Weaning is a critical developmental event in the young pig as it relates to the establishment of the commensal microbiota and immunological development. Furthermore farm production systems can have dramatic impacts on the development of these events and their continued progression later in the production cycle. Terminal restriction fragment length polymorphism (TRFLP) and flow cytometry analyses were performed to investigate the microbial community and associated immune system development between pigs weaned to an on-site conventional (CONV) and a segregated early weaning (SEW) facility. Ordination methods were performed to determine the relationship of specific TRF peaks and immune measurements to each management system. Jejunal intraepithelial (IEL) activated and γδ lymphocyte populations were positively associated with CONV pigs, whereas activated CD8+ T cells and T cells with memory phenotypes in IEL were positively associated with SEW pigs. TRFLP analysis indicated peaks putatively containing Lactobacillus sp. and Pediococcus sp. whose presence in the gastrointestinal tract was positively correlated to SEW pigs post-weaning. TRF peak B100 was positively correlated to CD8+ and memory T cell phenotypes in the peripheral blood and jejunal IEL compartment, and negatively correlated to CD3+ T cells in blood. Peaks B262 and B269 were positively correlated to activated and γδ T cell populations in IEL and blood, and negatively correlated to T cells with memory phenotypes in IEL. TRF peak H341 was positively correlated to memory T cell phenotypes in the blood and activated leukocytes in IEL, and negatively correlated to γδ T cell populations. These data demonstrate divergent development of specific members of the microbial community and their relationship to immune development between swine management systems.

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