Shift of Microbiota and Modulation of Resistome in the Ceca of Broiler Chicken Fed Berry Pomace Alone or in Combination of a Multienzyme Mixture

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Alternative feed additives are being investigated due to the restriction of antibiotics use to decrease antimicrobial resistance (AMR) in food-producing animals. This study investigated the effects of dietary American cranberry (Vaccinium macrocarpon) and wild blueberry (V. angustifolium) pomaces on the cecal microbiota and resistome profiles as well as the short-chain fatty acid levels. Male broiler chickens Cobb500 were fed a basal diet with either 55 ppm bacitracin methylene disalicylate (BMD); 0.5% (CRP0.5) and 1% (CRP1) cranberry pomace; and 0.5% (LBP0.5) and 1% (LBP1) lowbush blueberry pomace with or without a multienzyme mixture (ENZ). The results showed that at 21 days of age, the total coliform counts decreased in the CRP0.5-fed birds compared to BMD (p < 0.05). The use of pomace significantly increased the abundance of Lactobacillus and Bacteroides regardless of ENZ, while CRP decreased the Proteobacteria phylum abundance. In-feed ENZ tended to increase the relative abundance of genes conferring aminoglycoside resistance. Treatment with CRP0.5 decreased the abundance of cepA genes encoding for macrolide (MACROLIDE) and lincomycin (InuD) resistance while increasing those for tetracycline (tetO and tetX) resistance. These results showed, for the first time, the potential of the studied enzymes in influencing berry pomace’s effects on antimicrobial resistance gene profiles in broilers.