Eliminating pathogenic groups with antibiotics is an obvious approach to beneficially modifying the intestinal microbiota. However, perturbation of indigenous microbial ecosystems caused by the collateral damage to desirable populations can lead to potentially serious side effects. These include antibiotic-associated diarrhea and pseudomembranous colitis involving overgrowth of Clostridium difficile as well as oral or vaginal candidiasis (173-175). Prebiotics and probiotics can ameliorate the potential of opportunistic infections caused by disturbances to the microbiota by restoring populations of beneficial bacteria (176-179). No long-term side effects have been reported for either prebiotic or probiotic ingredients, enabling their safe long-term use in prophylactic strategies to minimize disease. In contrast, long-term use of antibiotics may elicit a range of side-effects including liver damage, hypersensitivity, sensitivity to sunlight, and increasing the risk of developing antibiotic-resistant bacterial strains (180,181). This latter risk is particularly serious, and applies also to the sub-therapeutic use of antibiotics in intensive livestock farming in order to minimize infections and maximize yields, particularly for poultry and pork. Alternatives to antibiotics are urgently sought, and there has been considerable interest in the use of both prebiotics and probiotics in animal feeds to aid production. Although they have shown some promise (182,183), further research is needed into their application within an overall management strategy in order to match the performance of antibiotics.
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