Effect of infection with and treatment of sensitive and resistant strains of Teladorsagia circumcincta on the ovine intestinal microbiota

The pathogenic nature of gastro-intestinal round worms has a significant effect on absorption in the gut. However, quantifying precisely the dynamics of the microbial community has not been possible until the advent of culture-independent 16S rDNA-based sequence analysis and whole genome shot gun high throughput sequencing. In this study, Illumina MiSeq technology was used to sequence amplicons of the V4 region of the 16S rRNA gene, to determine the inherent variability of the gut microbiota between samples obtained from two different areas of the intestinal tract (rectal and terminal ileum) in six identically treated sheep. The same approach was used to further define the effect of infection with and treatment of sensitive and resistant strains of T.circumcincta on the ovine intestinal microbiota, and rectal faecal composition.