Antibiotic Use and Microbiota

Year 2017, - Mikrobiyota, 39 - 43, 15.11.2017

Ümit Kılıç Mustafa Altındiş

Abstract

Our microbiota is one of the most complex components of the human body. The use of antibiotics, primarily beta-lactam antibiotics, is one of the main factors affecting the microbiotic composition. Factors that cause microbiotic changes with antibiotics are not just chemical structures of antibiotics. The duration of treatment, dose, pharmacodynamic and pharmacokinetic effects, as well as the level of resistance of each microbiota member affect the extent of these changes. Studies have shown that microbial bacteria may be vulnerable or resistant to different antibiotics. Therefore, different effects of antibiotic interventions in terms of microbial composition, metabolism have been observed. (Therefore different effects on microbial composition and metabolism have been observed due to antibiotic interventions.) Antibiotics are used on a large scale worldwide, and antibiotic prescriptions are increasing. However, the effects on microbiota have been shown with limited studies. This article presents a review of antibiotics or antibiotic combinations in relation to changes in the microbiota composition and their molecular agents (genes, proteins, and metabolites), primarily the bowel. (This article presents a review about antibiotics or antibiotic combinations being linked to the changes in the microbiota composition, mainly bowel and their molecular agents (genes, proteins, and metabolites).

Keywords

microbiota, antibiotics

Antibiyotik Kullanımı ve Mikrobiyota

Abstract

Mikrobiyotamız, insan vücudunun en karmaşık bileşenleri arasında yer almaktadır. Başta beta-laktam antibiyotikler olmak üzere antibiyotiklerin kullanımı, mikrobiyota bileşimini etkileyen başlıca faktörlerden biridir. Antibiyotiklerle ilgili mikrobiyotik değişikliklere neden olan faktör antibiyotiklerin sadece kimyasal yapıları değildir. Tedavinin süresi, dozu, farmakodinamik ve farmakokinetik etkileri, ayrıca her bir mikrobiyota üyesinin direnç seviyesi bu değişikliklerin kapsamını etkilemektedir. Yapılan çalışmalarla mikrobiyotamızdaki bakterilerin farklı antibiyotiklere karşı savunmasız ya da dirençli olabileceği görülmüştür. Dolayısıyla antibiyotik müdahalelerinin mikrobiyal bileşim ve metabolizma açısından farklı etkileri de gözlemlenmiştir. Antibiyotikler dünya çapında büyük ölçekte kullanılmaktadır ve antibiyotik reçeteleri artarak devam etmektedir. Bununla birlikte, mikrobiyotamız üzerindeki etkileri sınırlı çalışmalarla gösterilmiştir. Bu makale, insanlarda kullanımı olan antibiyotikler veya antibiyotik kombinasyonlarının başlıca barsak olmak üzere mikrobiyota kompozisyonundaki ve bunların moleküler ajanlarındaki (genler, proteinler ve metabolitler) değişikliklerle bağlantılı olmasıyla ilgili bir inceleme sunmaktadır.

Keywords

mikrobiyota, antibiyotikler

References

• 1. Sommer, F. and Backhed, F. The gut microbiota–masters of host development and physiology. Nat. Rev. Microbiol. 2013; 11: 227–238.
• 2. Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, Weir TL, Ehrentraut SF, Pickel C, Kuhn KA, Lanis JM, Nguyen V, Taylor CT, Colgan SP. Crosstalk between MicrobiotaDerived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function. Cell Host Microbe. 2015 May 13;17(5):662-71.
• 3. Brestoff JR, Artis D. Commensal bacteria at the interface of host metabolism and the immune system. Nat Immunol. 2013 Jul;14(7):676-84.
• 4. Buffi e CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol. 2013 Nov;13(11):790-801.
• 5. Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014 May 15;509(7500):357-60.
• 6. Ferrer M, Méndez-García C, Rojo D, Barbas C, Moya A. Antibiotic use and microbiome function Biochem Pharmacol. 2017 Jun 15;134:114-126.
• 7. (ESPAUR): Report, 2014. Public Health England, English surveillance programme for antimicrobial utilisation and resistance
• 8. Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016 Apr 29;352(6285):565-9.
• 9. Jernberg, C. et al.Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 2007; 1: 56–66
• 10. Kim DH. Gut Microbiota-Mediated Drug-Antibiotic Interactions. Drug Metab Dispos. 2015 Oct;43(10):1581-9.
• 11. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008 Nov 18;6(11):e280.
• 12. Zhang L, Huang Y, Zhou Y, Buckley T, Wang HH. Antibiotic administration routes signifi cantly infl uence the levels of antibiotic resistance in gut microbiota. Antimicrob Agents Chemother. 2013 Aug;57(8):3659-66.
• 13. Ponziani FR, Pecere S, Lopetuso L, Scaldaferri F, Cammarota G, Gasbarrini A. Rifaximin for the treatment of irritable bowel syndrome - a drug safety evaluation. Expert Opin Drug Saf. 2016 Jul;15(7):983-91.
• 14. Lopetuso LR, Petito V, Scaldaferri F, Gasbarrini A. Gut Microbiota Modulation and Mucosal Immunity: Focus on Rifaximin. Mini Rev Med Chem. 2015;16(3):179-85.
• 15. Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Santiago A, Cuenca S, Guarner F, Manichanh C. Short-term effect of antibiotics on human gut microbiota. PLoS One. 2014 Apr 18;9(4):e95476.
• 16. Pérez-Cobas AE, Artacho A, Knecht H, Ferrús ML, Friedrichs A, Ott SJ, Moya A, Latorre A, Gosalbes MJ. Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS One. 2013 Nov 25;8(11):e80201.
• 17. Ladirat SE, Schols HA, Nauta A, Schoterman MH, Keijser BJ, Montijn RC, Gruppen H, Schuren FH. High-throughput analysis of the impact of antibiotics on the human intestinal microbiota composition. J Microbiol Methods. 2013 Mar;92(3):387-97.
• 18. Liao X, Li B, Zou R, Dai Y, Xie S, Yuan B. Biodegradation of antibiotic ciprofl oxacin: pathways, infl uential factors, and bacterial community structure. Environ Sci Pollut Res Int. 2016 Apr;23(8):7911-8.
• 19. Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J, Boudreau DK, Simard JL, Chabot I, Domingo MC, Trottier S, Boissinot M, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. The initial state of the human gut microbiome determines its reshaping by antibiotics. ISME J. 2016 Mar;10(3):707-20.
• 20. Iapichino G, Callegari ML, Marzorati S, Cigada M, Corbella D, Ferrari S, Morelli L. Impact of antibiotics on the gut microbiota of critically ill patients. J Med Microbiol. 2008 Aug;57(Pt 8):1007-14.
• 21. O'Sullivan O, Coakley M, Lakshminarayanan B, Conde S, Claesson MJ, Cusack S, Fitzgerald AP, O'Toole PW, Stanton C, Ross RP; ELDERMET Consortium. Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy. J Antimicrob Chemother. 2013 Jan;68(1):214-21
• 22. Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine. 2016;8:39.
• 23. Ben-Amor K, Heilig H, Smidt H, Vaughan EE, Abee T, de Vos WM. Genetic diversity of viable, injured, and dead fecal bacteria assessed by fl uorescenceactivated cell sorting and 16S rRNA gene analysis. Appl Environ Microbiol. 2005 Aug;71(8):4679-89.
• 24. Knecht H, Neulinger SC, Heinsen FA, Knecht C, Schilhabel A, Schmitz RA, Zimmermann A, dos Santos VM, Ferrer M, Rosenstiel PC, Schreiber S, Friedrichs AK, Ott SJ. Effects of β-lactam antibiotics and fl uoroquinolones on human gut microbiota in relation to Clostridium diffi cile associated diarrhea. PLoS One. 2014 Feb 28;9(2):e89417.
• 25. Suzuki S, Horinouchi T, Furusawa C. Prediction of antibiotic resistance by gene expression profi les. Nature Communications. 2014;5:5792.
• 26. Gosalbes MJ, Vázquez-Castellanos JF, Angebault C, et al. Carriage of Enterobacteria Producing Extended-Spectrum β-Lactamases and Composition of the Gut Microbiota in an Amerindian Community. Antimicrobial Agents and Chemotherapy. 2016;60(1):507-514.
• 27. Hernandez E, Bargiela R, Diez MS, Friedrichs A, Perez-Cobas AE, Gosalbes MJ, et al. Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity. Gut Microbes. 2013;4:306– 15. doi:10.4161/gmic.25321
• 28. Lambert-Zechovsky N, Bingen E, Aujard Y, Mathieu H. Impact of cefotaxime on the fecal fl ora in children. Infection. 1985;13 Suppl 1:S140–4.
• 29. Bergan T, Nord CE, Thorsteinsson SB. Effect of meropenem on the intestinal microfl ora. Eur J Clin Microbiol Infect Dis. 1991;10:524–7
• 30. Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013;152:39–50. doi:10.1016/j.cell.2012.10.052.
• 31. Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One. 2010;5:e9836. doi:10.1371/journal.pone.0009836..
• 32. Zaura E, Brandt BW, Teixeira de Mattos MJ, Buijs MJ, Caspers MP, Rashid MU, et al. Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term microbial shifts in feces. mBio. 2015;6:e01693–15. doi:10.1128/mBio.01693-15.
• 33. Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE. Hostmicrobiota interactions in the pathogenesis of antibiotic-associated diseases. Cell Rep. 2016;14:1049–61. doi:10.1016/j.celrep.2016.01.009
• 34. Brismar B, Edlund C, Nord CE. Comparative effects of clarithromycin and erythromycin on the normal intestinal microfl ora. Scand J Infect Dis. 1991;23:635–42.
• 35. Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, et al. Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter. J Pediatr. 2014;165:23–9. doi:10.1016/j.jpeds.2014.01.010.
• 36. Nord CE, Sillerström E, Wahlund E. Effect of tigecycline on normal oropharyngeal and intestinal microfl ora. Antimicrob Agents Chemother. 2006;50:3375–80. doi:10.1128/aac.00373-06
• 37. Bassis CM, Theriot CM, Young VB. Alteration of the murine gastrointestinal microbiota by tigecycline leads to increased susceptibility to Clostridium diffi cile infection. Antimicrob Agents Chemother. 2014;58:2767–74. doi:10.1128/aac.02262-13.
• 38. Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, et al. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut. 2015;64:1732–43. doi:10.1136/gutjnl-2014-308820.