Causality of diarrhoea occurrence in young lambs

The aim of this study was to establish microbial colonisation in twin or triplet lambs separated into two or three experimental groups. For twin lambs, one of the siblings remained with the mother until weaning, while the other was separated from the mother shortly after birth and fed a milk replacer to avoid any contact with adult animals. For the triplet lambs, the additional experimental group consisted of lambs separated from their mothers shortly after weaning but allowed to have physical contact with other animals. Samples of the digestive contents were taken weekly from one week to one month after weaning. The microbial community was monitored using amplicon MiSeq sequencing targeting the genes of rRNA16S for bacteria and archaea, rRNA18S for eucaryotes and the D1D2 region for fungi. Additional samples were taken when diarrhoea symptoms were observed. Ewes were also sampled for digestive contents two weeks before lambing and at weaning. Microbial analysis was performed in the same way.