Applied Microbiology and Biotechnology

, Volume 102, Issue 5, pp 2289–2299 | Cite as

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs

Applied microbial and cell physiology


We investigated the time-course effects of therapeutic antibiotics on intestinal microbial composition and metabolism in an ileal-cannulated pig model. Sixteen ileal-cannulated piglets (12 ± 0.5 kg) were assigned to two groups (n = 8) and fed standard diets with or without antibiotics. At 4 days before, and at days 2, 7, and 13 after antibiotic administration, ileal and fecal samples were collected for analysis of microbiota composition via 16S rRNA MiSeq sequencing and metabolites (short-chain fatty acids, biogenic amines, and indole). It was found that Lactobacillus and Bifidobacterium had decreased by an average 2.68-fold and 508-fold in ileum on days 2–13, and by an average 45.08-fold and 71.50-fold in feces on days 7–13 (P < 0.05). Escherichia/Shigella had increased by an average 265-fold in ileum on days 2–13, and by an average 36.70-fold in feces on days 7–13 (P < 0.05). Acetate concentration had decreased in ileum by an average 2.88-fold on days 2–13, and by 1.83-fold in feces on day 7 (P < 0.05). Cadaverine concentration had increased by an average 7.03-fold in ileum on days 2–13, and by an average 9.96-fold in feces on days 7–13 (P < 0.05), and fecal indole concentration had increased by an average 2.51-fold on days 7–13 (P < 0.05). Correlation analysis between significant microbes and metabolites indicated that the antibiotic-induced microbiota shift appeared to result in the changes of intestinal metabolism. In conclusion, antibiotic administration led to dynamic changes in microbial communities and metabolism in ileum and feces, with ileal microbiota being more prone to shift than fecal microbiota.


Antibiotics Dynamic impact of antibiotics Temporal change of gut microbiota Microbial metabolites 



This research was supported by the National Natural Science Foundation of China (31430082) and National Key Basic Research Program of China, 973 program (Beijing, grant no. 2013CB127300).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Supplementary material

253_2018_8774_MOESM1_ESM.pdf (837 kb)
ESM 1 (PDF 837 kb)


  1. Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. Isme J 7(7):1344–1353. CrossRefPubMedPubMedCentralGoogle Scholar
  2. Becattini S, Taur Y, Pamer EG (2016) Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol Med 22(6):458–478. CrossRefPubMedPubMedCentralGoogle Scholar
  3. Belenguer A, Duncan SH, Holtrop G, Anderson SE, Lobley GE, Flint HJ (2007) Impact of pH on lactate formation and utilization by human fecal microbial communities. Appl Environ Microbiol 73(20):6526–6533. CrossRefPubMedPubMedCentralGoogle Scholar
  4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300. Google Scholar
  5. Birck MM, Nguyen DN, Cilieborg MS, Kamal SS, Nielsen DS, Damborg P, Olsen JE, Lauridsen C, Sangild PT, Thymann T (2016) Enteral but not parenteral antibiotics enhance gut function and prevent necrotizing enterocolitis in formula-fed newborn preterm pigs. Am J Physiol-Gastr Liver 310(5):G323–G333. CrossRefGoogle Scholar
  6. Chen W, Liu F, Ling Z, Tong X, Xiang C (2012) Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 7(6):e39743. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cilieborg MS, Boye M, Molbak L, Thymann T, Sangild PT (2011) Preterm birth and necrotizing enterocolitis alter gut colonization in pigs. Pediatr Res 69(1):10–16. CrossRefPubMedGoogle Scholar
  8. Dai ZL, Zhang J, Wu G, Zhu WY (2010) Utilization of amino acids by bacteria from the pig small intestine. Amino Acids 39(5):1201–1215. CrossRefPubMedGoogle Scholar
  9. Davila AM, Blachier F, Gotteland M, Andriamihaja M, Benetti PH, Sanz Y, Tome D (2013) Intestinal luminal nitrogen metabolism: role of the gut microbiota and consequences for the host. Pharmacol Res 68(1):95–107. CrossRefPubMedGoogle Scholar
  10. de Lange CF, Sauer WC, Souffrant WB, Lien KA (1992) 15N-leucine and 15N-isoleucine isotope dilution techniques versus the 15N-isotope dilution technique for determining the recovery of endogenous protein and amino acids in digesta collected from the distal ileum in pigs. J Anim Sci 70(6):1848–1856. CrossRefPubMedGoogle Scholar
  11. Duncan SH, Barcenilla A, Stewart CS, Pryde SE, Flint HJ (2002) Acetate utilization and butyryl coenzyme A (CoA): acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl Environ Microbiol 68(10):5186–5190. CrossRefPubMedPubMedCentralGoogle Scholar
  12. Farup PG, Rudi K, Hestad K (2016) Faecal short-chain fatty acids—a diagnostic biomarker for irritable bowel syndrome? BMC Gastroenterol 16(1):51. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8(7):e1002606. CrossRefPubMedPubMedCentralGoogle Scholar
  14. Flint HJ, Scott KP, Louis P, Duncan SH (2012) The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9(10):577–589. CrossRefPubMedGoogle Scholar
  15. Holmes E, Li JV, Athanasiou T, Ashrafian H, Nicholson JK (2011) Understanding the role of gut microbiome-host metabolic signal disruption in health and disease. Trends Microbiol 19(7):349–359. CrossRefPubMedGoogle Scholar
  16. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5(3):299–314. Google Scholar
  17. Jensen ML, Thymann T, Cilieborg MS, Lykke M, Molbak L, Jensen BB, Schmidt M, Kelly D, Mulder I, Burrin DG, Sangild PT (2014) Antibiotics modulate intestinal immunity and prevent necrotizing enterocolitis in preterm neonatal piglets. Am J Physiol Gastrointest Liver Physiol 306(1):G59–G71. CrossRefPubMedGoogle Scholar
  18. Koh A, De Vadder F, Kovatcheva-Datchary P, Backhed F (2016) From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165(6):1332–1345. CrossRefPubMedGoogle Scholar
  19. Li S, Sauer WC, Fan MZ (1993) The effect of dietary crude protein level on ileal and fecal amino-acid digestibility in early-weaned pigs. J Anim Physiol Anim Nutr 70(1-5):117–128. CrossRefGoogle Scholar
  20. Looft T, Allen HK, Cantarel BL, Levine UY, Bayles DO, Alt DP, Henrissat B, Stanton TB (2014) Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. ISME J 8(8):1566–1576. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Louis P, Hold GL, Flint HJ (2014) The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol 12(10):661–672. CrossRefPubMedGoogle Scholar
  22. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12):8228–8235. CrossRefPubMedPubMedCentralGoogle Scholar
  23. Makras L, Triantafyllou V, Fayol-Messaoudi D, Adriany T, Zoumpopoulou G, Tsakalidou E, Servin A, De Vuyst L (2006) Kinetic analysis of the antibacterial activity of probiotic lactobacilli towards Salmonella enterica serovar Typhimurium reveals a role for lactic acid and other inhibitory compounds. Res Microbiol 157(3):241–247. CrossRefPubMedGoogle Scholar
  24. Mao SY, Zhang ML, Liu JH, Zhu WY (2015) Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function. Sci Rep 5(1):16116. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Mu CL, Yang YX, Luo Z, Guan LL, Zhu WY (2016) The colonic microbiome and epithelial transcriptome are altered in rats fed a high-protein diet compared with a normal-protein diet. J Nutr 146(3):474–483. CrossRefPubMedGoogle Scholar
  26. Mu CL, Yang YX, Su Y, Zoetendal EG, Zhu WY (2017) Differences in microbiota membership along the gastrointestinal tract of piglets and their differential alterations following an early-life antibiotic intervention. Front Microbiol 8:797. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Perez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, Otto W, Rojo D, Bargiela R, von Bergen M, Neulinger SC, Daumer C, Heinsen FA, Latorre A, Barbas C, Seifert J, dos Santos VM, Ott SJ, Ferrer M, Moya A (2013) Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 62(11):1591–1601. CrossRefPubMedGoogle Scholar
  28. Sangild PT, Siggers RH, Schmidt M, Elnif J, Bjornvad CR, Thymann T, Grondahl ML, Hansen AK, Jensen SK, Boye M, Moelbak L, Buddington RK, Westrom BR, Holst JJ, Burrin DG (2006) Diet- and colonization-dependent intestinal dysfunction predisposes to necrotizing enterocolitis in preterm pigs. Gastroenterology 130(6):1776–1792. CrossRefPubMedGoogle Scholar
  29. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541. CrossRefPubMedPubMedCentralGoogle Scholar
  30. Schüssler W, Nitschke L (1999) Death of fish due to surface water pollution by liquid manure or untreated wastewater: analytical preservation of evidence by HPLC. Water Res 33(12):2884–2887. CrossRefGoogle Scholar
  31. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12(6):R60. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Wang XF, Mao SY, Liu JH, Zhang LL, Cheng YF, Jin W, Zhu WY (2011) Effect of the gynosaponin on methane production and microbe numbers in a fungus-methanogen co-culture. J Anim Feed Sci 20(2):272–284. CrossRefGoogle Scholar
  33. Yang YX, Mu CL, Zhang JF, Zhu WY (2014) Determination of biogenic amines in digesta by high performance liquid chromatography with precolumn dansylation. Anal Lett 47(8):1290–1298. CrossRefGoogle Scholar
  34. Yang YX, Mu CL, Luo Z, Zhu WY (2015) Bromochloromethane, a methane analogue, affects the microbiota and metabolic profiles of the rat gastrointestinal tract. Appl Environ Microbiol 82(3):778–787. CrossRefPubMedGoogle Scholar
  35. Ze X, Duncan SH, Louis P, Flint HJ (2012) Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 6(8):1535–1543. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Kan Gao
    • 1
  • Yu Pi
    • 1
  • Yu Peng
    • 1
  • Chun-Long Mu
    • 1
  • Wei-Yun Zhu
    • 1
  1. 1.Laboratory of Gastrointestinal Microbiology, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingPeople’s Republic of China

Personalised recommendations