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Review

Why targeting the microbiome is not so successful: can randomness overcome the adaptation that occurs following gut manipulation?

Pages 209-217 | Published online: 08 May 2019

References

  • Baktash A, Terveer EM, Zwittink RD, et al. Mechanistic insights in the success of fecal microbiota transplants for the treatment of clostridium difficile infections. Front Microbiol. 2018;9:1242. doi:10.3389/fmicb.2018.0124229946308
  • Khanna S. Microbiota replacement therapies: innovation in gastrointestinal care. Clin Pharmacol Ther. 2018;103:102–111. doi:10.1002/cpt.92329071710
  • Kho ZY, Lal SK. The human gut microbiome - a potential controller of wellness and disease. Front Microbiol. 2018;9:1835. doi:10.3389/fmicb.2018.0183530154767
  • Human Microbiome Project C. A framework for human microbiome research. Nature. 2012;486:215–221. doi:10.1038/nature1120922699610
  • Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–214. doi:10.1038/nature1123422699609
  • Gagliardi A, Totino V, Cacciotti F, et al. Rebuilding the gut microbiota ecosystem. Int J Environ Res Public Health. 2018;15(8):pii:E1679. doi:10.3390/ijerph15081679.
  • Holleran G, Scaldaferri F, Ianiro G, et al. Fecal microbiota transplantation for the treatment of patients with ulcerative colitis and other gastrointestinal conditions beyond clostridium difficile infection: an update. Drugs Today (Barc). 2018;54:123–136. doi:10.1358/dot.2018.54.2.276076529637938
  • Ooijevaar RE, van Beurden YH, Terveer EM, et al. Update of treatment algorithms for clostridium difficile infection. Clin Microbiol Infect. 2018;24:452–462. doi:10.1016/j.cmi.2017.12.02229309934
  • Jeon SR, Chai J, Kim C, Lee CH. Current evidence for the management of inflammatory bowel diseases using fecal microbiota transplantation. Curr Infect Dis Rep. 2018;20:21. doi:10.1007/s11908-018-0627-829804272
  • Costello SP, Hughes PA, Waters O, et al. Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: a randomized clinical trial. JAMA. 2019;321:156–164. doi:10.1001/jama.2018.2004630644982
  • Paramsothy S, Nielsen S, Kamm MA, et al. Specific bacteria and metabolites associated with response to fecal microbiota transplantation in patients with ulcerative colitis. Gastroenterology.  2019;156(5):1440.e2–1454.e2. doi:10.1053/j.gastro.2018.12.001.
  • Paramsothy S, Kamm MA, Kaakoush NO, et al. Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet. 2017;389:1218–1228. doi:10.1016/S0140-6736(17)30182-428214091
  • Cao Y, Zhang B, Wu Y, Wang Q, Wang J, Shen F. The value of fecal microbiota transplantation in the treatment of ulcerative colitis patients: a systematic review and meta-Analysis. Gastroenterol Res Pract. 2018;2018:5480961. doi:10.1155/2018/548096129849592
  • Fairhurst NG, Travis SPL. Why is it so difficult to evaluate faecal microbiota transplantation as a treatment for ulcerative colitis? Intest Res. 2018;16:209–215. doi:10.5217/ir.2018.16.2.20929743833
  • Wang H, Cui B, Li Q, et al. The safety of fecal microbiota transplantation for Crohn‘s disease: findings from a long-term study. Adv Ther. 2018;35:1935–1944. doi:10.1007/s12325-018-0800-330328062
  • He Z, Li P, Zhu J, et al. Multiple fresh fecal microbiota transplants induces and maintains clinical remission in Crohn‘s disease complicated with inflammatory mass. Sci Rep. 2017;7:4753. doi:10.1038/s41598-017-04984-z28684845
  • D‘Odorico I, Di Bella S, Monticelli J, Giacobbe DR, Boldock E, Luzzati R. Role of fecal microbiota transplantation in inflammatory bowel disease. J Dig Dis. 2018;19:322–334. doi:10.1111/1751-2980.1260329696802
  • Matijasic M, Mestrovic T, Peric M, et al. Modulating composition and metabolic activity of the gut microbiota in IBD patients. Int J Mol Sci. 2016;17(4): pii:E578. doi:10.3390/ijms17040578.
  • El-Salhy M, Mazzawi T. Fecal microbiota transplantation for managing irritable bowel syndrome. Expert Rev Gastroenterol Hepatol. 2018;12:439–445. doi:10.1080/17474124.2018.144738029493330
  • Rodino-Janeiro BK, Vicario M, Alonso-Cotoner C, Pascua-García R, Santos J. A review of microbiota and irritable bowel syndrome: future in therapies. Adv Ther. 2018;35:289–310. doi:10.1007/s12325-018-0673-529498019
  • Huang L, Zhu Q, Qu X, Qin H. Microbial treatment in chronic constipation. Sci China Life Sci. 2018;61:744–752. doi:10.1007/s11427-017-9220-729388040
  • Schmulson M, Bashashati M. Fecal microbiota transfer for bowel disorders: efficacy or hype? Curr Opin Pharmacol. 2018;43:72–80. doi:10.1016/j.coph.2018.08.01230218939
  • De Luca F, Shoenfeld Y. The microbiome in autoimmune diseases. Clin Exp Immunol. 2019;195(1):74–85. doi:10.1111/cei.13158.
  • Kang Y, Cai Y. Future prospect of faecal microbiota transplantation as a potential therapy in asthma. Allergol Immunopathol (Madr). 2018;46:307–309. doi:10.1016/j.aller.2017.04.00828803667
  • Haak BW, Prescott HC, Wiersinga WJ. Therapeutic potential of the gut microbiota in the prevention and treatment of sepsis. Front Immunol. 2018;9:2042. doi:10.3389/fimmu.2018.0204230250472
  • Yu LC, Wei SC, Ni YH. Impact of microbiota in colorectal carcinogenesis: lessons from experimental models. Intest Res. 2018;16:346–357. doi:10.5217/ir.2018.16.3.34630090033
  • Fuentes S, Rossen NG, van der Spek MJ, et al. Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. ISME J. 2017;11:1877–1889. doi:10.1038/ismej.2017.4428398347
  • Human Microbiome Jumpstart Reference Strains C, Nelson KE, Weinstock GM, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328:994–999. doi:10.1126/science.118360520489017
  • Tasse L, Bercovici J, Pizzut-Serin S, et al. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 2010;20:1605–1612. doi:10.1101/gr.108332.11020841432
  • Bremel RD, Homan EJ. Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self. Front Immunol. 2015;6:538. doi:10.3389/fimmu.2015.0053826557118
  • Presti RM, Handley S, Droit L, et al. Alterations in the oral microbiome in HIV-infected participants after ART administration are influenced by immune status. Aids. 2018;32:1279–1287. doi:10.1097/QAD.000000000000181129851662
  • Chen EZ, Li H. A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. Bioinformatics. 2016;32:2611–2617. doi:10.1093/bioinformatics/btw30827187200
  • Zhan X, Xue L, Zheng H, et al. A small-sample kernel association test for correlated data with application to microbiome association studies. Genet Epidemiol. 2018. doi:10.1002/gepi.22160
  • Luo YM, Liu FT, Chen MX, et al. [A machine learning model based on initial gut microbiome data for predicting changes of Bifidobacterium after prebiotics consumption]. Nan Fang Yi Ke Da Xue Xue Bao. 2018;38:251–260.29643029
  • Lu JQ, Wang S, Yin J, et al. [A machine learning model using gut microbiome data for predicting changes of trimethylamine-N-oxide in healthy volunteers after choline consumption]. Nan Fang Yi Ke Da Xue Xue Bao. 2017;37:290–295.28377341
  • Schmidt M, Unterer S, Suchodolski JS, et al. The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets. PLoS One. 2018;13:e0201279. doi:10.1371/journal.pone.020127930110340
  • Ren Z, Li A, Jiang J, et al. Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma. Gut. 2018. doi:10.1136/gutjnl-2017-315084
  • Ding ZF, Cao MJ, Zhu XS, Xu GH, Wang RL. Changes in the gut microbiome of the Chinese mitten crab (Eriocheir sinensis) in response to white spot syndrome virus (WSSV) infection. J Fish Dis. 2017;40:1561–1571. doi:10.1111/jfd.1262428429823
  • Sherrill-Mix S, McCormick K, Lauder A, et al. Allometry and ecology of the bilaterian gut microbiome. MBio. 2018;9(2):pii:e00319–18. doi:10.1128/mBio.00319-18.
  • Matar GK, Bagchi S, Zhang K, Oerther DB, Saikaly PE. Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome. Water Res. 2017;123:124–133. doi:10.1016/j.watres.2017.06.05228658633
  • Beghini F, Pasolli E, Truong TD, Putignani L, Cacciò SM, Segata N. Large-scale comparative metagenomics of blastocystis, a common member of the human gut microbiome. ISME J. 2017;11:2848–2863. doi:10.1038/ismej.2017.13928837129
  • Lamoureux EV, Grandy SA, Langille MGI. Moderate exercise has limited but distinguishable effects on the mouse microbiome. mSystems. 2017;2(4):pii:e00006–e00017.doi:10.1128/mSystems.00006-17.
  • McIlroy J, Ianiro G, Mukhopadhya I, Hansen R, Hold GL. Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management. Aliment Pharmacol Ther. 2018;47:26–42. doi:10.1111/apt.1438429034981
  • Sun MF, Shen YQ. Dysbiosis of gut microbiota and microbial metabolites in Parkinson‘s disease. Ageing Res Rev. 2018;45:53–61. doi:10.1016/j.arr.2018.04.00429705121
  • Yang Y, Tian J, Yang B. Targeting gut microbiome: A novel and potential therapy for autism. Life Sci. 2018;194:111–119. doi:10.1016/j.lfs.2017.12.02729277311
  • Jasarevic E, Howerton CL, Howard CD, Bale TL. Alterations in the vaginal microbiome by maternal stress are associated with metabolic reprogramming of the offspring gut and brain. Endocrinology. 2015;156:3265–3276. doi:10.1210/en.2015-117726079804
  • He Z, Cui BT, Zhang T, et al. Fecal microbiota transplantation cured epilepsy in a case with Crohn‘s disease: the first report. World J Gastroenterol. 2017;23:3565–3568. doi:10.3748/wjg.v23.i19.356528596693
  • Sze MA, Schloss PD. Looking for a signal in the noise: revisiting obesity and the microbiome. MBio. 2016;7(4):pii:e01018–e01216. doi:10.1128/mBio.01018-16.
  • Laudadio I, Fulci V, Palone F, Stronati L, Cucchiara S, Carissimi C. Quantitative assessment of shotgun metagenomics and 16S rDNA amplicon sequencing in the study of human gut microbiome. OMICS. 2018;22:248–254. doi:10.1089/omi.2018.001329652573
  • Zhai J, Kim J, Knox KS, Twigg HL, Zhou H, Zhou JJ. Variance component selection with applications to microbiome taxonomic data. Front Microbiol. 2018;9:509. doi:10.3389/fmicb.2018.0050929643839
  • Zhang X, Mallick H, Tang Z, et al. Negative binomial mixed models for analyzing microbiome count data. BMC Bioinformatics. 2017;18:4. doi:10.1186/s12859-016-1441-728049409
  • Panek M, Cipcic Paljetak H, Baresic A, et al. Methodology challenges in studying human gut microbiota - effects of collection, storage, DNA extraction and next generation sequencing technologies. Sci Rep. 2018;8:5143. doi:10.1038/s41598-018-23296-429572539
  • Zhang F, Cui B, He X, Nie Y, Wu K, Fan D. Microbiota transplantation: concept, methodology and strategy for its modernization. Protein Cell. 2018;9:462–473. doi:10.1007/s13238-018-0541-829691757
  • Chu ND, Smith MB, Perrotta AR, Kassam Z, Alm EJ, Zoetendal EG. Profiling living bacteria informs preparation of fecal microbiota transplantations. PLoS One. 2017;12:e0170922. doi:10.1371/journal.pone.017092228125667
  • Ernst G. Hidden signals-the history and methods of heart rate variability. Front Public Health. 2017;5:265. doi:10.3389/fpubh.2017.0008129085816
  • Kyriazis M. Editorial: novel approaches to an old problem: insights, theory and practice for eliminating aging. Curr Aging Sci. 2014;7:1–2.25056407
  • Kyriazis M. Practical applications of chaos theory to the modulation of human ageing: nature prefers chaos to regularity. Biogerontology. 2003;4:75–90.12766532