Abstract
The intestinal microbiota contributes to the metabolism of its host. Adequate identification of the microbiota’s impact on the host plasma metabolites is lacking. As antibiotics have a profound effect on the microbial composition and hence on the mammalian-microbiota co-metabolism, we studied the effects of antibiotics on the “functionality of the microbiome”—defined as the production of metabolites absorbed by the host. This metabolomics study presents insights into the mammalian-microbiome co-metabolism of endogenous metabolites. To identify plasma metabolites related to microbiome changes due to antibiotic treatment, we have applied broad-spectrum antibiotics belonging to the class of aminoglycosides (neomycin, gentamicin), fluoroquinolones (moxifloxacin, levofloxacin) and tetracyclines (doxycycline, tetracycline). These were administered orally for 28 days to male rats including blood sampling for metabolic profiling after 7, 14 and 28 days. Fluoroquinolones and tetracyclines can be absorbed from the gut; whereas, aminoglycosides are poorly absorbed. Hippuric acid, indole-3-acetic acid and glycerol were identified as key metabolites affected by antibiotic treatment, beside changes mainly concerning amino acids and carbohydrates. Inter alia, effects on indole-3-propionic acid were found to be unique for aminoglycosides, and on 3-indoxylsulfate for tetracyclines. For each class of antibiotics, specific metabolome patterns could be established in the MetaMap®Tox data base, which contains metabolome data for more than 550 reference compounds. The results suggest that plasma-based metabolic profiling (metabolomics) could be a suitable tool to investigate the effect of antibiotics on the functionality of the microbiome and to obtain insight into the mammalian-microbiome co-metabolism.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- CKD:
-
Chronic kidney disease
- HA:
-
Hippuric acid
- IAA:
-
Indole-3-acetic acid
- IPA:
-
Indole-3-propionic acid
- IS:
-
3-Indoxylsulfate
- GC:
-
Gas chromatography
- LC:
-
Liquid chromatography
- MOA:
-
Mode of action
- MS:
-
Mass spectrometry
- SPE:
-
Solid phase extraction
References
Adir J (1975) Enterohepatic circulation of tetracycline in rats. J Pharm Sci 64:1847–1850. doi:10.1002/jps.2600641121
Ahmadi R, Ahmadifar M, Safarpour E et al (2016) The effects of levofloxacin on testis tissue and spermatogenesis in rat. Cell J 18:112–116
Arumugam M, Raes J, Pelletier E et al (2011) Enterotypes of the human gut microbiome. 1–7. doi:10.1038/nature09944
Barreto FC, Barreto DV, Liabeuf S et al (2009) Serum indoxyl sulfate is associated with vascular disease and mortality in chronic kidney disease patients. Clin J Am Soc Nephrol 4:1551–1558. doi:10.2215/CJN.03980609
Beger RD, Sun J, Schnackenberg LK (2010) Metabolomics approaches for discovering biomarkers of drug-induced hepatotoxicity and nephrotoxicity. Toxicol Appl Pharmacol 243:154–166
Bendheim PE, Poeggeler B, Neria E, Ziv V, Pappolla MA, Chain DG (2002) Development of indole-3-propionic Acid (OXIGONTM) for alzheimer’ s disease. J Mol Neurosci 19:213–217. doi:10.1007/s12031-002-0036-0
Bergogne-Bérézin E, Bryskier A (1999) The suppository form of antibiotic administration: pharmacokinetics and clinical application. J Antimicrob Chemother 43:177–185. doi:10.1093/jac/43.2.177
Boothe DM (2015) The merck veterinary manual: tetracyclines. http://www.merckvetmanual.com/mvm/pharmacology/antibacterial_agents/tetracyclines.html
Brown SA, Riviere JE (1991) Comparative pharmacokinetics of amionoglycoside antibiotics. J Vet Pharmacol Ther 14:1–35. doi:10.3109/14992027.2010.524253
Center for Drug Evaluation and Research (2003) Application number: 21–598
Center for Drug Evaluation and Research (2013) Application Number:204063Orig1s000
Chiba M, Poon K, Hollands J, Pang K (1994) Glycine conjugation activity of benzoic acid and its acinar localization in the perfused rat liver. J Pharmacol Exp Ther 268:409–416
Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:260–270. doi:10.1038/nrg3182
Chyan YJ, Poeggeler B, Omar RA et al (1999) Potent neuroprotective properties against the Alzheimer β-amyloid by an endogenous melatonin-related indole structure, indole-3-propionic acid. J Biol Chem 274:21937–21942. doi:10.1074/jbc.274.31.21937
Clarke G, Stilling RM, Kennedy PJ et al (2014) Gut microbiota: the neglected endocrine organ. Mol Endocrinol 28:1221–1238. doi:10.1210/me.2014-1108
Dai ZL, Li XL, Xi P Bin et al (2013) L-Glutamine regulates amino acid utilization by intestinal bacteria. Amino Acids 45:501–512. doi:10.1007/s00726-012-1264-4
Dalhoff A (2001) Comparative in vitro and in vivo activity of the C-8 methoxy quinolone moxifloxacin and the C-8 chlorine quinolone BAY y 3118. Clin Infect Dis 32(Suppl 1):S16–S22. doi:10.1086/319371
David LA, Maurice CF, Carmody RN et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563. doi:10.1038/nature12820
Davila AM, Blachier F, Gotteland M et al (2013) Re-print of “intestinal luminal nitrogen metabolism: role of the gut microbiota and consequences for the host”. Pharmacol Res 69:114–126. doi:10.1016/j.phrs.2013.01.003
De Weirdt R, Possemiers S, Vermeulen G et al (2010) Human faecal microbiota display variable patterns of glycerol metabolism. FEMS Microbiol Ecol 74:601–611. doi:10.1111/j.1574-6941.2010.00974.x
Dhillon S (2006) Clinical pharmacokinetics. Pharmaceutical Press
Dietz D (1989) Toxicology and carcinogenesis studies of tetracycline hydrochloride. US Dep Heal Hum Serv 344:1–171
Dortantz PM, Devices M (1999) Comparison of tobramycin nephrotoxicity in young adult and aged female rats. Pharmacol Toxicol 84(4):147–153
Dou L, Sallée M, Cerini C et al (2014) The cardiovascular effect of the uremic solute indole-3 acetic acid. J Am Soc Nephrol 1–12. doi:10.1681/ASN.2013121283
Drugs.com (2016a) Gentamicin Dosage. In: Gentamicin Inf. from drugs.com, Updat. 2016 Sept. https://www.drugs.com/dosage/gentamicin.html. Accessed 14 Sep 2016a
Drugs.com (2016b) Neomycin Dosage. In: Neomycin Inf. from drugs.com, Updat. 2016 Sept. https://www.drugs.com/dosage/neomycin.html. Accessed 14 Sep 2016b
European Medicines Agency (2016) European public MRL assessment report (EPMAR) European public MRL: Gentamicin
Frost GS, Walton GE, Swann JR et al (2014) Impacts of plant-based foods in ancestral hominin diets on the metabolism and function of gut microbiota in vitro. 5:1–11. doi:10.1128/mBio.00853-14.Editor
Frye RE, Rose S, Slattery J, MacFabe DF (2015) Gastrointestinal dysfunction in autism spectrum disorder: the role of the mitochondria and the enteric microbiome. Microb Ecol Health Dis 26:27458
Guarner F, Malagelada JR (2003) Gut flora in health and disease. The Lancet 361:1831. doi:10.1016/S0140-6736(03)12489-0
Heinken A, Thiele I (2015a) Systems biology of host–microbe metabolomics. WIREs Syst Biol Med 7:195–219. doi:10.1002/wsbm.1301
Heinken A, Thiele I (2015b) Gut microbes systematic prediction of health-relevant human- microbial co-metabolism through a computational framework. doi:10.1080/19490976.2015.1023494
Holmes E, Li JV, Athanasiou T et al (2011) Understanding the role of gut microbiome–host metabolic signal disruption in health and disease. Trends Microbiol 19:349–359. doi:10.1016/j.tim.2011.05.006
Huse SM, Dethlefsen L, Huber JA et al (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4:e1000255. doi:10.1371/journal.pgen.1000255
Igarashi K, Kashiwagi K (2010) Modulation of cellular function by polyamines. Int J Biochem Cell Biol 42:39–51. doi:10.1016/j.biocel.2009.07.009
Kamp H, Fabian E, Groeters S et al (2012a) Application of in vivo metabolomics to preclinical/toxicological studies: case study on phenytoin-induced systemic toxicity
Kamp H, Strauss V, Wiemer J et al (2012b) Reproducibility and robustness of metabolome analysis in rat plasma of 28-day repeated dose toxicity studies. Toxicol Lett 215:143–149
Kirpich IA, Marsano LS, McClain CJ (2015) Gut-liver axis, nutrition, and non-alcoholic fatty liver disease. Clin Biochem 48:923–930
Kohli R, Kirby M, Xanthakos SA et al (2011) High-fructose medium-chain-trans-fat diet induces liver fibrosis & elevates plasma coenzyme Q9 in a novel murine model of obesity and NASH. 52:934–944. doi:10.1002/hep.23797.High-Fructose
Kuroda T, Namba K, Torimaru T et al (2001) Variability of oral bioavailability for low dose methotrexate in rats. Eur J Drug Metab Pharmacokinet 26:227–234
Lecomte V, Kaakoush NO, Maloney CA et al (2015) Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters. PLoS One 10:e0126931. doi:10.1371/journal.pone.0126931
Li M, Wang B, Zhang M et al (2008) Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 105:2117–2122. doi:10.1073/pnas.0712038105
Lindon JC, Holmes E, Bollard ME et al (2004) Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers 9:1–31. doi:10.1080/13547500410001668379
Looser R, Krotzky AJ, Trethewey N (2005) Metabolite profiling with GC-MS and LC-MS - a key tool for contemporary biology. In: Vaidyanathan S, Harrigan G, Goodacre R (eds) Metabolome analyses - strategies for systems biology. Springer, New York, p 103–118
Marchesi JR, Holmes E, Khan F et al (2007) Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 6:546–551. doi:10.1021/pr060470d
Marcobal A, Kashyap PC, Nelson TA et al (2013) A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice. ISME J 7:1933–1943. doi:10.1038/ismej.2013.89
Marcobal A, Yusufaly T, Higginbottom S et al (2015) Metabolome progression during early gut microbial colonization of gnotobiotic mice. Sci Rep 5:11589. doi:10.1038/srep11589
Martin FPJ, Wang Y, Yap IKS et al (2009) Topographical variation in murine intestinal metabolic profiles in relation to microbiome speciation and functional ecological activity. J Proteome Res 8:3464–3474. doi:10.1021/pr900099x
Mellert W, Kapp M, Strauss V et al (2011) Nutritional impact on the plasma metabolome of rats. Toxicol Lett 207:173–181. doi:10.1016/j.toxlet.2011.08.013
Mingeot-Leclercq MP, Glupczynski Y, Tulkens PM (1999) Aminoglycosides: activity and resistance. Antimicrob Agents Chemother 43:727–737
Modi SR, Collins JJ, Relman DA (2014) Antibiotics and the gut microbiota. J Clin Invest 124:4212–4218. doi:10.1172/JCI72333.themselves
Musther H, Olivares-Morales A, Hatley OJD et al (2014) Animal versus human oral drug bioavailability: do they correlate? Eur J Pharm Sci 57:280–291. doi:10.1016/j.ejps.2013.08.018
Nicholls AW, Mortishire-Smith RJ, Nicholson JK (2003) NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats. Chem Res Toxicol 16:1395–1404. doi:10.1021/tx0340293
Nicholson JK, Holmes E, Kinross J et al (2012) Metabolic Interactions. 108:1262–1268
Ottman N, Smidt H, de Vos WM, Belzer C (2012) The function of our microbiota: who is out there and what do they do? Front Cell Infect Microbiol 2:1–11. doi:10.3389/fcimb.2012.00104
Phipps AN, Stewart J, Wright B, Wilson ID (1998) Effect of diet on the urinary excretion of hippuric acid and other dietary-derived aromatics in rat. A complex interaction between diet, gut microflora and substrate specificity. Xenobiotica 28:527–537. doi:10.1080/004982598239443
Poon K, Pang K (1995) Benzoic acid glycine conjugation in the isolated perfused rat kidney. Drug Metab Dispos 23:255–260
Ramezani A, Massy ZA, Meijers B et al (2015) Role of the gut microbiome in uremia: a potential therapeutic target. Am J Kidney Dis 1–16. doi:10.1053/j.ajkd.2015.09.027
Ravenzwaay B Van, Kamp H, Montoya-parra GA et al (2016) The development of a database for metabolomics – looking back on ten years of experience. 14:47–68
Remer T, Manz F (2003) Paleolithic diet, sweet potato eaters, and potential renal acid load. Am J Clin Nutr 78:802–803 (author reply 803)
Renshaw D, Cerniglia C, Mitsumori K NEOMYCIN (addendum, WHO Food Additives Series 51). http://www.inchem.org/documents/jecfa/jecmono/v51je02.htm. Accessed 11 Aug 2016
Roberts G (1995) Gentamicin (WHO Food Additives Series 34). In: WHO Food Addit. http://www.inchem.org/documents/jecfa/jecmono/v34je06.htm. Accessed 23 Aug 2016
Roessner U, Wagner C, Kopka J et al (2000) Technical advance: simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23:131–142. doi:10.1046/j.1365-313x.2000.00774.x
Saric J, Wang Y, Li J et al (2008) Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res 7:352–360. doi:10.1021/pr070340k
Satoh M, Hayashi H, Watanabe M et al (2003) Uremic toxins overload accelerates renal damage in a rat model of chronic renal failure. Nephron Exp Nephrol 95:e111–e118. doi:10.1159/000074327
Schoonen WGEJ, Kloks CPAM, Ploemen JPHTM et al (2007) Uniform procedure of 1 H NMR analysis of rat urine and toxicometabonomics Part II: Comparison of NMR profiles classification of hepatotoxicity. Toxicol Sci 98:286–297. doi:10.1093/toxsci/kfm077
Scoper SV (2008) Review of third-and fourth-generation fluoroquinolones in ophthalmology: in-vitro and in-vivo efficacy. Adv Ther 25:979–994
Shah P, Swiatlo E (2008) A multifaceted role for polyamines in bacterial pathogens. Mol Microbiol 68:4–16
Shiomi Y, Nishiumi S, Ooi M et al (2011) GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium. Inflamm Bowel Dis 17:2261–2274. doi:10.1002/ibd.21616
Strahl N, Barr W (1971) Intestinal drug absorption and metabolism. 3. Glycine conjugation and accumulation of benzoic acid in rat intestinal tissue. J Pharm Sci 60:278–281
Strauss V, Wiemer J, Leibold E et al (2009) Influence of strain and sex on the metabolic profile of rats in repeated dose toxicological studies. Toxicol Lett 191:88–95. doi:10.1016/j.toxlet.2009.08.004
Strauss V, Mellert W, Wiemer J et al (2012) Increased toxicity when fibrates and statins are administered in combination - A metabolomics approach with rats. Toxicol Lett 211:187–200. doi:10.1016/j.toxlet.2012.03.798
Swann JR, Want EJ, Geier FM et al (2011) Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci 108:4523–4530. doi:10.1073/pnas.1006734107
Tabor CW, Tabor H (1985) Polyamines in microorganisms. Microbiol Rev 49:81–99
Tanaka M, Takashina H, Tsutsumi S (2004) Comparative assessment of ocular tissue distribution of drug-related radioactivity after chronic oral administration of 14C-levofloxacin and 14C-chloroquine in pigmented rats. J Pharm Pharmacol 56:977–983. doi:10.1211/0022357043932
Thomas S, Prabhu R, Balasubramanian KA (2005) Surgical manipulation of the intestine and distant organ damage-Protection by oral glutamine supplementation. Surgery 137:48–55. doi:10.1016/j.surg.2004.04.038
Toh MC, Allen-Vercoe E (2015) The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts. Microb Ecol Health Dis 26:26309. doi:10.3402/mehd.v26.26309
U.S. Food and Drug Administration (2008) Levofloxacin - Prescribing Information
U.S. Food and Drug Administration (2013) FDA requires label changes to warn of risk for possibly permanent nerve damage from antibacterial fluoroquinolone drugs taken by mouth or by injection. http://www.fda.gov/Drugs/DrugSafety/ucm365050.htm. Accessed 7 Jun 2016
U.S. Food and Drug Administration (2015) TETRACYCLINE HYDROCHLORIDE-tetracycline hydrochloride capsule. In: Ref. ID 3740369. http://www.accessdata.fda.gov/drugsatfda_docs/label/2015/050278s037lbl.pdf. Accessed 7 Jun 2016
U.S. Food and Drug Administration Prescribing Information for DORYX Tablets. Reference ID: 2921043. http://www.accessdata.fda.gov/drugsatfda_docs/label/2011/050795s013lbl.pdf. Accessed 5 Jul 2016
Van Koten-Vermeulen JEM, van Leeuwen FXR (1995) Neomycin (WHO Food Additives Series 34). http://www.inchem.org/documents/jecfa/jecmono/v34je07.htm. Accessed 5 Jul 2016
Van Ravenzwaay B, Cunha GCP, Leibold E et al (2007) The use of metabolomics for the discovery of new biomarkers of effect. Toxicol Lett 172:21–28. doi:10.1016/j.toxlet.2007.05.021
Van Ravenzwaay B, Coelho-Palermo CG, Strauss V et al (2010a) The use of metabolomics in cancer research. In: Cho WCS (ed) An omics perspective of cancer. SpringerScience + Business Media BV, New York, pp 141–166
Van Ravenzwaay B, Coelho-Palermo Cunha G, Strauss V et al (2010b) The individual and combined metabolite profiles (metabolomics) of dibutylphthalate and di(2-ethylhexyl)phthalate following a 28-day dietary exposure in rats. Toxicol Lett 198:159–170. doi:10.1016/j.toxlet.2010.06.009
Van Ravenzwaay B, Herold M, Kamp H et al (2012) Metabolomics: a tool for early detection of toxicological effects an opportunity for biology based grouping of chemicals-from QSAR to QBAR. Mutat Res Genet Toxicol Environ Mutagen 746:144–150. doi:10.1016/j.mrgentox.2012.01.006
Vargas-Estrada D, Gutiérrez L, Juarez-Rodríguez I, Sumano H (2008) Pharmacokinetics of doxycycline and tissue concentrations of an experimental long-acting parenteral formulation of doxycycline in Wistar rats. Arzneimittelforschung 58:310–315. doi:10.1055/s-0031-1296512.Pharmacokinetics
Velasquez-Manoff M (2015) 2. Gut microbiome: the peacekeepers. Nature 518:S3–S11. doi:10.1038/518S3a
Von Keutz E, Schlüter G (1999) Preclinical safety evaluation of moxifloxacin, a novel fluoroquinolone. J Antimicrob Chemother 43:91–100. doi:10.1093/jac/43.suppl_2.91
Wikoff WR, Anfora AT, Liu J et al (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci USA 106:3698–3703. doi:10.1073/pnas.0812874106
Williams RE, Eyton-Jones HW, Farnworth MJ et al (2002) Effect of intestinal microflora on the urinary metabolic profile of rats: a 1 H-nuclear magnetic resonance spectroscopy study. Xenobiotica 32:783–794. doi:10.1080/00498250210143047
Wu IW, Hsu KH, Lee CC et al (2011) P-cresyl sulphate and indoxyl sulphate predict progression of chronic kidney disease. Nephrol Dial Transplant 26:938–947. doi:10.1093/ndt/gfq580
Yamada H, Yamahara A, Yasuda S et al (2002) Dansyl chloride derivatization of methamphetamine: a method with advantages for screening and analysis of methamphetamine in urine. J Anal Toxicol 26:17–22. doi:10.1093/jat/26.1.17
Zeng Y, Dai Z, Lu F et al (2016) Emodin via colonic irrigation modulates gut microbiota and reduces uremic toxins in rats with chronic kidney disease. Oncotarget 7:17468–17478. doi:10.18632/oncotarget.8160
Zhang Y, Limaye PB, Renaud HJ, Klaassen CD (2014) Effect of various antibiotics on modulation of intestinal microbiota and bile acid profile in mice. Toxicol Appl Pharmacol 277:138–145. doi:10.1016/j.taap.2014.03.009
Zhang Y-J, Li S, Gan R-Y et al (2015) Impacts of gut bacteria on human health and diseases. Int J Mol Sci 16:7493–7519. doi:10.3390/ijms16047493
Zheng X, Xie G, Zhao A et al (2011) The footprints of gut microbial à mammalian co-metabolism. 10:5512–5522. doi:10.1021/pr2007945
Acknowledgements
We would like to thank Ms Irmgard Weber for her skillful assistance.
Funding
The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties. No writing assistance was utilized in the production of this manuscript.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Behr, C., Kamp, H., Fabian, E. et al. Gut microbiome-related metabolic changes in plasma of antibiotic-treated rats. Arch Toxicol 91, 3439–3454 (2017). https://doi.org/10.1007/s00204-017-1949-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00204-017-1949-2