Antimicrobial use (AMU) in broiler production is highly regulated in many countries due to antimicrobial resistance (AMR) concerns, resulting in the use of alternative products including probiotics and phytochemicals. There are many studies that investigated the impacts of AMU on AMR in broilers, but there are limited studies evaluating how alternative production systems such as organic and raised without antibiotics (RWA) impact AMR. First study investigated the AMR and gut microbiota profiles of broilers raised in different feeding programs: conventional (CON), raised without medically important antibiotics (RWMIA), and raised without antibiotics (RWA). Results demonstrated the prevalence of AMR Escherichia coli in all three feeding programs, however, revealed sex-specific differences in AMR to ciprofloxacin, tetracycline, and gentamicin. Gut microbiota analyses revealed significantly different cecal community diversities and bacterial taxa between feeding programs. Specifically, Enterococcus was more abundant in RWA compared to other programs, where abundances in RWA females were higher than males. Second study evaluated the in-vitro characteristics of Lactobacillus reuteri isolated from cranberry pomace-fed broilers for their probiotic potential. Lactic acid bacteria (LAB) strains were identified as L. salivarius, L. johnsonii, L. reuteri, and L. crispatus, where they demonstrated tolerance and stability in acidic environments and presence of bile salts and ability to autoaggregate and bind to hydrophobic surfaces. Of all Lactobacillus isolates, L. reuteri was demonstrated the best probiotic characteristics, with low presence of antimicrobial resistance genes (ARGs) and no virulence genes. Reuterin (L. reuteri bacteriocin) exhibited antimicrobial activity against gram-negative and gram-positive bacteria, while exposed to digestive enzymes, and stable in acidic environments, NaCl, and bile salts. The third study evaluated the in-vivo impacts of the L. reuteri isolate in broilers alone or in combination with cranberry and blueberry pomaces on anti-coccidial effects, growth performance, and AMR. Growth performance, body parameters, lesion scores, and oocyst counts revealed that broilers fed berry pomace in combination with L. reuteri showed potential in controlling coccidiosis while maintaining performance. Microbiota analysis revealed L. reuteri was prevalent in high abundance in market weight broilers fed the combination.