Comparison of rumen bacterial communities in dairy herds of different production

Abstract

Background: The purpose of this study was to compare the rumen bacterial composition in high and low yielding dairy cows within and between two dairy herds. Eighty five Holstein dairy cows in mid-lactation (79-179 days in milk) were selected from two farms: Farm 12 (M305 = 12,300 kg; n = 47; 24 primiparous cows, 23 multiparous cows) and Farm 9 (M305 = 9700 kg; n = 38; 19 primiparous cows, 19 multiparous cows). Each study cow was sampled once using the stomach tube method and processed for 16S rRNA gene amplicon sequencing using the Ion Torrent (PGM) platform.

Results: Differences in bacterial communities between farms were greater (Adonis: R² = 0.16; p < 0.001) than within farm. Five bacterial lineages, namely Prevotella (48-52%), unclassified Bacteroidales (10-12%), unclassified bacteria (5-8%), unclassified Succinivibrionaceae (1-7%) and unclassified Prevotellaceae (4-5%) were observed to differentiate the community clustering patterns among the two farms. A notable finding is the greater (p < 0.05) contribution of Succinivibrionaceae lineages in Farm 12 compared to Farm 9. Furthermore, in Farm 12, Succinivibrionaceae lineages were higher (p < 0.05) in the high yielding cows compared to the low yielding cows in both primiparous and multiparous groups. Prevotella, S24-7 and Succinivibrionaceae lineages were found in greater abundance on Farm 12 and were positively correlated with milk yield.

Conclusions: Differences in rumen bacterial populations observed between the two farms can be attributed to dietary composition, particularly differences in forage type and proportion in the diets. A combination of corn silage and alfalfa silage may have contributed to the increased proportion of Proteobacteria in Farm 12. It was concluded that Farm 12 had a greater proportion of specialist bacteria that have the potential to enhance rumen fermentative digestion of feedstuffs to support higher milk yields.

Keywords: Dairy cows; Dairy herds; Rumen microbiota.

Fig. 1

Biplot of weighted UniFrac beta diversity plot, labels for the most 5 abundant genus-level taxa added. The size of the sphere for each taxon is proportional to the mean relative abundance of that taxon across all samples. This plot is created by the QIIME command make_emperor.py

Fig. 2

Heatmap showing the distribution of OTUs assigned to Succinivibrionaceae family in dairy cows in Farm 12 and Farm 9

Fig. 3

Correlation between production variables and abundant ruminal bacterial genera. The scale colors denote whether the correlation is positive (closer to 1, blue squares) or negative (closer to −1, red squares) between the taxa and the production parameters. The taxa colors red, dark green and blue denotes the genus of Bacteroidetes, Firmicutes and Proteobacteria respectively