Effects of intestinal infection on the microbiome of sheep: a focused study on Johne’s disease and round worms

Abstract

The gastrointestinal microbiome plays an invaluable role in the maintenance and wellbeing of their host. They are important in the development of host immunity and host digestion. Despite their vital importance, there is still much to be known about their role in the host and their diversity during bacterial and parasitic infections. In the first part of this study, we examined the gut microbiome of 40 sheep (gimmers) infected only with gastrointestinal nematodes. Rectal faecal samples were taken before treatment and after treatment with anthelminthic. In the second part of the study, a total of 125 rectal faecal samples were collected from a sheep flock infected with Mycobacterium avium subspecies paratuberculosis and nematodes. Bacterial DNA was isolated from all rectal faecal samples using the MOBIO PowerFecal® DNA Isolation Kit. The faecal samples acted as a surrogate to the gastrointestinal microbiota. Bacterial and archaeal ecosystems were examined by sequencing the 16sRNA gene V4 amplicons employing the Illumina sequencing platform. Raw sequenced data was then analysed by the use of QIIME (Quantitative Insight into Microbial Ecology) with the assigning of taxonomy to the raw sequenced data and the determination of diversity within the samples. Statistical analysis was carried out using PRIMER (Plymouth Routine into Microbial Ecological Research). PERMANOVA and PERMDISP statistical tools were used to analyse the multivariate data. In the first part of the study with the nematode only infected sheep, we discovered that the gastrointestinal microbiome of sheep before and after treatment showed few differences (P>0.05). This suggest that anthelminthic treatment did not have much effect on the bacterial and archaeal community in the gastrointestinal tract. In the second part of the study with the MAP and helminth infected sheep, it was discovered that the Year 3 samples differ from the Year 2 and Year 1 samples with a P value of 0.001, suggesting that the progression of disease alters the gastrointestinal microbiome of sheep.