Effects of a simple or a complex starter microbiota on intestinal microbiota composition in caesarean derived piglets

Variations in early gut microbial colonization has been implicated in mucosal and systemic immune development. Early microbial colonization of the intestine in piglets may be influenced by conditions and management in the farrowing house. The objective of this study was to investigate the effect of the management on the long-term development of intestinal immunity in growing pigs. Three management system were compared that only differed from each other in the use of antibiotics and stress factor at d 4 after birth. The used antibiotic is commonly applied in practice to prevent and/or reduce infections of the respiratory tract. The stress factors included the commonly applied practices of weighing, ear-tagging, and tail docking in pig husbandry. To investigate the effects on intestinal immunity, we performed genome-wide gene expression analyses at 2 different intestinal locations, jejunum and ileum, and at 3 different time points (8, 40, and 180 d) after birth. Differentially expressed genes were identified by pair-wise comparisons between treatment groups and tissues per time point. Functional analysis of the differentially expressed genes was used to identify intestinal processes that differed between the experimental groups. Luminal contents of the intestines were stored for analysis of microbiota composition. The results indicate that the antibiotic treatment and the applied stress factors at d 4 after birth greatly affect the expression of immune related genes in jejunum and ileum later in life. This suggest that both treatments have an effect on the development and/or activity of immune related processes in the gut of growing pigs. We hypothesize that these differences may be related to management-mediated variations in the early colonization of the gut by microbiota.