Correlating feed efficiency with ruminal bacterial, fungal and archaeal community composition in dairy cows over two lactations

A same-aged group of 14 Holstein cows was followed through the course of their first two lactation cycles (2012-2014). During each lactation cycle the ruminal solids and liquids, milk samples and production data, and feed consumption values were collected for Early (76-82 days in milk, or DIM), Middle (151-157 DIM), and Late (251-257 DIM) lactation periods. Using the Illumina MiSeq, we sequenced the V4 region of the 16S rRNA gene for bacterial identification, ITS4 for fungal identification and V6-V8 region of the 16S rRNA gene for archaeal identification. These sequences were used to investigate links between the ruminal microbial community and host production over time.