The dynamics of the microbiome of Swiss dairy cows Thesis by Karin Meier

Increasing herd sizes and animal movements intensify the exchange of microbiota in livestock -between individuals as well as herds. Next Generation Sequencing (NGS) allows to study the dynamics of this exchange and how it may influence animal health.
The aim of the present study is to compare the virome and the microbiome of dairy cows before and after herds are intermingled. This can provide novel information on how diverse viral and bacterial communities of different dairy herds may be and how they interact if herds are mixed.
Three independent dairy herds were united to one herd of 120 cows in a newly built barn. Of each cow a nasal swab and a faecal sample were taken before and 6 months after the herds were brought together. The virome is determined using our in-house ViroScreen (PDF, 376 KB) protocol that includes a relative enrichment of virus particles, followed by shotgun sequencing. The Microbiome is analysed by NGS of the bacterial 16S gene after PCR amplification.
Preliminary results show that changes in bacterial abundance in nasal swabs are different than in faeces. The nasal microbiome, once established, shows a herd specific pattern to a new environment while the faecal microbiome changes for all animals similarly upon moving to the new barn. 
Virome analysis is still ongoing. Preliminary results show the presence of Rotavirus A, Sapelovirus, Ungulate bocaparvovirus 6, CRESS (circular Rep-encoding ssDNA) virus and Faecal-associated gemycircularvirus 6 in the nasal swabs. Specific testing for known pathogens of the respiratory tract of cattle will follow as well as the analysis of the faecal virome.