Gut Microbiome and Incidence of Foodborne Pathogens are affected by diet in pasture-raised Chickens.

Authors: LOURENCO, JEFERSON - University Of Georgia; Rothrock, Michael; SANAD, YASSAR - University Of Arkansas; FLUHARTY, FRANCIS - University Of Georgia; CALLAWAY, TODD - University Of Georgia

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/15/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary: Consumer demands have led many pastured poultry operations to feed soy-free diets to their birds. However, the impacts of such diets on the gastrointestinal microbiome of pasture-raised chickens is still unclear. Using a farm-to-fork approach, this study aimed to examine the effects of feeding two distinct diets – soy-containing (SB), and soy-free (SF) – on the gut microbiome of pasture-raised chickens. Microbial DNA was extracted, and 16r RNA gene sequencing was performed on: cecal contents of 1-day-old birds, feces collected from their pastures (at 4, 7 and 12-weeks-old), cecal contents obtained at the slaughter house, whole carcass rinses (WCR) obtained at the slaughterhouse, and WCR obtained from final products (after carcasses were frozen for 1 month). Results showed that the number of observed OTUs significantly increased (P < 0.001) as birds fed the SF diet aged (from 1-day-old to 12-weeks old); however, no significant differences (P = 0.11) in the number of OTUs were observed as SB-fed birds aged. Furthermore, regardless of diet and the type of sample collected, there was a predominance of the phylum Firmicutes in all samples throughout the birds lifecycle, which ranged from 58 to 91% of all OTUs. The abundance of the genera Oscillospira, Faecalibacterium and Ruminococcus increased as birds aged (P ' 0.001), whereas abundance of Lactobacillus decreased (P ' 0.02) in both SB and SF diets. For bacterial groups regarded as foodborne pathogens, there was no difference (P ' 0.15) in Salmonella abundance between SB and SF in any sample type; however, SF broilers had a lower abundance of Campylobacter during their entire lifecycle. This effect was particularly pronounced in the fecal material collected when birds were 12-weeks-old (P = 0.003) as well as in the WCR obtained from the final product (P = 0.04). Acinetobacter abundance was also lower (P = 0.05) in the WCR from birds consuming SF. These findings demonstrate that the feed offered to pasture-raised broilers can significantly affect their gut microbial populations. Moreover, they suggest that the use of soy-free diets may represent a viable strategy to reduce contamination of carcasses in pasture-raised chicken production systems, since the incidence of foodborne pathogens such as Campylobacter and Acinetobacter were reduced in broilers fed SF.

Technical Abstract: Consumer demands have led many pastured poultry operations to feed soy-free diets to their birds. However, the impacts of such diets on the gastrointestinal microbiome of pasture-raised chickens is still unclear. Using a farm-to-fork approach, this study aimed to examine the effects of feeding two distinct diets – soy-containing (SB), and soy-free (SF) – on the gut microbiome of pasture-raised chickens. Microbial DNA was extracted, and 16r RNA gene sequencing was performed on: cecal contents of 1-day-old birds, feces collected from their pastures (at 4, 7 and 12-weeks-old), cecal contents obtained at the slaughter house, whole carcass rinses (WCR) obtained at the slaughterhouse, and WCR obtained from final products (after carcasses were frozen for 1 month). Results showed that the number of observed OTUs significantly increased (P < 0.001) as birds fed the SF diet aged (from 1-day-old to 12-weeks old); however, no significant differences (P = 0.11) in the number of OTUs were observed as SB-fed birds aged. Furthermore, regardless of diet and the type of sample collected, there was a predominance of the phylum Firmicutes in all samples throughout the birds lifecycle, which ranged from 58 to 91% of all OTUs. The abundance of the genera Oscillospira, Faecalibacterium and Ruminococcus increased as birds aged (P ' 0.001), whereas abundance of Lactobacillus decreased (P ' 0.02) in both SB and SF diets. For bacterial groups regarded as foodborne pathogens, there was no difference (P ' 0.15) in Salmonella abundance between SB and SF in any sample type; however, SF broilers had a lower abundance of Campylobacter during their entire lifecycle. This effect was particularly pronounced in the fecal material collected when birds were 12-weeks-old (P = 0.003) as well as in the WCR obtained from the final product (P = 0.04). Acinetobacter abundance was also lower (P = 0.05) in the WCR from birds consuming SF. These findings demonstrate that the feed offered to pasture-raised broilers can significantly affect their gut microbial populations. Moreover, they suggest that the use of soy-free diets may represent a viable strategy to reduce contamination of carcasses in pasture-raised chicken production systems, since the incidence of foodborne pathogens such as Campylobacter and Acinetobacter were reduced in broilers fed SF.