Use of a Microbiome Signature to Determine Health, Productivity and Welfare Status in Dairy Cattle

Abstract

Dairy products remain an important source of nutrition for people globally. As dairy cattle farming intensifies, there is a need to introduce innovative strategies to monitor the health, welfare and productivity of these animals. A growing number of studies highlight the use of gut microbiome signatures as diagnostic indicators for health conditions. To date, a large proportion of microbiome research in cattle has focused on 16S rRNA studies of the rumen, some of which have highlighted the association between prokaryotic taxa and certain health and productivity traits. The current study sought to investigate the oral and faecal microbiomes of dairy cows and heifers around the time of calving. Pre- and post-calving oral and faecal samples were obtained from 150 animals on two commercial UK dairy farms. Body condition, rumen fill and hock scores were assigned at each sampling timepoint and health and productivity data were collected during the lactation period. Shotgun metagenomic sequencing was employed to characterise microbial populations present in the samples and may provide an insight into the functionality of these communities. Further analysis will determine whether an association exists between these microbiome signatures and cattle health, welfare and production parameters. Data from this project will expand the currently limited bovine oral and faecal microbiome knowledge base. This may be of practical significance given the relatively accessibility of these microbiomes compared to that of the rumen; the oral and faecal microbiomes could serve as important tools to predict and monitor the wellbeing and productivity of dairy cattle