Probiotic Effects On Bacterial Community Structure And Antibiotic Resistance Of Gut Microbiota In Broiler Chickens Raised Under Three Different Dietary Conditions

Open Access
Bailey, Megan Louise
Graduate Program:
Master of Science
Document Type:
Master Thesis
Date of Defense:
Committee Members:
  • Subhashinie Kariyawasam, Thesis Advisor
  • Microbiota
  • Probiotic
  • Organic
  • Conventional
  • Antimicrobial Resistance
Antimicrobial resistance of bacterial pathogens has developed into a global issue and has become an imminent threat to both human and animal health. The sub-therapeutic levels of antimicrobial supplementation in food animal feed are consistently argued to contribute to antimicrobial resistance. Not only do poultry producers use antimicrobials as feed additives, but they also utilize probiotics as a live microbial feed supplement. Probiotic supplementation positively affects the chicken by improving its intestinal balance and can be used as an alternative to antimicrobial supplementation during poultry production. The United States (U.S.) is the world’s largest poultry producer and the second largest poultry exporter, with broiler chickens comprising over four-fifths of U.S. poultry production. Because broiler producers in the U.S. use antimicrobials for disease therapy, prophylaxis, and growth promotion, it is important to understand the contribution of antimicrobial use to the emergence of antimicrobial resistant bacteria and their associated genes as well as changes in resident microbiota. The effect of supplementing commercial broiler diet with probiotics, including conventionally-fed broiler chickens, is an important concept, as the resident microbiota may be significant for the prevention of such colonization. Using a field-based trial approach, the gut microbiota and antibiotic resistance genes in broiler chickens fed with three commercial diet types: conventional (antibiotic-supplemented with and without probiotics), natural (antibiotic-free and probiotic-supplemented) and organic (antibiotic-free with organic standard probiotics), were compared with real-time polymerase chain reaction assay using the Comparative Ct method. To determine phenotypic validation of antimicrobial resistance, microbial DNA recovered from broiler chicken feces was utilized for DNA library construction. Genotypic presence of resistance genes was compared among diet types using the Comparative Ct method. It was hypothesized that the microbiota of conventionally-fed broiler chickens would be significantly different than both the microbiotas of chickens fed natural or organic diets. Furthermore, it was also hypothesized that there would be an increased amount of antimicrobial resistance genes found among broiler chickens that had been fed conventional diets when compared to broiler chickens fed a natural or organic diet. At variable levels, antimicrobial resistance can be found among every microbiota from each diet type (conventional with and without probiotics, natural, and organic). The antimicrobial resistance found in both the antibiotic-free diets (organic and natural) was not a result of the supplementation of antimicrobials in feed. However, even with antimicrobial resistance found within each broiler chicken microbiota from each diet type, chickens fed with conventional diets contained more resistance genes in feces than chickens fed with natural and organic diets suggesting the addition of antimicrobials in diet may influence the microbial community structure and increase the antibiotic resistance gene repertoire in the commercial broiler gut.