Comparison of rumen microbial communities in dairy herds of different production

In the US, there is a substantial difference in annual milk production between dairy herds.  We hypothesized that the rumen microbial composition will be different between higher and lower yielding dairy herds and that each dairy herd will have a distinct microbial  fingerprint.  This study included 85 Holstein dairy cows from two farms: Farm12 (M305;, 12,324 kg; n=47; primiparous cows: 24, multiparous cows: 23) and Farm9 (M305;, 9,693 kg; n=38; primiparous cows: 19, multiparous cows: 19).  Bacterial diversity from rumen samples was characterized using 16S rRNA gene sequencing using Ion Torrent (PGM)Ion Torrent platform.   Differences in microbial communities between farms were greater  (p<0.001) (adonisAdonis:; R2=0.16;, p<0.001) than within farm.  Five bacterial lineages namely Prevotella (48-51 %), Bacteroidales (10-12 %), Unclassified bacteria (5-8 %), Succinivibrionaceae (1.4-6.6 %) and Prevotellaceae (3.8-4.7 %) were observed to differentiate the community clustering patterns between the two farms. A notable finding is the greater (p<0.05) contribution of Succinivibrionaceae in Farm12 compared to Farm9. Furthermore, in Farm12, this bacterial populations was higher (p<0.05)  in the high yielding cows compared to low yielding cows in both parity groups. Prevotella, S24-7 and Succinivibrionaceae were found to be positively correlated with fat corrected milk and feed efficiency, and a majority of Firmicutes genera were found to be positively correlated with milk fat ( %) and protein ( %). It was concluded that characterizing ruminal microbiota across elite herds is required to identify specialist rumen microbes across herds varying in milk production.