Effects of Antibiotic Growth Promoter and Characterization of Ecological Succession in Swine Gut Microbiota (original) (raw)

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Research article

Microbial Ecology and Diversity

Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea

Received: August 26, 2014; Accepted: November 3, 2014

J. Microbiol. Biotechnol. 2015; 25(4): 431-438

Published April 28, 2015 https://doi.org/10.4014/jmb.1408.08063

Copyright © The Korean Society for Microbiology and Biotechnology.

Abstract

Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has increased owing to pathogenic bacterial infections. There is a need of developing AGP alternatives; however, the mechanisms by which AGP enhances livestock growth performance are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the effects of AGPs on swine gut microbiota. Microbial community analysis was done based on bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect, but inhibited the growth of potential pathogens during the early growth stage. Our results showed the significant increase in species richness after the stabilization of gut microbiota during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was divided into four clusters based on the distribution of operational taxonomic units, which was significantly correlated to the swine weight regardless of AGP treatments. Taxonomic abundance analysis indicated a negative correlation between host weight and the abundance of the family Prevotellaceae species, but showed positive correlation to the abundance of the family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth performance enhancement was observed, the use of AGP inhibited the potential pathogens in the early growth stage of swine. In addition, our results indicated the ecological succession of swine gut microbiota according to swine weight. Here, we present a characterization of swine gut microbiota with respect to the effects of AGPs on growth performance.

Keywords

gut microbiota, swine, miseq, mothur, antibiotics, growth promoter

References

1. Awad WA, Ghareeb K, Abdel-Raheem S, Bohm J. 2009. Effects of dietary inclusion of probiotic and synbiotic on growth performance, organ weights, and intestinal histomorphology of broiler chickens. Poult. Sci. 88: 49-56.
   
2. Bhandari SK, Xu B, Nyachoti CM, Giesting DW, Krause DO. 2008. Evaluation of alternatives to antibiotics using an Escherichia coli K88+ model of piglet diarrhea: effects on gut microbial ecology. J. Anim. Sci. 86: 836-847.
   
3. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6: 1621-1624.
   
4. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA 108(Suppl 1): 4516-4522.
   
5. Casewell M, Friis C, Marco E, McMullin P, Phillips I. 2003. The European ban on growth-promoting antibiotics and emerging consequences for human and animal health. J. Antimicrob. Chemother. 52: 159-161.
   
6. Castillo M, Martín-Orúe SM, Roca M, Manzanilla EG, Badiola I, P erez J F, G asa J. 2 006. T he r esponse of gastrointestinal microbiota to avilamycin, butyrate, and plant extracts in early-weaned pigs. J. Anim. Sci. 84: 2725-2734.
   
7. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
   
8. Cornick NA. 2010. Tylosin and chlorotetracycline decrease the duration of fecal shedding of E. coli O157:H7 by swine. Vet. Microbiol. 143: 417-419.
   
9. Degnan PH, Ochman H. 2012. Illumina-based analysis of microbial community diversity. ISME J. 6: 183-194.
   
10. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
    
11. Flint HJ. 2012. Microbiology: antibiotics and adiposity. Nature 488: 601-602.
    
12. Foster EK. 2003. METASTATS: behavioral science statistics for Microsoft Windows and the HP49G programmable calculator. Behav. Res. Methods Instrum. Comput. 35: 325-328.
    
13. Foxx-Orenstein AE, Chey WD. 2012. Manipulation of the gut microbiota as a novel treatment strategy for gastrointestinal disorders. Am. J. Gastroenterol. Suppl. 1: 41-46.
    
14. Hoese A, Clay SA, Clay DE, Oswald J, Trooien T, Thaler R, Carlson CG. 2009. Chlortetracycline and tylosin runoff from soils treated with antimicrobial containing manure. J. Environ. Sci. Health B 44: 371-378.
    
15. Holman DB, Chénier MR. 2013. Impact of subtherapeutic administration of tylosin and chlortetracycline on antimicrobial resistance in farrow-to-finish swine. FEMS Microbiol. Ecol. 85: 1-13.
    
16. Jernberg C, Löfmark S, Edlund C, Jansson JK. 2010. Longterm impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156: 3216-3223.
    
17. Joy SR, Li X, Snow DD, Gilley JE, Woodbury B, BarteltHunt SL. 2014. Fate of antimicrobials and antimicrobial resistance genes in simulated swine manure storage. Sci. Total Environ. 481C: 69-74.
    
18. Juntunen P, Heiska H, Olkkola S, Myllyniemi A-L, Hänninen M-L. 2010. Antimicrobial resistance in Campylobacter coli selected by tylosin treatment at a pig farm. Vet. Microbiol. 146: 90-97.
    
19. Kalmokoff M, Waddington LM, Thomas M, Liang K-L, Ma C, Topp E, et al. 2011. Continuous feeding of antimicrobial growth promoters to commercial swine during the growing/finishing phase does not modify faecal community erythromycin resistance or community structure. J. Appl. Microbiol. 110: 1414-1425.
    
20. Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, Nunez G. 2012. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336: 1325-1329.
    
21. Karlsson F, Svartstrom O, Belak K, Fellstrom C, Pringle M. 2013. Occurrence of Treponema spp. in porcine skin ulcers and gingiva. Vet. Microbiol. 165: 402-409.
    
22. Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, Isaacson RE. 2011. Longitudinal investigation of the agerelated bacterial diversity in the feces of commercial pigs. Vet. Microbiol. 153: 124-133.
    
23. Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, Isaacson RE. 2012. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. Proc. Natl. Acad. Sci. USA 109: 15485-15490.
    
24. Konstantinov SR, Smidt H, Akkermans ADL, Casini L, Trevisi P, Mazzoni M, et al. 2008. Feeding of Lactobacillus sobrius reduces Escherichia coli F4 levels in the gut and promotes growth of infected piglets. FEMS Microbiol. Ecol. 66: 599-607.
    
25. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79: 5112-5120.
    
26. Looft T, Allen HK, Casey TA, Alt DP, Stanton TB. 2014. Carbadox has both temporary and lasting effects on the swine gut microbiota. Front. Microbiol. 5: 276.
    
27. Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, et al. 2012. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl. Acad. Sci. USA 109:1691-1696.
    
28. Lowenthal JW, Lambrecht B, van den Berg TP, Andrew ME, Strom AD, Bean AG. 2000. Avian cytokines − the natural approach to therapeutics. Dev. Comp. Immunol. 24: 355-365.
    
29. Marshall BM, Levy SB. 2011. Food animals and antimicrobials:impacts on human health. Clin. Microbiol. Rev. 24: 718-733.
    
30. May KD, Wells JE, Maxwell CV, Oliver WT. 2012. Granulated lysozyme as an alternative to antibiotics improves growth performance and small intestinal morphology of 10day-old pigs. J. Anim. Sci. 90: 1118-1125.
    
31. Norris V, Molina F, Gewirtz AT. 2013. Hypothesis: bacteria control host appetites. J. Bacteriol. 195: 411-416.
    
32. Pedersen R, Ingerslev H-C, Sturek M, Alloosh M, Cirera S, Christoffersen BØ, et al. 2013. Characterisation of gut microbiota in Ossabaw and Göttingen minipigs as models of obesity and metabolic syndrome. PLoS One 8: e56612.
    
33. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and Web-based tools. Nucleic Acids Res. 41: D590-D596.
    
34. Queipo-Ortuno MI, Seoane LM, Murri M, Pardo M, GomezZumaquero JM, Cardona F, et al. 2013. Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels. PLoS One 8: e65465.
    
35. Redondo LM, Chacana PA, Dominguez JE, Fernandez Miyakawa ME. 2014. Perspectives in the use of tannins as alternative to antimicrobial growth promoter factors in poultry. Front. Microbiol. 5: 118.
    
36. Rettedal E, Vilain S, Lindblom S, Lehnert K, Scofield C, George S, et al. 2009. Alteration of the ileal microbiota of weanling piglets by the growth-promoting antibiotic chlortetracycline. Appl. Environ. Microbiol. 75: 5489-5495.
    
37. Sarmah AK, Meyer MT, Boxall AB. 2006. A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment. Chemosphere 65: 725-759.
    
38. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541.
    
39. Thompson CL, Wang B, Holmes AJ. 2008. The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J. 2: 739-748.
    
40. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457: 480-484.
    
41. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
    
42. Upadrasta A, O’Sullivan L, O’Sullivan O, Sexton N, Lawlor PG, Hill C, et al. 2013. The effect of dietary supplementation with spent cider yeast on the swine distal gut microbiome. PLoS One 8: e75714.
    
43. Willing BP, Russell SL, Finlay BB. 2011. Shifting the balance:antibiotic effects on host-microbiota mutualism. Nat. Rev. Microbiol. 9: 233-243.
    
44. Zhang J, Kobert K, Flouri T, Stamatakis A. 2014. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30: 614-620.
    

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Article

Research article

Effects of Antibiotic Growth Promoter and Characterization of Ecological Succession in Swine Gut Microbiota

Tatsuya Unno 1*, Jungman Kim 1, Robin B. Guevarra 1 and Son G. Nguyen 1

Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea

Received: August 26, 2014; Accepted: November 3, 2014

Abstract

Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has
increased owing to pathogenic bacterial infections. There is a need of developing AGP
alternatives; however, the mechanisms by which AGP enhances livestock growth performance
are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and
without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the
effects of AGPs on swine gut microbiota. Microbial community analysis was done based on
bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect,
but inhibited the growth of potential pathogens during the early growth stage. Our results
showed the significant increase in species richness after the stabilization of gut microbiota
during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was
divided into four clusters based on the distribution of operational taxonomic units, which was
significantly correlated to the swine weight regardless of AGP treatments. Taxonomic
abundance analysis indicated a negative correlation between host weight and the abundance
of the family Prevotellaceae species, but showed positive correlation to the abundance of the
family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth
performance enhancement was observed, the use of AGP inhibited the potential pathogens in
the early growth stage of swine. In addition, our results indicated the ecological succession of
swine gut microbiota according to swine weight. Here, we present a characterization of swine
gut microbiota with respect to the effects of AGPs on growth performance.

Keywords: gut microbiota, swine, miseq, mothur, antibiotics, growth promoter

• Abstract

References

1. Awad WA, Ghareeb K, Abdel-Raheem S, Bohm J. 2009. Effects of dietary inclusion of probiotic and synbiotic on growth performance, organ weights, and intestinal histomorphology of broiler chickens. Poult. Sci. 88: 49-56.
   
2. Bhandari SK, Xu B, Nyachoti CM, Giesting DW, Krause DO. 2008. Evaluation of alternatives to antibiotics using an Escherichia coli K88+ model of piglet diarrhea: effects on gut microbial ecology. J. Anim. Sci. 86: 836-847.
   
3. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6: 1621-1624.
   
4. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA 108(Suppl 1): 4516-4522.
   
5. Casewell M, Friis C, Marco E, McMullin P, Phillips I. 2003. The European ban on growth-promoting antibiotics and emerging consequences for human and animal health. J. Antimicrob. Chemother. 52: 159-161.
   
6. Castillo M, Martín-Orúe SM, Roca M, Manzanilla EG, Badiola I, P erez J F, G asa J. 2 006. T he r esponse of gastrointestinal microbiota to avilamycin, butyrate, and plant extracts in early-weaned pigs. J. Anim. Sci. 84: 2725-2734.
   
7. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
   
8. Cornick NA. 2010. Tylosin and chlorotetracycline decrease the duration of fecal shedding of E. coli O157:H7 by swine. Vet. Microbiol. 143: 417-419.
   
9. Degnan PH, Ochman H. 2012. Illumina-based analysis of microbial community diversity. ISME J. 6: 183-194.
   
10. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
    
11. Flint HJ. 2012. Microbiology: antibiotics and adiposity. Nature 488: 601-602.
    
12. Foster EK. 2003. METASTATS: behavioral science statistics for Microsoft Windows and the HP49G programmable calculator. Behav. Res. Methods Instrum. Comput. 35: 325-328.
    
13. Foxx-Orenstein AE, Chey WD. 2012. Manipulation of the gut microbiota as a novel treatment strategy for gastrointestinal disorders. Am. J. Gastroenterol. Suppl. 1: 41-46.
    
14. Hoese A, Clay SA, Clay DE, Oswald J, Trooien T, Thaler R, Carlson CG. 2009. Chlortetracycline and tylosin runoff from soils treated with antimicrobial containing manure. J. Environ. Sci. Health B 44: 371-378.
    
15. Holman DB, Chénier MR. 2013. Impact of subtherapeutic administration of tylosin and chlortetracycline on antimicrobial resistance in farrow-to-finish swine. FEMS Microbiol. Ecol. 85: 1-13.
    
16. Jernberg C, Löfmark S, Edlund C, Jansson JK. 2010. Longterm impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156: 3216-3223.
    
17. Joy SR, Li X, Snow DD, Gilley JE, Woodbury B, BarteltHunt SL. 2014. Fate of antimicrobials and antimicrobial resistance genes in simulated swine manure storage. Sci. Total Environ. 481C: 69-74.
    
18. Juntunen P, Heiska H, Olkkola S, Myllyniemi A-L, Hänninen M-L. 2010. Antimicrobial resistance in Campylobacter coli selected by tylosin treatment at a pig farm. Vet. Microbiol. 146: 90-97.
    
19. Kalmokoff M, Waddington LM, Thomas M, Liang K-L, Ma C, Topp E, et al. 2011. Continuous feeding of antimicrobial growth promoters to commercial swine during the growing/finishing phase does not modify faecal community erythromycin resistance or community structure. J. Appl. Microbiol. 110: 1414-1425.
    
20. Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, Nunez G. 2012. Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science 336: 1325-1329.
    
21. Karlsson F, Svartstrom O, Belak K, Fellstrom C, Pringle M. 2013. Occurrence of Treponema spp. in porcine skin ulcers and gingiva. Vet. Microbiol. 165: 402-409.
    
22. Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, Isaacson RE. 2011. Longitudinal investigation of the agerelated bacterial diversity in the feces of commercial pigs. Vet. Microbiol. 153: 124-133.
    
23. Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, Isaacson RE. 2012. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. Proc. Natl. Acad. Sci. USA 109: 15485-15490.
    
24. Konstantinov SR, Smidt H, Akkermans ADL, Casini L, Trevisi P, Mazzoni M, et al. 2008. Feeding of Lactobacillus sobrius reduces Escherichia coli F4 levels in the gut and promotes growth of infected piglets. FEMS Microbiol. Ecol. 66: 599-607.
    
25. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79: 5112-5120.
    
26. Looft T, Allen HK, Casey TA, Alt DP, Stanton TB. 2014. Carbadox has both temporary and lasting effects on the swine gut microbiota. Front. Microbiol. 5: 276.
    
27. Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, et al. 2012. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl. Acad. Sci. USA 109:1691-1696.
    
28. Lowenthal JW, Lambrecht B, van den Berg TP, Andrew ME, Strom AD, Bean AG. 2000. Avian cytokines − the natural approach to therapeutics. Dev. Comp. Immunol. 24: 355-365.
    
29. Marshall BM, Levy SB. 2011. Food animals and antimicrobials:impacts on human health. Clin. Microbiol. Rev. 24: 718-733.
    
30. May KD, Wells JE, Maxwell CV, Oliver WT. 2012. Granulated lysozyme as an alternative to antibiotics improves growth performance and small intestinal morphology of 10day-old pigs. J. Anim. Sci. 90: 1118-1125.
    
31. Norris V, Molina F, Gewirtz AT. 2013. Hypothesis: bacteria control host appetites. J. Bacteriol. 195: 411-416.
    
32. Pedersen R, Ingerslev H-C, Sturek M, Alloosh M, Cirera S, Christoffersen BØ, et al. 2013. Characterisation of gut microbiota in Ossabaw and Göttingen minipigs as models of obesity and metabolic syndrome. PLoS One 8: e56612.
    
33. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and Web-based tools. Nucleic Acids Res. 41: D590-D596.
    
34. Queipo-Ortuno MI, Seoane LM, Murri M, Pardo M, GomezZumaquero JM, Cardona F, et al. 2013. Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels. PLoS One 8: e65465.
    
35. Redondo LM, Chacana PA, Dominguez JE, Fernandez Miyakawa ME. 2014. Perspectives in the use of tannins as alternative to antimicrobial growth promoter factors in poultry. Front. Microbiol. 5: 118.
    
36. Rettedal E, Vilain S, Lindblom S, Lehnert K, Scofield C, George S, et al. 2009. Alteration of the ileal microbiota of weanling piglets by the growth-promoting antibiotic chlortetracycline. Appl. Environ. Microbiol. 75: 5489-5495.
    
37. Sarmah AK, Meyer MT, Boxall AB. 2006. A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment. Chemosphere 65: 725-759.
    
38. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541.
    
39. Thompson CL, Wang B, Holmes AJ. 2008. The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J. 2: 739-748.
    
40. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457: 480-484.
    
41. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
    
42. Upadrasta A, O’Sullivan L, O’Sullivan O, Sexton N, Lawlor PG, Hill C, et al. 2013. The effect of dietary supplementation with spent cider yeast on the swine distal gut microbiome. PLoS One 8: e75714.
    
43. Willing BP, Russell SL, Finlay BB. 2011. Shifting the balance:antibiotic effects on host-microbiota mutualism. Nat. Rev. Microbiol. 9: 233-243.
    
44. Zhang J, Kobert K, Flouri T, Stamatakis A. 2014. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30: 614-620.