Effects of enriched pig housing on gut microbiome and immunology

A previous study showed that enriched housing increased disease resilience of piglets. The present study assessed whether disease resilience could be associated with housing-induced changes in gut microbiota composition. We studied the microbiota of piglet faeces at weeks 2, 4, 5, 7, and 9 after birth, and of the lumen of jejunum, ileum, and colon at week 9 by 16S rRNA gene sequencing, as well as various immunological parameters, comparing 8 piglets per group in enriched (E) and standard barren (B) housing, respectively. Piglets were weaned after sampling at week 4. Enriched housing provided double space and rooting substrate of peat and wood shavings.Both in faeces and gut luminal contents, and regardless of group or time point, the microbiota of individual piglets was dominated by Firmicutes, with Lactobacillusbeing in general the most predominant genus. Groups did not differ in overall community structure and composition in faeces or gut luminal contents. Before weaning, the faecal microbiota of piglets was numerically more diverse in E than in B, and inter-individual distance in microbiota composition within E was larger than within B. After weaning, these differences between groups became smaller. Ileal (week9) microbiota showed distinct grouping of B and E group animals when using Principal Coordinate Analysis of weighted Unifrac and Bray-Curtis distances (p<0.05). Moreover, inter-individual variation for ileum and colon communities was clearly lower within E than within B (p<0.005). Next step is to link these results to the performance, behavioural, and immunological parameters studied in both groups.