“…Under normal rearing conditions, chickens adapted to rearing-related factors have a balanced gut microbiota composition, maintaining its optimal function in feed digestion, nutrient resorption, synthesis of biochemicals, and neural and immune regulation [ 112 , 113 ]. However, under certain conditions, these management-associated stressors have negative effects on the gut microbial structure and functions by (1) disrupting the commensal bacterial populations and colonization (the stability of the gut microbiota), thus reducing beneficial bacteria and increasing pathogenic variant (low-grade inflammation); (2) increasing pathogen survival and invasive capability (bacterial translocation to increase neuroinflammation); (3) disrupting the absorption of nutrients and minerals including calcium, a key bone mineral; (4) disrupting microbial neuroendocrine functions (producing several signaling molecules and neurochemicals including serotonin (5-HT); (5) disrupting the gut epithelial barrier, thereby increasing intestinal permeability causing the gut to leak certain bacteria and harmful substances into the bloodstream (leaky gut), resulting in inflammation and or infection; and (6) damaging epithelial cells, thus producing free radicals and reducing antioxidant efficacy (oxidative stress) [ 31 , 114 , 115 , 116 , 117 , 118 ]. These changes resulted from the gut microbiota alterations (imbalanced microbiota composition with dysfunction) that influenced host behavioral display and health status via the nerve systems (i.e., the vagus nerve, enteric nerve, and autonomic nervous system), hormone signaling, immune system, and microbial metabolites (such as short chain fatty acids) to regulate the function of the gut–brain and gut–immune axes ( Figure 3 ).…”