Microbial diversity in the large intestine of pigs born and reared in different environments

Pigs born outdoors and reared on deep litter (straw) have been reported to experience less of a growth check after weaning and have a higher dressing percentage than counterparts born and reared under conventional (indoor) systems. The reason(s) for this difference is/are presently unknown, but differences in the gut environment might contribute to these observations. PCR-DGGE techniques were used in this study to examine microbial diversity and banding patterns in the large intestine of piglets that were reared under different rearing conditions. Six piglets per treatment were euthanised at weaning (21 days) and at 7 days and 21 days after weaning from two extreme treatments indoor-born: conventionally-raised after weaning (‘Indoor’) or outdoor-born, deep-litter raised after weaning (‘Outdoor’)]. The Shannon diversity index was calculated, and multivariate analysis of banding patterns was performed. Indoor pigs had a more diverse bacterial population at weaning and 21 days after weaning than Outdoor pigs. However at the end of the first week after weaning, outdoor-born and deep-litter pigs had a more diverse microbiota. The Shannon diversity index continued to increase with time after weaning in Outdoor pigs, which did not occur in Indoor pigs. Multivariate analysis of banding patterns showed there was a trend (P = 0.109) for a difference in microbial structure depending on housing type. There was also a significant (P < 0.001) effect of sampling time after weaning and a significant interaction (P < 0.001) between housing and time after weaning.