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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #412210
Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: A metagenomics perspective to evaluate probiotics combating Salmonella Infantis in poultry settings – a case study

Author
item Li, Xiang
item Oladeinde, Adelumola - Ade
item Rothrock, Michael
item AGGREY, SAMUEL - University Of Georgia
item HAMAOKA, TOMOHIRO - Calpis America
item ABDO, ZAID - Colorado State University
item Buhr, Richard - Jeff
item Pokoo-Aikins, Anthony

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 3/6/2024
Publication Date: 6/13/2024
Citation: Li, X., Oladeinde, A.A., Rothrock Jr, M.J., Aggrey, S.E., Hamaoka, T., Abdo, Z., Buhr, R.J., Pokoo-Aikins, A. 2024. A metagenomics perspective to evaluate probiotics combating Salmonella Infantis in poultry settings – a case study. American Society for Microbiology. ASM Microbe: 2024.

Interpretive Summary:

Technical Abstract: Probiotics, as alternatives to antibiotics, are used as feed supplements; however, their efficacy in controlling food-borne pathogens remains uncertain. In this study, 260 male and 260 female 1-day-old Cobb 500 broiler chicks were randomly assigned (a total of 13 males and 13 females in each floor pen; 4 - 6 floor pens per treatment) to four categorical groups: (T1) Commercial probiotic (added to feed), (T2) ARS probiotic (applied to litter), (T3) No probiotic (Salmonella positive control), and (T4) No probiotic (Salmonella negative control). At day zero, six birds from each pen in T1, T2, and T3 were gavaged with a cocktail of an antibiotic-susceptible and multidrug-resistant strain of Salmonella Infantis. After 7 days of infection, cecal DNA samples from six chickens in each of the treatment groups (T1, T2, T3, and T4) were extracted and sequenced using shotgun metagenomics. Shannon alpha diversity index results showed chickens exposed to probiotics (T1 and T2) exhibited a more diverse microbiome, and the most abundant species were Faecalibacterium spp. (8.04±9.29% in T1), Lachnospiraceae spp. (12.50±10.88% in T2), Enterococcus hirae (4.17±3.91% and 6.93±6.51% and in T1 and T2, respectively), and Lactobacillus crispatus (4.89±5.45% and 4.40±5.53% in T1 and T2, respectively). Notably, taxa related to Enterobacteriaceae represented only 0.61% to 2.17% of the total cecal microbiome for each treatment group; however, within Enterobacteriaceae, the relative abundance of Salmonella was significantly lower (p<0.019) in the probiotic treatments (15.13±22.12% and 11.20±8.02% for T1 and T2, respectively) compared to the no-probiotic, positive control treatment (T3; 31.28±22.25%). Lastly, aminoglycoside resistance genes (aad(6) and aph(3')-IIIa) were significantly higher in T1 and T2 compared to T3 (p<0.01), but no significant differences were noted between T1 and T2 (p>0.05). Tetracycline resistance gene tet(O) and total copper compound resistance genes were significantly higher in T2 than T1 (p<0.01). In summary, our study demonstrated that probiotics altered the cecal microbiome of chickens and reduced the relative abundance of Salmonella, however, the magnitude of change differed between probiotics.