Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast

The objective of the current study was to employ a DNA-based sequencing technology to study the effect of active dry yeast (ADY) supplementation, diet type, and sample location within the rumen on rumen bacterial community diversity and composition, and to use an RNA-based method to study the effect of ADY supplementation on rumen microbial metabolism during high-grain feeding (HG). Our previous report demonstrated that the supplementation of lactating dairy cows with ADY attenuated the effect of subacute ruminal acidosis. Therefore, we used samples from that study, where 16 multiparous, rumen-cannulated lactating Holstein cows were randomly assigned to 1 of 2 dietary treatments: ADY (Saccharomyces cerevisiae strain Y1242, 80 billion cfu/animal per day) or control (carrier only). Cows received a high-forage diet (77:23, forage:concentrate), then were abruptly switched to HG (49:51, forage:concentrate). Rumen bacterial community diversity and structure were highly influenced by diet and sampling location (fluid, solids, epimural). The transition to HG reduced bacterial diversity, but epimural bacteria maintained a greater diversity than fluid and solids. Analysis of molecular variance indicated a significant separation due to diet × sampling location, but not due to treatment. Across all samples, the analysis yielded 6,254 nonsingleton operational taxonomic units (OTU), which were classified into several phyla: mainly Firmicutes, Bacteroidetes, Fibrobacteres, Tenericutes, and Proteobacteria. High forage and solids were dominated by OTU from Fibrobacter, whereas HG and fluid were dominated by OTU from Prevotella. Epimural samples, however, were dominated in part by Campylobacter. Active dry yeast had no effect on bacterial community diversity or structure. The phylum SR1 was more abundant in all ADY samples regardless of diet or sampling location. Furthermore, on HG, OTU2 and OTU3 (both classified into Fibrobacter succinogenes) were more abundant with ADY in fluid and solids than control samples. This increase with ADY was paralleled by a reduction in prominent Prevotella OTU. Metatranscriptomic profiling of rumen microbiome conducted on random samples from the HG phase showed that ADY increased the abundance of the cellulase endo-β-1,4-glucanase and had a tendency to increase the hemicellulase α-glucuronidase. In conclusion, the shift from high forage to HG and sampling location had a more significant influence on ruminal bacterial community abundance and structure compared with ADY. However, evidence suggested that ADY can increase the abundance of some dominant anaerobic OTU belonging to F. succinogenes and phylum SR1. Further, microbial mRNA-based evidence suggested that ADY can increase the abundance of a specific microbial fibrolytic enzymes.