Cow microbiome from antepartum to postpartum: a long-term study covering two physiological challenges

This long-term study investigated the ruminal and duodenal microbiota during calving as individual challenge and an LPS induced inflammation as standardized challenge. An intensive sampling along the trial showed the impact of the two individual stress situations on the host and the intestinal microbiome. Eight rumen and duodenum fistulated Holstein dairy cows were sampled at 12 time points from 42 days antepartum (ap) to 126 days postpartum (pp). The cows were divided into a control and a carnitine supplemented group (n=4 each). From 73 rumen fluid (RUM) and 75 duodenal fluid (DUO) samples, metabolites were identified and quantified using nuclear magnetic resonance technique (NMR). Illumina amplicon sequencing of 16S rRNA gene was done with both sample types and time points leading to 2,658 operational taxonomic units (OTUs) that were grouped into 16 bacterial phyla, 65 families (including 26 unclassified), 102 genera (including 53 unclassified). The bacteriome in the rumen and duodenal fluid changed remarkably over the transition period (p=<0.001) and an abrupt shift was caused by the LPS injection. Carnitine supplementation did not have an impact on the microbial or metabolite composition. Strong animal individual shifts were noted during the complete trial period. Differences were seen between time points as well as for single OTUs such as Bifidobacterium spp. and Treponema spp.. Metabolites, such as fatty and amino acids, amines and urea showed clear variations along the trial period.Conclusion: The present study demonstrated the differential changes of the microbial community composition and metabolic processes during two individual physiologic challenges. This is the first long-term challenge study comparing microbial and metabolic interactions in rumen and duodenal fluid during the critical transition calving time of the dairy cow.