Investigation and subsequent manipulation of the\ud intestinal microbiota of pigs, with a view to\ud optimising feed efficiency

The objectives of this thesis were (1) to explore a possible link between the intestinal\ud microbiota and feed efficiency (FE) in pigs and (2) to investigate microbiotamodulating\ud strategies to improve FE. Two studies were conducted in pigs ranked on\ud divergence in residual feed intake (RFI; a metric for FE); one in Ireland only and one\ud across three geographical locations. Microbial diversity, composition and potential\ud functionality were assessed in faecal and digesta samples, using high-throughput 16S\ud rRNA gene sequencing. In both studies, RFI-associated microbes were identified, albeit\ud most at low relative abundance, with increases in bacterial taxa associated with\ud improved metabolism and health found in low RFI (highly efficient) pigs. These\ud bacterial taxa could potentially be exploited in the future as biomarkers for FE, targets\ud for nutritional strategies, or probiotics, to improve FE. However, no FE-associated\ud microbial taxon was common to all geographical locations, highlighting the influence of\ud rearing environment on the intestinal microbiome. Manipulation of the microbiome\ud with a view to improving FE was investigated in two studies. Firstly, faecal microbiota\ud transplantation (FMT) was performed in pregnant sows and/or their offspring.\ud Although RFI tended to be lower (better FE), slaughter weight was reduced by FMT,\ud and offspring harboured more potentially pathogenic and fewer beneficial microbes.\ud Secondly, inulin was fed to weaner pigs born to sows in the FMT study. No\ud improvements in growth were observed, but RFI was lower in inulin-fed pigs from\ud FMT sows, and decreases in potentially pathogenic microbes were observed. While\ud these findings have negative implications for the use of FMT to improve FE in pigs,\ud they demonstrate the considerable impact of early life intestinal microbiota on pig\ud growth. In conclusion, the work from this thesis demonstrates a possible link between\ud the intestinal microbiota and FE in pigs, but further work is needed to investigate\ud causality