New insights into cow holobiont in relation to health

Infectious diseases have been traditionally considered as the result of the bipartite interaction between a given pathogen and its host. Recent advances in high-throughput sequencing technology have uncovered the complexity of the various microbiomes associated with the host and symbiotic microbiota have emerged as a main player of the infectious process. In cattle, major efforts have been devoted to the characterization of the microbiome associated to different anatomical sites in relation to animal performance and health. However, these have mainly focused on the comparison of microbiomes of healthy versus diseased animals. Issues that remained to be addressed include the role in disease development of the microbiome associated to the affected organ as well as the impact of microbiome located at remote body sites. Here, we propose to explore the structure, diversity and dynamics of microbiomes associated to 4 anatomical sites in cows before and after calving. The interdependence of these microbiomes in relation to animal health and genetics will also be investigated. 2.Material and methods Over one thousand samples were collected from 45 primiparous prim’ Holstein cows selected from two divergent lineages that are respectively more or less susceptible to mastitis. Sampling were performed at 4 time points from 1week pre-partum to 7 months post-partum and from 4 anatomic sites: nasal, genital, buccal (as a proxy for rumen), and foremilk (as a proxy for internal teat microbiome). For each sample, we performed 16S and ITS metabarcoding sequencing and used DADA2 [1] to characterize the communities using Amplicon Sequence Variant (ASV, analogue of OTU) table. We then performed diversity analyses on the ASV count table using Phyloseq [2]. 3.Results We first show that the 4 sites harbor different microbiota both in terms of richness and ASV repertoire. We then use alpha- and beta-diversity analyses to show how the composition evolves in time and differs between lineages. Finally, we will also present the results obtained while performing differential abundance analysis within each site to identify the differentially abundant taxa, i.e. taxa whose abundances that differ between lineages.