[ 1 ] Lynch JB, Hsiao EY. Microbiomes as sources of emergent host phenotypes. Science 2019; 365(6460):1405‒9. 链接1

[ 2 ] Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 2016; 14(1):20‒32. 链接1

[ 3 ] Stearns JC, Lynch MDJ, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, et al. Bacterial biogeography of the human digestive tract. Sci Rep 2011; 1(1):170. 链接1

[ 4 ] Yasuda K, Oh K, Ren B, Tickle T, Franzosa E, Wachtman L, et al. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe 2015; 17(3):385‒91. 链接1

[ 5 ] Zeng Y, Zeng D, Zhou Y, Niu L, Deng J, Li Y, et al. Microbial biogeography along the gastrointestinal tract of a red panda. Front Microbiol 2018; 9:1411. 链接1

[ 6 ] Ahern PP, Maloy KJ. Understanding immune‒microbiota interactions in the intestine. Immunology 2020; 159(1):4‒14. 链接1

[ 7 ] Manuzak JA, Zevin AS, Cheu R, Richardson B, Modesitt J, Hensley-McBain T, et al. Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques. Mucosal Immunol 2020; 13(3):471‒80. 链接1

[ 8 ] Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, et al. Transient osmotic perturbation causes long-term alteration to the gut microbiota. Cell 2018; 173(7):1742‒54.e17. 链接1

[ 9 ] Wang Y, Kuang Z, Yu X, Ruhn KA, Kubo M, Hooper LV. The intestinal microbiota regulates body composition through NFIL3 and the circadian clock. Science 2017; 357(6354):912‒6. 链接1

[10] Kuang Z, Wang Y, Li Y, Ye C, Ruhn KA, Behrendt CL, et al. The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3. Science 2019; 365(6460):1428‒34. 链接1

[11] Gasparrini AJ, Crofts TS, Gibson MK, Tarr PI, Warner BB, Dantas G. Antibiotic perturbation of the preterm infant gut microbiome and resistome. Gut Microbes 2016; 7(5):443‒9. 链接1

[12] 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

[13] Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, et al. Daily sampling reveals personalized diet‒microbiome associations in humans. Cell Host Microbe 2019; 25(6):789‒802.e5. 链接1

[14] Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334 (6052):105‒8. 链接1

[15] Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 2019; 570(7762):462‒7. 链接1

[16] Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 2018; 555(7698):623‒8. 链接1

[17] Haak BW, Lankelma JM, Hugenholtz F, Belzer C, de Vos WM, Wiersinga WJ. Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. J Antimicrob Chemother 2019; 74(3):782‒6. 链接1

[18] Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, et al. LifeLines cohort study. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 2016; 352(6285):565‒9. 链接1

[19] Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, et al. Population- level analysis of gut microbiome variation. Science 2016; 352(6285):560‒4. 链接1

[20] Becattini S, Taur Y, Pamer EG. Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol Med 2016; 22(6):458‒78. 链接1

[21] Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, et al. Durable coexistence of donor and recipient strains after fecal microbiota transplantation. Science 2016; 352(6285):586‒9. 链接1

[22] Bharucha AE, Lacy BE. Mechanisms, evaluation, and management of chronic constipation. Gastroenterology 2020; 158(5):1232‒49.e3. 链接1

[23] Luthra P, Camilleri M, Burr NE, Quigley EMM, Black CJ, Ford AC. Efficacy of drugs in chronic idiopathic constipation: a systematic review and network meta-analysis. Lancet Gastroenterol Hepatol 2019; 4(11):831‒44. 链接1

[24] Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Diversity Knight R., stability and resilience of the human gut microbiota. Nature 2012; 489(7415):220‒30. 链接1

[25] Relman DA. The human microbiome: ecosystem resilience and health. Nutr Rev 2012; 70(Suppl 1):S2‒9. 链接1

[26] Peng Z, Xiang J, He Z, Zhang T, Xu L, Cui B, et al. Colonic transendoscopic enteral tubing: a novel way of transplanting fecal microbiota. Endosc Int Open 2016; 4(6):E610‒3.

[27] Ding X, Li Q, Li P, Zhang T, Cui B, Ji G, et al. Long-term safety and efficacy of fecal microbiota transplant in active ulcerative colitis. Drug Saf 2019; 42(7):869‒80. 链接1

[28] Fecal Microbiota Transplantation-standardization Study Group. Nanjing consensus on methodology of washed microbiota transplantation. Chin Med J 2020; 133(19):2330‒2. 链接1

[29] Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30(15):2114‒20. 链接1

[30] Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 2018; 15(11):962‒8. 链接1

[31] Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 2012; 9(8):811‒4. 链接1

[32] Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9(4):357‒9. 链接1

[33] Dunn WB, Broadhurst D, Begley P, Zelena E, Francis-McIntyre S, Anderson N, et al. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 2011; 6(7):1060‒83. 链接1

[34] Hou W, Zhong D, Zhang P, Li Y, Lin M, Liu G, et al. A strategy for the targeted metabolomics analysis of 11 gut microbiota‒host co-metabolites in rat serum, urine and feces by ultra high performance liquid chromatography-tandem mass spectrometry. J Chromatogr A 2016; 1429:207‒17.

[35] Rohart F, Gautier B, Singh A, Lê Cao KA, Schneidman D. mixOmics: an R package for ‘omics feature selection and multiple data integration. PLOS Comput Biol 2017; 13(11):e1005752. 链接1

[36] Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13(11):2498‒504. 链接1

[37] Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, et al. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol 2018; 3(3):347‒55. 链接1

[38] Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol 2018; 3(3):337‒46. 链接1

[39] Chong J, Wishart DS, Xia J. Using MetaboAnalyst 4.0 for comprehensive and integrative metabolomics data analysis. Curr Protoc Bioinformatics 2019; 68(1):e86. 链接1

[40] Jin M, Kalainy S, Baskota N, Chiang D, Deehan EC, McDougall C, et al. Faecal microbiota from patients with cirrhosis has a low capacity to ferment non- digestible carbohydrates into short-chain fatty acids. Liver Int 2019; 39(8):1437‒47. 链接1

[41] Vital M, Howe A, Bergeron N, Krauss RM, Jansson JK, Tiedje JM. Metagenomic insights into the degradation of resistant starch by human gut microbiota. Appl Environ Microbiol 2018; 84(23):e01562‒18. 链接1

[42] Takahashi K, Nishida A, Fujimoto T, Fujii M, Shioya M, Imaeda H, et al. Reduced abundance of butyrate-producing bacteria species in the fecal microbial community in Crohn’s disease. Digestion 2016; 93(1):59‒65. 链接1

[43] Rosario D, Benfeitas R, Bidkhori G, Zhang C, Uhlen M, Shoaie S, et al. Understanding the representative gut microbiota dysbiosis in metformintreated type 2 diabetes patients using genome-scale metabolic modeling. Front Physiol 2018; 9:775. 链接1

[44] Liu H, Han M, Li SC, Tan G, Sun S, Hu Z, et al. Resilience of human gut microbial communities for the long stay with multiple dietary shifts. Gut 2019; 68(12):2254‒5. 链接1

[45] Ng KM, Aranda-Díaz A, Tropini C, Frankel MR, Van Treuren W, O’Loughlin CT, et al. Recovery of the gut microbiota after antibiotics depends on host diet, community context, and environmental reservoirs. Cell Host Microbe 2019; 26(5):650‒65.e4. 链接1

[46] Liu C, Zhang J, Li M, Zhao L, Ji C, Ma Q. Alterations and structural resilience of the gut microbiota under dietary fat perturbations. J Nutr Biochem 2018; 61:91‒100. 链接1

[47] MacPherson CW, Mathieu O, Tremblay J, Champagne J, Nantel A, Girard SA, et al. Gut bacterial microbiota and its resistome rapidly recover to basal state levels after short-term amoxicillin-clavulanic acid treatment in healthy adults. Sci Rep 2018; 8(1):11192. 链接1

[48] Goethel A, Turpin W, Rouquier S, Zanello G, Robertson SJ, Streutker CJ, et al. Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure. Mucosal Immunol 2019; 12(3):720‒32. 链接1

[49] Mortensen MS, Hebbelstrup Jensen B, Williams J, Brejnrod AD, O‍’‍Brien Andersen L, Röser D, et al. Stability and resilience of the intestinal microbiota in children in daycare—a 12 month cohort study. BMC Microbiol 2018; 18(1):223. 链接1

[50] Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate- producing bacteria from the human large intestine. FEMS Microbiol Lett 2009; 294(1):1‒8. 链接1

[51] Tahara Y, Yamazaki M, Sukigara H, Motohashi H, Sasaki H, Miyakawa H, et al. Gut microbiota-derived short chain fatty acids induce circadian clock entrainment in mouse peripheral tissue. Sci Rep 2018; 8(1):1395. 链接1

[52] Segers A, Desmet L, Thijs T, Verbeke K, Tack J, Depoortere I. The circadian clock regulates the diurnal levels of microbial short-chain fatty acids and their rhythmic effects on colon contractility in mice. Acta Physiol 2019; 225(3): e13193. 链接1

[53] Fellows R, Denizot J, Stellato C, Cuomo A, Jain P, Stoyanova E, et al. Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nat Commun 2018; 9(1):105. 链接1

[54] Waldecker M, Kautenburger T, Daumann H, Busch C, Schrenk D. Inhibition of histone-deacetylase activity by short-chain fatty acids and some polyphenol metabolites formed in the colon. J Nutr Biochem 2008; 19 (9):587‒93. 链接1

[55] Zhang T, Long C, Cui B, Buch H, Wen Q, Li Q, et al. Colonic transendoscopic tube-delivered enteral therapy (with video): a prospective study. BMC Gastroenterol 2020; 20(1):135. 链接1