. Sivan A, Corrales L, Hubert N, Williams JB, AquinoMichaels K, Earley ZM, Benyamin FW, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 2015;350:10841089.
66. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012;490:55-60.
67. Forbes JD, Van Domselaar G, Bernstein CN. Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2016;22:817-825.
68. Forbes JD, Van Domselaar G, Bernstein CN. The Gut Microbiota in Immune-Mediated Inflammatory Diseases. Front Microbiol 2016;7:1081.
69. Cantarel BL, Waubant E, Chehoud C, Kuczynski J, DeSantis TZ, Warrington J, Venkatesan A, et al. Gut microbiota in multiple sclerosis: possible influence of immunomodulators. J Investig Med 2015;63:729-734.
70. Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, Patel B, et al. Alterations of the human gut microbiome in multiple sclerosis. Nat Commun 2016;7:12015.
71. Chen J, Wright K, Davis JM, Jeraldo P, Marietta EV, Murray J, Nelson H, et al. An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis. Genome Med 2016;8:43.
72. Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, Marmon S, et al. Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol 2015;67:128-139.
73. Haque TR, Barritt ASt. Intestinal microbiota in liver disease. Best Pract Res Clin Gastroenterol 2016;30:133142.
74. Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014;513:59-64.
75. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, et al. A core gut microbiome in obese and lean twins. Nature 2009;457:480484.
76. Shen J, Obin MS, Zhao L. The gut microbiota, obesity and insulin resistance. Mol Aspects Med 2013;34:39-58.
77. Mazidi M, Rezaie P, Kengne AP, Mobarhan MG, Ferns GA. Gut microbiome and metabolic syndrome. Diabetes Metab Syndr 2016;10: S150-157.
78. Sonnenburg JL, Backhed F. Diet-microbiota interactions as moderators of human metabolism. Nature 2016;535:5664.
79. Choi GB, Yim YS, Wong H, Kim S, Kim H, Kim SV, Hoeffer CA, et al. The maternal interleukin-17a pathway in mice promotes autism-like phenotypes in offspring. Science 2016;351:933-939.
80. Aizawa E, Tsuji H, Asahara T, Takahashi T, Teraishi T, Yoshida S, Ota M, et al. Possible association of Bifidobacterium and Lactobacillus in the gut microbiota of patients with major depressive disorder. J Affect Disord 2016;202:254-257.
81. Bu XL, Yao XQ, Jiao SS, Zeng F, Liu YH, Xiang Y, Liang CR, et al. A study on the association between infectious burden and Alzheimer’s disease. Eur J Neurol 2015;22:1519-1525.
82. Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, et al. Gut microbiota are related to Parkinson’s disease and clinical phenotype. Mov Disord 2015;30:350-358.
Для цитирования:
Хуберт Е.Б. Кишечный микробиом - основной фактор поддержания здоровья и развития болезней человека. Российский журнал гастроэнтерологии, гепатологии, колопроктологии. 2017;27(5):4-10. https://doi.org/10.22416/1382-4376-2017-27-5-4-10
For citation:
Hubert E.B. INTESTINAL MICROBIOME - A LEADING FACTOR IN HUMAN HEALTH AND DISEASES. Russian Journal of Gastroenterology, Hepatology, Coloproctology. 2017;27(5):4-10. (In Russ.) https://doi.org/10.22416/1382-4376-2017-27-5-4-10
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