Assessment of the Impact of Different Feeding Strategies on Chicken Gastrointestinal Tract by Shotgun Metagenomic Sequencing to Fight Colonization by Potential Foodborne Pathogens

The objective of my study was to characterize the impact of the administration of different feed additives on gut and skin microbiome of commercial chickens in order to find nutritional strategies able to fight foodborne pathogens colonization in these animals, improving safety of poultry meat and avoiding the use of antibiotics. The administration of Lactobacillus acidophilus D2/CSL in the feed showed to positively affect species belonging to Clostridium clusters IV (Faecalibacterium prausnitzzi, Subdonigranulum variabile) and XIVa (Roseburia intestinalis) producing butyric acid involved in the protection against pathogens. Furthermore, R. torques, which degrade gut mucin potentially exposing the gut cells to pathogens, was significantly lowered by the probiotic administration. The chicken fed with the probiotic showed a significantly higher level of β-glucosidase contributing to the hydrolysis of glucose monomers from non-starch polysaccharides, playing an important role in the fermentation of undigested carbohydrates. The administration of serine protease in the feed decreased abundance of Lactobacillaceae at 14 days even if they increased over time. Faecalibacterium praustnizii, as well as Sudoligranum variabile decreased in the caeca of chickens fed with serine protease in comparison to the control at 42 days. All signature species of the caeca of chickens fed with serine protease at 14 days belonged to Bacteroidetes. In the caeca of chickens fed with phytase, the abundance of Erysipelotrichaceae, a family associated to butyryl-CoA production enzymes, significantly decreased along with Lactobacillaceae family which is involved in the stimulation of immune responses and in the improvement of digestive health and growth performance in poultry. The effect of phytase on chicken skin microbiota lead to mostly the reduction of spoilage genera and species in the treated groups compared to the control. The reduction of these genera and species, responsible of the spoilage of meat, could allow to heighten the quality of poultry meat product.