Gut microbiota: what is its place in pharmacology?

References

• Jandhyala SM, Talukdar R, Subramanyam C, et al. Role of the normal gut microbiota. World J Gastroenterol. 2015 Aug;21(29):8787–8803.
   PubMed Web of Science ®Google Scholar
• Libudzisz Z, “Małgorzata lewandowska microbiota of human gastrointestinal tract,” 1081.
   Google Scholar
• Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823–1836.
   PubMed Web of Science ®Google Scholar
• Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev. 2014 Sep;38(5):996–1047.
   PubMed Web of Science ®Google Scholar
• Li H, He J, Jia W. The influence of gut microbiota on drug metabolism and toxicity. Expert Opin Drug Metab Toxicol. 2016 Jan;12(1):31–40.
   PubMed Web of Science ®Google Scholar
• Dieterich W, Schink M, Zopf Y. Microbiota in the gastrointestinal tract. Med Sci (Basel, Switzerland). 2018 Dec;6(4):116.
   Google Scholar
• Helander HF, Fändriks L. Surface area of the digestive tract – revisited. Scand J Gastroenterol. 2014 Jun;49(6):681–689.
   PubMed Web of Science ®Google Scholar
• Gavini F, Cayuela, C, Antoine, JM, et al. Differences in the distribution of bifidobacterial and enterobacterial species in human faecal microflora of three different (children, adults, elderly) age groups. Microb Ecol Health Dis. 2001 Jan;13(1):40–45.
   Google Scholar
• Hopkins MJ, Sharp R, Macfarlane GT. Variation in human intestinal microbiota with age. Dig Liver Dis. 2002 Sep;34(2):S12–8.
   PubMedGoogle Scholar
• Nagpal R, Mainali R, Ahmadi S, et al. Gut microbiome and aging: physiological and mechanistic insights. Nutr Health Aging. 2018 Jun;4(4):267–285.
   Google Scholar
• Choi J, Hur T-Y, Hong Y. Influence of altered gut microbiota composition on aging and aging-related diseases. J Lifestyle Med. 2018 Jan;8(1):1–7.
   PubMedGoogle Scholar
• Bibbò S, Ianiro G, Giorgio V, et al. The role of diet on gut microbiota composition. Eur Rev Med Pharmacol Sci. 2016;20(22):4742–4749.
   PubMed Web of Science ®Google Scholar
• Greenwood-Van Meerveld B, Johnson AC, Grundy D. Gastrointestinal physiology and function. In: Greenwood-Van Meerveld B, editor. Handbook of experimental pharmacology. Cham: Springer. Vol. 239. 2017. p. 1–16.
   Google Scholar
• Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell. 2016 Jan;164(3):337–340.
   PubMed Web of Science ®Google Scholar
• Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016 Aug;14(8):e1002533.
   PubMed Web of Science ®Google Scholar
• Zuo T, Ng SC. The gut microbiota in the pathogenesis and therapeutics of inflammatory bowel disease. Front Microbiol. 2018 Sep;9:2247.
   PubMed Web of Science ®Google Scholar
• Al-Assal K, Martinez AC, Torrinhas RS, et al. Gut microbiota and obesity. Clin Nutr Exp. 2018 Aug;20:60–64.
   Google Scholar
• Pascal M, Perez-Gordo M, Caballero T, et al. Microbiome and allergic diseases. Front Immunol. 2018;9:1584.
   PubMed Web of Science ®Google Scholar
• Helmink BA, Khan MAW, Hermann A, et al. The microbiome, cancer, and cancer therapy. Nat Med. 2019 Mar;25(3):377–388.
   PubMed Web of Science ®Google Scholar
• Stewart CJ, Chown SL, DeConto RM, et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018 Oct;562(7728):583–588.
   PubMed Web of Science ®Google Scholar
• Walker RW, Clemente JC, Peter I, et al. The prenatal gut microbiome: are we colonized with bacteria in utero ? Pediatr Obes. 2017 Aug;12:3–17.
   PubMed Web of Science ®Google Scholar
• Perez-Muñoz ME, Arrieta M-C, Ramer-Tait AE, et al. A critical assessment of the ‘sterile womb’ and ‘in utero colonization’ hypotheses: implications for research on the pioneer infant microbiome. Microbiome. 2017 Dec;5(1):48.
   PubMed Web of Science ®Google Scholar
• Barko PC, McMichael MA, Swanson KS, et al. The Gastrointestinal microbiome: a review. J Vet Intern Med. 2018 Jan;32(1):9–25.
   PubMed Web of Science ®Google Scholar
• Blackwell M. The Fungi: 1, 2, 3 … 5.1 million species? Am J Bot. 2011 Mar;98(3):426–438.
   PubMed Web of Science ®Google Scholar
• Nash AK, Auchtung TA, Wong MC, et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome. 2017 Nov;5(1):153.
   PubMedGoogle Scholar
• Forbes JD, Bernstein CN, Tremlett H, et al. A fungal world: could the gut mycobiome be involved in neurological disease? Front Microbiol. 2018;9:3249.
   PubMed Web of Science ®Google Scholar
• Chiaro TR, Soto R, Zac Stephens W, et al. A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Sci Transl Med. 2017 Mar;9(380):eaaf9044.
   PubMed Web of Science ®Google Scholar
• Gaitanis G, Magiatis P, Stathopoulou K, et al. AhR ligands, malassezin, and indolo[3,2-b]carbazole are selectively produced by malassezia furfur strains isolated from seborrheic dermatitis. J Invest Dermatol. 2008 Jul;128(7):1620–1625.
   PubMed Web of Science ®Google Scholar
• Lamas B, Natividad JM, Sokol H. Aryl hydrocarbon receptor and intestinal immunity. Mucosal Immunol. 2018 Jul;11(4):1024–1038.
   PubMed Web of Science ®Google Scholar
• Lai GC, Tan TG, Pavelka N. The mammalian mycobiome: A complex system in a dynamic relationship with the host. Wiley Interdiscip Rev Syst Biol Med. 2019 Jan;11(1):e1438.
   PubMed Web of Science ®Google Scholar
• Velegraki A, Cafarchia C, Gaitanis G, et al. malassezia infections in humans and animals: pathophysiology, detection, and treatment. PLoS Pathog. 2015 Jan;11(1):e1004523.
   PubMed Web of Science ®Google Scholar
• Mukhopadhya I, Segal JP, Carding SR, et al. The gut virome: the ‘missing link’ between gut bacteria and host immunity? Therap Adv Gastroenterol. 2019 Jan;12:175628481983662.
   Web of Science ®Google Scholar
• Ash C. Revelation in the gut virome. Science. 2018 Dec;362(6421):1373.4–1374.
   Google Scholar
• Neil JA, Cadwell K. The Intestinal Virome and Immunity. J Immunol. 2018 Sep;201(6):1615–1624.
   PubMed Web of Science ®Google Scholar
• Tremaroli V, Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012 Sep;489(7415):242–249.
   PubMed Web of Science ®Google Scholar
• Robles Alonso V, Guarner F. Linking the gut microbiota to human health. Br J Nutr. 2013 Jan;109(S2):S21–S26.
   PubMedGoogle Scholar
• Sekirov I, Russell SL, Antunes LCM, et al. Gut microbiota in health and disease. Physiol Rev. 2010 Jul;90(3):859–904.
   PubMed Web of Science ®Google Scholar
• Den Besten G, van Eunen K, Groen AK, et al. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013 Sep;54(9):2325–2340.
   PubMed Web of Science ®Google Scholar
• Ohira H, Tsutsui W, Fujioka Y. Are short chain fatty acids in gut microbiota defensive players for inflammation and atherosclerosis? J Atheroscler Thromb. 2017 Jul;24(7):660–672.
   PubMed Web of Science ®Google Scholar
• Ratajczak W, Rył A, Mizerski A, et al. Immunomodulatory potential of gut microbiome-derived short-chain fatty acids (SCFAs). Acta Biochim Pol. 2019 Mar.
   PubMed Web of Science ®Google Scholar
• Rowland I, Gibson, G, Heinken, A, et al. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018 Feb;57(1):1–24.
   PubMed Web of Science ®Google Scholar
• Ma J, Rubin BK, Voynow JA. Mucins, mucus, and goblet cells. Chest. 2018 Jul:154(1):169–176.
   Google Scholar
• Sicard J-F, Le Bihan G, Vogeleer P, et al. Interactions of intestinal bacteria with components of the intestinal mucus. Front Cell Infect Microbiol. 2017;7:387.
   PubMed Web of Science ®Google Scholar
• Corfield AP. the interaction of the gut microbiota with the mucus barrier in health and disease in human. Microorganisms. 2018 Aug;6(3):78.
   PubMed Web of Science ®Google Scholar
• Purchiaroni F, Tortora, A, Gabrielli, M et al. The role of intestinal microbiota and the immune system. Eur Rev Med Pharmacol Sci. 2013 Feb;17(3):323–333.
   PubMed Web of Science ®Google Scholar
• Hibbing ME, Fuqua C, Parsek MR, et al. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol. 2010 Jan;8(1):15–25.
   PubMed Web of Science ®Google Scholar
• Cianci R, Pagliari D, Piccirillo CA, et al. the microbiota and immune system crosstalk in health and disease. Mediators Inflamm. 2018;2018:1–3.
   Google Scholar
• Pagliari D, Piccirillo CA, Larbi A, et al. The Interactions between innate immunity and microbiota in gastrointestinal diseases. J Immunol Res. 2015 May;2015:1–3.
   Google Scholar
• Stanley LA. Drug metabolism. Pharmacognosy. 2017 Jan. Chapter 27 - Drug Metabolism forom the book Pharmacognosy Fundamentals, Applications and Strategies; p. 527–545.
   Google Scholar
• Kim D-H. Gut microbiota-mediated drug-antibiotic interactions. Drug Metab Dispos. 2015 Sep;43(10):1581–1589.
   PubMed Web of Science ®Google Scholar
• Swanson HI. Drug metabolism by the host and gut microbiota: A partnership or rivalry? Drug Metab Dispos. 2015 Oct;43(10):1499–1504.
   PubMed Web of Science ®Google Scholar
• Yoo D-H, Kim IS, Van Le TK, et al. Gut microbiota-mediated drug interactions between lovastatin and antibiotics. Drug Metab Dispos. 2014 Aug;42(9):1508–1513.
   PubMed Web of Science ®Google Scholar
• Spanogiannopoulos P, Bess EN, Carmody RN, et al. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Microbiol. 2016 May;14(5):273–287.
   PubMed Web of Science ®Google Scholar
• Yip LY, Chun E, Chan Y. Special section on drug metabolism and the microbiome-minireview investigation of host-gut microbiota modulation of therapeutic outcome. Drug Metab Dispos. 2015;43:1619–1631.
   PubMed Web of Science ®Google Scholar
• Sousa T, Paterson R, Moore V, et al. The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm. 2008 Nov;363(1–2):1–25.
   PubMed Web of Science ®Google Scholar
• Haiser HJ, Gootenberg DB, Chatman K, et al. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science. 2013 Jul;341(6143):295–298.
   PubMed Web of Science ®Google Scholar
• Saha JR, Butler VP, Neu HC, et al. Digoxin-inactivating bacteria: identification in human gut flora. Science. 1983 Apr;220(4594):325–327.
   PubMed Web of Science ®Google Scholar
• Haiser HJ, Seim KL, Balskus EP, et al. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes. 2014;5(2):233–238.
   PubMed Web of Science ®Google Scholar
• Clark DR, Kalman SM. Dihydrodigoxin: a common metabolite of digoxin in man. Drug Metab Dispos. 1974;2(2):148-150.
   PubMed Web of Science ®Google Scholar
• Makiyama A, Arimizu K, Hirano G, et al. Irinotecan monotherapy as third-line or later treatment in advanced gastric cancer. Gastric Cancer. 2018 May;21(3):464–472.
   PubMed Web of Science ®Google Scholar
• Nielsen DL, Palshof J, Brünner N, et al. Implications of ABCG2 expression on irinotecan treatment of colorectal cancer patients: a review. Int J Mol Sci. 2017 Sep;18(9):1926.
   PubMed Web of Science ®Google Scholar
• Hahn RZ, Arnhold, PC, Andriguetti, NB, et al. Determination of irinotecan and its metabolite SN-38 in dried blood spots using high-performance liquid-chromatography with fluorescence detection. J Pharm Biomed Anal. 2018;150:51–58.
   PubMed Web of Science ®Google Scholar
• Basu S, Zeng M, Yin T, et al. Development and validation of an UPLC–MS/MS method for the quantification of irinotecan, SN-38 and SN-38 glucuronide in plasma, urine, feces, liver and kidney: application to a pharmacokinetic study of irinotecan in rats. J Chromatogr B. 2016 Mar;1015–1016:34–41.
   PubMed Web of Science ®Google Scholar
• Atasilp C, Chansriwong P, Sirachainan E, et al. Determination of irinotecan, SN-38 and SN-38 glucuronide using HPLC/MS/MS: application in a clinical pharmacokinetic and personalized medicine in colorectal cancer patients. J Clin Lab Anal. 2018 Jan;32(1):e22217.
   Web of Science ®Google Scholar
• Guthrie L, Gupta S, Daily J, et al. Human microbiome signatures of differential colorectal cancer drug metabolism. Npj Biofilms Microbiomes. 2017 Dec;3(1):27.
   PubMedGoogle Scholar
• Davis CD, Milner JA. Gastrointestinal microflora, food components and colon cancer prevention. J Nutr Biochem. 2009 Oct;20(10):743–752.
   PubMed Web of Science ®Google Scholar
• Sjoukes A, Venekamp, RP, van de Pol, AC, et al. Paracetamol (acetaminophen) or non-steroidal anti-inflammatory drugs, alone or combined, for pain relief in acute otitis media in children. Cochrane Database Syst Rev. 2016;12(12):CD011534.
   PubMedGoogle Scholar
• Ohlsson A, Shah PS. Paracetamol (acetaminophen) for patent ductus arteriosus in preterm or low birth weight infants. Cochrane Database Syst Rev. 2018;4(4):CD010061.
   PubMedGoogle Scholar
• Meremikwu MM, Oyo-Ita A. Paracetamol versus placebo or physical methods for treating fever in children. Cochrane Database Syst Rev. 2002 Apr.
   Google Scholar
• Chiew AL, Gluud C, Brok J, et al. Interventions for paracetamol (acetaminophen) overdose. Cochrane Database Syst Rev. 2018;2(2):CD003328.
   PubMedGoogle Scholar
• Klaassen CD, Cui JY. Review: mechanisms of how the intestinal microbiota alters the effects of drugs and bile acids. Drug Metab Dispos. 2015 Oct;43(10):1505–1521.
   PubMed Web of Science ®Google Scholar
• Forrest JAH, Clements JA, Prescott LF. Clinical pharmacokinetics of paracetamol. Clin Pharmacokinet. 1982;7(2):93–107.
   PubMed Web of Science ®Google Scholar
• Prescott LF. Kinetics and metabolism of paracetamol and phenacetin. Br J Clin Pharmacol. 1980 Oct;10(2):291S–298S.
   PubMedGoogle Scholar
• Clayton TA, Baker D, Lindon JC, et al. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci. 2009 Aug;106(34):14728–14733.
   PubMed Web of Science ®Google Scholar
• Zimmermann P, Curtis N. The effect of aspirin on antibiotic susceptibility. Expert Opin Ther Targets. 2018 Nov;22(11):967–972.
   PubMed Web of Science ®Google Scholar
• Kim IS, Yoo D-H, Jung I-H, et al. Reduced metabolic activity of gut microbiota by antibiotics can potentiate the antithrombotic effect of aspirin. Biochem Pharmacol. 2016;122:72–79.
   PubMed Web of Science ®Google Scholar
• Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, et al. Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science. 2019 Feb;363(6427):eaat9931.
   PubMed Web of Science ®Google Scholar
• Markowiak P, Śliżewska K. The role of probiotics, prebiotics and synbiotics in animal nutrition. Gut Pathog. 2018;10:21.
   PubMed Web of Science ®Google Scholar
• Gong J, Chehrazi-Raffle A, Placencio-Hickok V, et al. The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies. Clin Transl Med. 2019 Mar;8(1):9.
   PubMedGoogle Scholar
• Ahlmann M, Hempel G. The effect of cyclophosphamide on the immune system: implications for clinical cancer therapy. Cancer Chemother Pharmacol. 2016 Oct;78(4):661–671.
   PubMed Web of Science ®Google Scholar
• Viaud S, Daillère R, Boneca IG, et al. Gut microbiome and anticancer immune response: really hot Sh*t!. Cell Death Differ. 2015 Feb;22(2):199–214.
   PubMed Web of Science ®Google Scholar
• Liu Y, Tang H, Liu Y, et al. gut microbiome associates with lipid-lowering effect of rosuvastatin in vivo. Front Microbiol. 2018;9:530.
   PubMed Web of Science ®Google Scholar
• Matthies A, Clavel T, Gutschow M, et al. Conversion of daidzein and genistein by an anaerobic bacterium newly isolated from the mouse intestine. Appl Environ Microbiol. 2008 Aug;74(15):4847–4852.
   PubMed Web of Science ®Google Scholar
• Schneider H, Simmering R, Hartmann L, et al. Degradation of quercetin-3-glucoside in gnotobiotic rats associated with human intestinal bacteria. J Appl Microbiol. 2000 Dec;89(6):1027–1037.
   PubMed Web of Science ®Google Scholar
• Shim S-B, Kim N-J, Kim D-H. β-glucuronidase inhibitory activity and hepatoprotective effect of 18β-glycyrrhetinic acid from the rhizomes of glycyrrhiza uralensis. Planta Med. 2000 Feb;66(1):40–43.
   PubMed Web of Science ®Google Scholar
• Akao T, Beylin I, Sluzky V, et al. Intestinal bacterial hydrolysis is indispensable to absorption of 18 beta-glycyrrhetic acid after oral administration of glycyrrhizin in rats. J Pharm Pharmacol. 1994 Feb;46(2):135–137.
   PubMed Web of Science ®Google Scholar
• Matthies A, Loh G, Blaut M, et al. Daidzein and genistein are converted to equol and 5-hydroxy-equol by human intestinal Slackia isoflavoniconvertens in gnotobiotic rats. J Nutr. 2012 Jan;142(1):40–46.
   PubMed Web of Science ®Google Scholar
• Akao T, Kida H, Kanaoka M, et al. drug metabolism: intestinal bacterial hydrolysis is required for the appearance of compound k in rat plasma after oral administration of ginsenoside Rb1 from panax ginseng. J Pharm Pharmacol. 1998 Oct;50(10):1155–1160.
   PubMed Web of Science ®Google Scholar
• Watanabe K, Yamashita S, Furuno K, et al. Metabolism of omeprazole by gut flora in rats. J Pharm Sci. 1995 Apr;84(4):516–517.
   PubMed Web of Science ®Google Scholar
• Caldwell J, Hawksworth GM. The demethylation of methamphetamine by intestinal microflora. J Pharm Pharmacol. 1973 May;25(5):422–424.
   PubMed Web of Science ®Google Scholar
• Shu Y-Z, Kingston DGI, Van Tassell RL, et al. Metabolism of levamisole, an anti-colon cancer drug, by human intestinal bacteria. Xenobiotica. 1991 Jan;21(6):737–750.
   PubMed Web of Science ®Google Scholar
• Mikov M, Caldwell J, Dolphin CT, et al. The role of intestinal microflora in the formation of the methylthio adduct metabolites of paracetamol. Studies in neomycin-pretreated and germ-free mice. Biochem Pharmacol. 1988 Apr;37(8):1445–1449.
   PubMed Web of Science ®Google Scholar
• Lindenbaum J, Rund DG, Butler VP, et al. Inactivation of digoxin by the gut flora: reversal by antibiotic therapy. N Engl J Med. 1981 Oct;305(14):789–794.
   PubMed Web of Science ®Google Scholar
• Renouf M, Hendrich S. Bacteroides uniformis is a putative bacterial species associated with the degradation of the isoflavone genistein in human feces. J Nutr. 2011 Jun;141(6):1120–1126.
   PubMed Web of Science ®Google Scholar
• Baker JM, Al-Nakkash L, Herbst-Kralovetz MM. Estrogen–gut microbiome axis: physiological and clinical implications. Maturitas. 2017 Sep;103:45–53.
   PubMed Web of Science ®Google Scholar