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《工程(英文)》 >> 2017年 第3卷 第1期 doi: 10.1016/J.ENG.2017.01.008

人体微生态与健康

National Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China

录用日期: 2017-01-19 发布日期: 2017-02-28

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摘要

数以万亿计的微生物寄生于人体表面和体内,并与人类起演变多种环境因素可影响胃肠道微生的平衡,这些改变与人体健康和疾病密切相关本文重点关注人体微生与宿主之间的相互作用,总体概括微生物在人体基本生命过程中以及主要疾病中起的作用,如感染性疾病肝脏疾病胃肠道肿瘤、代谢疾病呼吸系统疾病精神或心理疾病和自身免疫疾病等。我们还综述了微生物研究相关术的重要进展,如DNA 测序、代谢组学和基于计算生物信息学的蛋白质组学目前对人类微生态的研究已经更加复杂和全面建议研究应更多关注–宿主微生物的相互作用和因果关系,这有助于我们更好地了解肠道微生物在人类健康和疾病中的作用,并为临床实践提供新的治疗靶点和方法。

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参考文献

[ 1 ] O’Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep 2006;7(7):688–93 链接1

[ 2 ] Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, et al. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology 2014;146(6):1470–6 链接1

[ 3 ] Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 1998;95(12):6578–83 链接1

[ 4 ] Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977;31(1):107–33 链接1

[ 5 ] Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006;124(4):837–48 链接1

[ 6 ] Wang B, Li L. Who determines the outcomes of HBV exposure? Trends Microbiol 2015;23(6):328–29 链接1

[ 7 ] Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006;444(7122):1022–3 链接1

[ 8 ] Wang B, Jiang X, Cao M, Ge J, Bao Q, Tang L, et al. Altered fecal microbiota correlates with liver biochemistry in nonobese patients with non-alcoholic fatty liver disease. Sci Rep 2016;6:32002 链接1

[ 9 ] Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312(5778):1355–9 链接1

[10] Roberfroid MB, Bornet F, Bouley C, Cummings JH. Colonic microflora: nutrition and health. Summary and conclusions of an International Life Sciences Institute (ILSI) [Europe] workshop held in Barcelona, Spain. Nutr Rev 1995;53(5):127–30 链接1

[11] Cash HL, Whitham CV, Behrendt CL, Hooper LV. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 2006;313(5790):1126–30 链接1

[12] Hooper LV, Stappenbeck TS, Hong CV, Gordon JI. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol 2003;4(3):269–73 链接1

[13] Schauber J, Svanholm C, Termén S, Iffland K, Menzel T, Scheppach W, et al. Expression of the cathelicidin LL-37 is modulated by short chain fatty acids in colonocytes: relevance of signalling pathways. Gut 2003;52(5):735–41 链接1

[14] Bouskra D, Brézillon C, Bérard M, Werts C, Varona R, Boneca IG, et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 2008;456(7221):507–10 链接1

[15] Rakoff-Nahoum S, Medzhitov R. Innate immune recognition of the indigenous microbial flora. Mucosal Immunol 2008;1(Suppl 1):S10–4 链接1

[16] Macpherson AJ, Harris NL. Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol 2004;4(6):478–85 链接1

[17] Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev 2010;90(3):859–904 链接1

[18] Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008;134(2):577–94 链接1

[19] Liu Q, Duan Z, Ha D, Bengmark S, Kurtovic J, Riordan SM. Synbiotic modulation of gut flora: effect on minimal hepatic encephalopathy in patients with cirrhosis. Hepatology 2004;39(5):1441–9 链接1

[20] Scanlan PD, Shanaha n F, Clune Y, Collins JK, O’Sullivan GC, O’Riordan M, et al. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 2008;10(3):789–98 链接1

[21] Verhulst SL, Vael C, Beunckens C, Nelen V, Goossens H, Desager K. A longitudinal analysis on the association between antibiotic use, intestinal microflora, and wheezing during the first year of life. J Asthma 2008;45(9):828–32 链接1

[22] Finegold SM, Molitoris D, Song Y, Liu C, Vaisanen ML, Bolte E, et al. Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis 2002;35(Suppl 1):S6–16 链接1

[23] Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008;455(7216):1109–13 链接1

[24] Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444(7122):1027–31 链接1

[25] Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, et al. Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome. Nature 2016;534(7606):213–7 链接1

[26] Cani PD, Dewever C, Delzenne NM. Inulin-type fructans modulate gastrointestinal peptides involved in appetite regulation (glucagon-like peptide-1 and ghrelin) in rats. Br J Nutr 2004;92(3):521–6 链接1

[27] Hollister EB, Gao C, Versalovic J. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology 2014;146(6):1449–58 链接1

[28] Rogier EW, Frantz AL, Bruno ME, Wedlund L, Cohen DA, Stromberg AJ, et al. Lessons from mother: long-term impact of antibodies in breast milk on the gut microbiota and intestinal immune system of breastfed offspring. Gut Microbes 2014;5(5):663–8 链接1

[29] Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009;9(5):313–23 链接1

[30] Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, et al. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 2014;506(7489):498–502 链接1

[31] Goh YJ, Klaenhammer TR. Genetic mechanisms of prebiotic oligosaccharide metabolism in probiotic microbes. Annu Rev Food Sci Technol 2015;6:137–56 链接1

[32] Morowitz MJ, Carlisle EM, Alverdy JC. Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. Surg Clin North Am 2011;91(4):771–85 链接1

[33] Duncan SH, Louis P, Thomson JM, Flint HJ. The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol 2009;11(8):2112–22 链接1

[34] Cani PD, Everard A, Duparc T. Gut microbiota, enteroendocrine functions and metabolism. Curr Opin Pharmacol 2013;13(6):935–40 链接1

[35] Flint HJ, Scott KP, Louis P, Duncan SH. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 2012;9(10):577–89 链接1

[36] Kang Z, Zhang J, Zhou J, Qi Q, Du G, Chen J. Recent advances in microbial production of δ-aminolevulinic acid and vitamin B12. Biotechnol Adv 2012;30(6):1533–42 链接1

[37] Cebra JJ. Influences of microbiota on intestinal immune system development. Am J Clin Nutr 1999;69(5):1046S–51S.

[38] Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature 2016;535(7610):65–74 链接1

[39] Madsen KL, Doyle JS, Jewell LD, Tavernini MM, Fedorak RN. Lactobacillus species prevents colitis in interleukin 10 gene-deficient mice. Gastroenterology 1999;116(5):1107–14 链接1

[40] Magrone T, Jirillo E. The interplay between the gut immune system and microbiota in health and disease: nutraceutical intervention for restoring intestinal homeostasis. Curr Pharm Des 2013;19(7):1329–42.

[41] Brenchley JM, Douek DC. Microbial translocation across the GI tract. Annu Rev Immunol 2012;30:149–73 链接1

[42] Hand TW, Dos Santos LM, Bouladoux N, Molloy MJ, Pagán AJ, Pepper M, et al. Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses. Science 2012;337(6101):1553–6 链接1

[43] Ling Z, Liu X, Cheng Y, Jiang X, Jiang H, Wang Y, et al. Decreased diversity of the oral microbiota of patients with hepatitis B virus-induced chronic liver disease: a pilot report. Sci Rep 2015;5:17098 链接1

[44] Cohen J. Vaginal microbiome affects HIV risk. Science 2016;353(6297):331 链接1

[45] Gu S, Chen Y, Zhang X, Lu H, Lv T, Shen P, et al. Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population. Microbes Infect 2016;18(1):30–8 链接1

[46] Ling Z, Liu X, Jia X, Cheng Y, Luo Y, Yuan L, et al. Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children. Sci Rep 2014;4:7485 链接1

[47] Ling Z, Jin C, Xie T, Cheng Y, Li L, Wu N. Alterations in the fecal microbiota of patients with HIV-1 infection: an observational study in a Chinese population. Sci Rep 2016;6:30673 链接1

[48] Xu M, Wang B, Fu Y, Chen Y, Yang F, Lu H, et al. Changes of fecal Bifidobacterium species in adult patients with hepatitis B virus-induced chronic liver disease. Microb Ecol 2012;63(2):304–13 链接1

[49] Hu Z, Zhang Y, Li Z, Yu Y, Kang W, Han Y, et al. Effect of Helicobacter pylori infection on chronic periodontitis by the change of microecology and inflammation. Oncotarget 2016;7(41):66700–12.

[50] Ling Z, Kong J, Liu F, Zhu H, Chen X, Wang Y, et al. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics 2010;11:488 链接1

[51] Giannelli V, Di Gregorio V, Iebba V, Giusto M, Schippa S, Merli M, et al. Microbiota and the gut-liver axis: bacterial translocation, inflammation and infection in cirrhosis. World J Gastroenterol 2014;20(45):16795–810 链接1

[52] Nardone G, Rocco A. Probiotics: a potential target for the prevention and treatment of steatohepatitis. J Clin Gastroenterol 2004;38(Suppl 2):S121–2 链接1

[53] Cesaro C, Tiso A, Del Prete A, Cariello R, Tuccillo C, Cotticelli G, et al. Gut microbiota and probiotics in chronic liver diseases. Dig Liver Dis 2011;43(6): 431–8 链接1

[54] Lakshmi CP, Ghoshal UC, Kumar S, Goel A, Misra A, Mohindra S, et al. Frequency and factors associated with small intestinal bacterial overgrowth in patients with cirrhosis of the liver and extra hepatic portal venous obstruction. Dig Dis Sci 2010;55(4):1142–8 链接1

[55] Gupta A, Dhiman RK, Kumari S, Rana S, Agarwal R, Duseja A, et al. Role of small intestinal bacterial overgrowth and delayed gastrointestinal transit time in cirrhotic patients with minimal hepatic encephalopathy. J Hepatol 2010;53(5):849–55 链接1

[56] Chen Y, Yang F, Lu H, Wang B, Chen Y, Lei D, et al. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 2011;54(2):562–72 链接1

[57] Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014;513(7516):59–64 链接1

[58] Chen Y, Ji F, Guo J, Shi D, Fang D, Li L. Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology. Sci Rep 2016;6:34055 链接1

[59] Chen Y, Guo J, Qian G, Fang D, Shi D, Guo L, et al. Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality. J Gastroenterol Hepatol 2015;30(9):1429–37 链接1

[60] Dapito DH, Mencin A, Gwak GY, Pradere JP, Jang MK, Mederacke I, et al. Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell 2012;21(4):504–16 链接1

[61] Ozaslan E, Efe C. Further considerations in autoimmune hepatitis. J Hepatol 2016;64(6):1457–8 链接1

[62] Marchesi JR, Adams DH, Fava F, Hermes GD, Hirschfield GM, Hold G, et al. The gut microbiota and host health: a new clinical frontier. Gut 2016;65(2): 330–9 链接1

[63] Lv L, Fang D, Shi D, Chen D, Yan R, Zhu Y, et al. Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis. Environ Microbiol 2016;18(7):2272–86 链接1

[64] Bj?rnsson E, Cederborg A, ?kvist A, Simren M, Stotzer PO, Bjarnason I. Intestinal permeability and bacterial growth of the small bowel in patients with primary sclerosing cholangitis. Scand J Gastroenterol 2005;40(9):1090–4 链接1

[65] Tilg H, Moschen AR, Roden M. NAFLD and diabetes mellitus. Nat Rev Gastroenterol Hepatol 2017;14(1):32–42 链接1

[66] Wesolowski SR, Kasmi KC, Jonscher KR, Friedman JE. Developmental origins of NAFLD: a womb with a clue. Nat Rev Gastroenterol Hepatol. Epub 2016 Oct 26 链接1

[67] Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, et al. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 2016;63(3):764–75 链接1

[68] de Martel C, Ferlay J, Franceschi S, Vignat J, Bray F, Forman D, et al. Global burden of cancers attributable to infections in 2008: a review and synthetic analysis. Lancet Oncol 2012;13(6):607–15 链接1

[69] Wong BCY, Lam SK, Wong WM, Chen JS, Zheng TT, Feng RE, et al.; China Gastric Cancer Study Group. Helicobacter pylori eradication to prevent gastric cancer in a high-risk region of China: a randomized controlled trial. JAMA 2004;291(2):187–94 链接1

[70] Herrera V, Parsonnet J. Helicobacter pylori and gastric adenocarcinoma. Clin Microbiol Infect 2009;15(11):971–6 链接1

[71] El-Omar EM, Carrington M, Chow WH, McColl KE, Bream JH, Young HA, et al. Interleukin-1 polymorphisms associated with increased risk of gastric cancer. Nature 2000;404(6776):398–402 链接1

[72] de Sablet T, Piazuelo MB, Shaffer CL, Schneider BG, Asim M, Chaturvedi R, et al. Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk. Gut 2011;60(9):1189–95 链接1

[73] Rhead JL, Letley DP, Mohammadi M, Hussein N, Mohagheghi MA, Eshagh Hosseini M, et al. A new Helicobacter pylori vacuolating cytotoxin determinant, the intermediate region, is associated with gastric cancer. Gastroenterology 2007;133(3):926–36 链接1

[74] Cover TL, Krishna US, Israel DA, Peek RM Jr. Induction of gastric epithelial cell apoptosis by Helicobacter pylori vacuolating cytotoxin. Cancer Res 2003;63(5):951–7.

[75] Oertli M, Sundquist M, Hitzler I, Engler DB, Arnold IC, Reuter S, et al. DC-derived IL-18 drives Treg differentiation, murine Helicobacter pylori-specific immune tolerance, and asthma protection. J Clin Invest 2012;122(3):1082–96 链接1

[76] Blaser MJ, Perez-Perez GI, Kleanthous H, Cover TL, Peek RM, Chyou PH, et al. Infection with Helicobacter pylori strains possessing cagA is associated with an increased risk of developing adenocarcinoma of the stomach. Cancer Res 1995;55(10):2111–5.

[77] Kaparakis M, Turnbull L, Carneiro L, Firth S, Coleman HA, Parkington HC, et al. Bacterial membrane vesicles deliver peptidoglycan to NOD1 in epithelial cells. Cell Microbiol 2010;12(3):372–85 链接1

[78] Odenbreit S, Püls J, Sedlmaier B, Gerland E, Fischer W, Haas R. Translocation of Helicobacter pylori cagA into gastric epithelial cells by type IV secretion. Science 2000;287(5457):1497–500 链接1

[79] Lertpiriyapong K, Whary MT, Muthupalani S, Lofgren JL, Gamazon ER, Feng Y, et al. Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis. Gut 2014;63(1):54–63 链接1

[80] Sanapareddy N, Legge RM, Jovov B, McCoy A, Burcal L, Araujo-Perez F, et al. Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans. ISME J 2012;6(10):1858–68 链接1

[81] Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2012;22(2):299–306 链接1

[82] Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, et al. The gut microbiome modulates colon tumorigenesis. MBio 2013;4(6): e00692–13 链接1

[83] Keku TO, McCoy AN, Azcarate-Peril AM. Fusobacterium spp. and colorectal cancer: cause or consequence? Trends Microbiol 2013;21(10):506–8 链接1

[84] Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat Commun 2015;6:6528 链接1

[85] Rubinstein MR, Wang X, Liu W, Hao Y, Cai G, Han YW. Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/β-catenin signaling via its FadA adhesin. Cell Host Microbe 2013;14(2):195–206 链接1

[86] Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 2013;14(2): 207–15 链接1

[87] Sokol SY. Wnt signaling and dorso-ventral axis specification in vertebrates. Curr Opin Genet Dev 1999;9(4):405–10 链接1

[88] Sears CL. Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes. Clin Microbiol Rev 2009;22(2):349–69 链接1

[89] Shiryaev SA, Remacle AG, Chernov AV, Golubkov VS, Motamedchaboki K, Muranaka N, et al. Substrate cleavage profiling suggests a distinct function of Bacteroides fragilis metalloproteinases (fragilysin and metalloproteinase II) at the microbiome-inflammation-cancer interface. J Biol Chem 2013;288(48): 34956–67 链接1

[90] Wu S, Rhee KJ, Albesiano E, Rabizadeh S, Wu X, Yen HR, et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med 2009;15(9):1016–22 链接1

[91] Huycke MM, Abrams V, Moore DR. Enterococcus faecalis produces extracellular superoxide and hydrogen peroxide that damages colonic epithelial cell DNA. Carcinogenesis 2002;23(3):529–36 链接1

[92] Cuevas-Ramos G, Petit CR, Marcq I, Boury M, Oswald E, Nougayrède JP. Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells. Proc Natl Acad Sci USA 2010;107(25):11537–42 链接1

[93] Howe GR, Benito E, Castelleto R, Cornée J, Estève J, Gallagher RP, et al. Dietary intake of fiber and decreased risk of cancers of the colon and rectum: evidence from the combined analysis of 13 case-control studies. J Natl Cancer Inst 1992;84(24):1887–96 链接1

[94] Clausen MR, Bonnén H, Mortensen PB. Colonic fermentation of dietary fibre to short chain fatty acids in patients with adenomatous polyps and colonic cancer. Gut 1991;32(8):923–8 链接1

[95] Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R, Shi H, et al. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity 2014; 40(1):128–39 链接1

[96] Lagergren J, Bergstr?m R, Lindgren A, Nyrén O. Symptomatic gastroesophageal reflux as a risk factor for esophageal adenocarcinoma. N Engl J Med 1999;340(11):825–31 链接1

[97] Lagergren J. Adenocarcinoma of oesophagus: what exactly is the size of the problem and who is at risk? Gut 2005;54(Suppl 1):i1–5 链接1

[98] Anderson LA, Murphy SJ, Johnston BT, Watson RG, Ferguson HR, Bamford KB, et al. Relationship between Helicobacter pylori infection and gastric atrophy and the stages of the oesophageal inflammation, metaplasia, adenocarcinoma sequence: results from the FINBAR case-control study. Gut 2008;57(6):734–9 链接1

[99] Pei Z, Bini EJ, Yang L, Zhou M, Francois F, Blaser MJ. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci USA 2004;101(12):4250–5 链接1

[100] Yang L, Lu X, Nossa CW, Francois F, Peek RM, Pei Z. Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Gastroenterology 2009;137(2):588–97 链接1

[101] Finlay IG, Wright PA, Menzies T, McArdle CS. Microbial flora in carcinoma of oesophagus. Thorax 1982;37(3):181–4 链接1

[102] El-Serag HB, Sonnenberg A. Opposing time trends of peptic ulcer and reflux disease. Gut 1998;43(3):327–33 链接1

[103] Hamada H, Haruma K, Mihara M, Kamada T, Yoshihara M, Sumii K, et al. High incidence of reflux oesophagitis after eradication therapy for Helicobacter pylori: impacts of hiatal hernia and corpus gastritis. Aliment Pharmacol Ther 2000;14(6):729–35 链接1

[104] Sommer F, B?ckhed F. The gut microbiota-masters of host development and physiology. Nat Rev Microbiol 2013;11(4):227–38 链接1

[105] Franks PW, McCarthy MI. Exposing the exposures responsible for type 2 diabetes and obesity. Science 2016;354(6308):69–73 链接1

[106] Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al.; MetaHIT Consortium. Richness of human gut microbiome correlates with metabolic markers. Nature 2013;500(7464):541–6 链接1

[107] Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457(7228): 480–4 链接1

[108] Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013;341(6150):1241214 链接1

[109] David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014;505(7484):559–63 链接1

[110] Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, B?ckhed F. Crosstalk between gut microbiota and dietary lipids aggravates WAT inflammation through TLR signaling. Cell Metab 2015;22(4):658–68 链接1

[111] Sonnenburg JL, B?ckhed F. Diet-microbiota interactions as moderators of human metabolism. Nature 2016;535(7610):56–64 链接1

[112] Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, et al. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe 2015;17(5):681–9 链接1

[113] Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Suez J, Tengeler AC, et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 2014;159(3):514–29 链接1

[114] Tremaroli V, B?ckhed F. Functional interactions between the gut microbiota and host metabolism. Nature 2012;489(7415):242–9 链接1

[115] de Vos WM, Nieuwdorp M. Genomics: a gut prediction. Nature 2013;498(7452): 48–9 链接1

[116] Delzenne NM, Cani PD. Gut microflora is a key player in host energy homeostasis. Med Sci (Paris) 2008;24(5):505–10 链接1

[117] Wahlstr?m A, Sayin SI, Marschall HU, B?ckhed F. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab 2016;24(1):41–50 链接1

[118] Camilleri M. Peripheral mechanisms in appetite regulation. Gastroenterology 2015;148(6):1219–33 链接1

[119] Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012;490(7418):55–60 链接1

[120] Karlsson FH, Tremaroli V, Nookaew I, Bergstr?m G, Behre CJ, Fagerberg B, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 2013;498(7452):99–103 链接1

[121] Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, et al.; MetaHIT Consortium. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2015;528(7581): 262–6 链接1

[122] Burcelin R. Gut microbiota and immune crosstalk in metabolic disease. Mol Metab 2016;5(9):771–81 链接1

[123] Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, et al.; MetaHIT Consortium. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 2016;535(7612):376–81 链接1

[124] Mardinoglu A, Boren J, Smith U. Confounding effects of metformin on the human gut microbiome in type 2 diabetes. Cell Metab 2016;23(1):10–2 链接1

[125] Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Appl Environ Microbiol 2011;77(18):6718–21 链接1

[126] Ling Z, Li Z, Liu X, Cheng Y, Luo Y, Tong X, et al. Altered fecal microbiota composition associated with food allergy in infants. Appl Environ Microbiol 2014;80(8):2546–54 链接1

[127] Saarinen KM, Pelkonen AS, M?kel? MJ, Savilahti E. Clinical course and prognosis of cow’s milk allergy are dependent on milk-specific IgE status. J Allergy Clin Immunol 2005;116(4):869–75 链接1

[128] Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, et al. Early-life gut microbiome composition and milk allergy resolution. J Allergy Clin Immunol 2016;138(4):1122–30 链接1

[129] Tomova A, Husarova V, Lakatosova S, Bakos J, Vlkova B, Babinska K, et al. Gastrointestinal microbiota in children with autism in Slovakia. Physiol Behav 2015;138:179–87 链接1

[130] Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, et al. Altered fecal microbiota composition in patients with major depressive disorder. Brain Behav Immun 2015;48:186–94 链接1

[131] Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L, Wlodarska M, et al. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep 2012;13(5):440–7 链接1

[132] van Nimwegen FA,?Penders J,?Stobberingh EE,?Postma DS,?Koppelman GH,?Kerkhof M, et al. Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. J Allergy Clin Immunol 2011;128(5):948–55.e1-3.

[133] Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011;331(6015):337–41 链接1

[134] Charlson FJ, Baxter AJ, Cheng HG, Shidhaye R, Whiteford HA. The burden of mental, neurological, and substance use disorders in China and India: a systematic analysis of community representative epidemiological studies. Lancet 2016;388(10042):376–89 链接1

[135] Kendler KS. What psychiatric genetics has taught us about the nature of psychiatric illness and what is left to learn. Mol Psychiatry 2013;18(10):1058–66 链接1

[136] Maes M. Depression is an inflammatory disease, but cell-mediated immune activation is the key component of depression. Prog Neuropsychopharmacol Biol Psychiatry 2011;35(3):664–75 链接1

[137] Schmitt A, Malchow B, Hasan A, Falkai P. The impact of environmental factors in severe psychiatric disorders. Front Neurosci 2014;8:19 链接1

[138] Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci 2012;13(10):701–12 链接1

[139] Maes M, Kuber a M, Leunis JC, Berk M. Increased IgA and IgM responses against gut commensals in chronic depression: further evidence for increased bacterial translocation or leaky gut. J Affect Disord 2012;141(1):55–62 链接1

[140] Maes M, Kubera M, Leunis JC, Berk M, Geffard M, Bosmans E. In depression, bacterial translocation may drive inflammatory responses, oxidative and nitrosative stress (O&NS), and autoimmune responses directed against O&NS-damaged neoepitopes. Acta Psychiatr Scand 2013;127(5):344–54 链接1

[141] Gosalbes MJ, Durbán A, Pignatelli M, Abellan JJ, Jiménez-Hernández N, Pérez-Cobas AE, et al. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 2011;6(3):e17447 链接1

[142] Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, et al. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci USA 2014;111(22):E2329–38 链接1

[143] Santiago-Rodriguez TM, Naidu M, Abeles SR, Boehm TK, Ly M, Pride DT. Transcriptome analysis of bacteriophage communities in periodontal health and disease. BMC Genomics 2015;16:549 链接1

[144] Arnold JW, Roach J, Azcarate-Peril MA. Emerging technologies for gut microbiome research. Trends Microbiol 2016;24(11):887–901 链接1

[145] Connon SA, Giovannoni SJ. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 2002;68(8):3878–85 链接1

[146] Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, et al. Use of ichip for high-throughput in situ cultivation of “uncultivable” microbial species. Appl Environ Microbiol 2010;76(8):2445–50 链接1

[147] Jung D, Seo EY, Epstein SS, Joung Y, Han J, Parfenova VV, et al. Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia. FEMS Microbiol Ecol 2014;90(2):417–23 链接1

[148] Possemiers S, Verthé K, Uyttendaele S, Verstraete W. PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 2004;49(3):495–507 链接1

[149] Petrof EO, Khoruts A. From stool transplants to next-generation microbiota therapeutics. Gastroenterology 2014;146(6):1573–82 链接1

[150] McDonald JA, Fuentes S, Schroeter K, Heikamp-deJong I, Khursigara CM, de Vos WM, et al. Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model. J Microbiol Methods 2015;108:36–44 链接1

[151] Wang BL, Ghaderi A, Zhou H, Agresti J, Weitz DA, Fink GR, et al. Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption. Nat Biotechnol 2014;32(5):473–8 链接1

[152] Kim HJ, Huh D, Hamilton G, Ingber DE. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 2012;12(12):2165–74 链接1

[153] Rusconi R, Garren M, Stocker R. Microfluidics expanding the frontiers of microbial ecology. Annu Rev Biophys 2014;43:65–91 链接1

[154] Englert DL, Manson MD, Jayaraman A. Investigation of bacterial chemotaxis in flow-based microfluidic devices. Nat Protoc 2010;5(5):864–72 链接1

[155] Wang Y, Ahmad AA, Sims CE, Magness ST, Allbritton NL. In vitro generation of colonic epithelium from primary cells guided by microstructures. Lab Chip 2014;14(9):1622–31 链接1

[156] Gracz AD, Williamson IA, Roche KC, Johnston MJ, Wang F, Wang Y, et al. A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis. Nat Cell Biol 2015;17(3):340–9 链接1

[157] Forbester JL, Goulding D, Vallier L, Hannan N, Hale C, Pickard D, et al. Interaction of Salmonella enterica serovar Typhimurium with intestinal organoids derived from human induced pluripotent stem cells. Infect Immun 2015;83(7):2926–34 链接1

[158] Leslie JL, Huang S, Opp JS, Nagy MS, Kobayashi M, Young VB, et al. Persistence and toxin production by Clostridium difficile within human intestinal organoids result in disruption of epithelial paracellular barrier function. Infect Immun 2015;83(1):138–45 链接1

[159] Sommer MO. Advancing gut microbiome research using cultivation. Curr Opin Microbiol 2015;27:127–32 链接1

[160] Dao MC, Everard A, Aron-Wisnewsky J, Sokolovska N, Prifti E, Verger EO, et al.; MICRO-Obes Consortium. Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut 2016;65(3):426–36 链接1

[161] Chu J, Vila-Farres X, Inoyama D, Ternei M, Cohen LJ, Gordon EA, et al. Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nat Chem Biol 2016;12(12):1004–6 链接1

[162] Wang J, Jia H. Metagenome-wide association studies: fine-mining the microbiome. Nat Rev Microbiol 2016;14(8):508–22 链接1

[163] Lu H, Wu Z, Xu W, Yang J, Chen Y, Li L. Intestinal microbiota was assessed in cirrhotic patients with hepatitis B virus infection. Intestinal microbiota of HBV cirrhotic patients. Microb Ecol 2011;61(3):693–703 链接1

[164] Lu H, Zhang C, Qian G, Hu X, Zhang H, Chen C, et al. An analysis of microbiota-targeted therapies in patients with avian influenza virus subtype H7N9 infection. BMC Infect Dis 2014;14:359 链接1

[165] van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013;368(5):407–15 链接1

[166] Dhiman RK, Rana B,?Agrawal S,?Garg A,?Chopra M,?Thumburu KK, et al. Probiotic VSL#3 reduces liver disease severity and hospitalization in patients with cirrhosis: a randomized, controlled trial. Gastroenterology 2014;147(6):1327–37.e3 链接1

[167] Lv LX, Hu XJ, Qian GR, Zhang H, Lu HF, Zheng BW, et al. Administration of Lactobacillus salivarius LI01 or Pediococcus pentosaceus LI05 improves acute liver injury induced by D-galactosamine in rats. Appl Microbiol Biotechnol 2014;98(12):5619–32 链接1

[168] Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 2013;500(7461):232–6 链接1

[169] Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Weingarten RA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 2013;342(6161):967–70 链接1

[170] Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 2013;342(6161):971–6 链接1

[171] West CE, Jenmalm MC, Kozyrskyj AL, Prescott SL. Probiotics for treatment and primary prevention of allergic diseases and asthma: looking back and moving forward. Expert Rev Clin Immunol 2016;12(6):625–39 链接1

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