Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep

Abstract Background Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. It has been the subject of decades of research, but little attention has been paid to the role of the gut microbiota in the responses to infection. The present study characterized the microbiome along the gastro-intestinal tract (GIT) of sheep and tested whether it had been affected by three decades of breeding for resistance to helminth infection. Australian Sheep Breeding Values (ASBVs) for faecal egg count (FEC) were used to select the 10 most worm-susceptible (High-FEC) and 10 most worm-resistant (Low-FEC) animals. DNA was extracted and sequenced for 16S rRNA gene from faeces and from the lumen of the rumen, abomasum, duodenum, jejunum, ileum, caecum, and colon. Results The most frequent genera identified along the GIT were Eubacterium, Oscillibacter, and Ruminococcus. Intersectoral-specialization zones were identified along the GIT, with the duodenum revealing major differences between the High-FEC (helminth-susceptible) and Low-FEC (helminth-resistant) animals in values for Alpha and Beta diversity. The High-FEC and Low-FEC sheep differed significantly for three phyla (Firmicutes, Elusimicrobia, Chloroflexi) and 11 genera. At other GIT sites, Firmicutes was the most abundant phylum followed by Bacteroidetes, and Proteobacteria presenting no major differences between High-FEC and Low-FEC. Conclusions The gastro-intestinal microbial profile varies widely between helminth-resistant and helminth-susceptible sheep. Each GIT section appears to supports a particular bacterial composition leading to inter-sectoral differences among the various microbial communities. The animal’s duodenum creates the right environment which results in a more diverse and richness microbial population in the helminth-resistant sheep and suggests that this population favours bacterial genera that generally ferment carbohydrates. The energy metabolism of sheep is largely based on the production of volatile fatty acids (acetate, butyrate, propionate) in the rumen, raising the possibility that butyrate-producing bacteria in the duodenum of helminth-resistant sheep, modulate the host’s metabolism and assist in the regulation of the parasite burden.