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Initial effects of supplemental forages and feedstuffs on bovine rumen ecology in vitro as determined by DNA-based molecular procedures

ABSTRACT This research aided in determining the impacts on rumen microbial ecology when supplemental forages and feedstuffs were added for 48 h after an initial 24-h in vitro rumen fermentation of orchardgrass (Dactylis glomerata L.) hay. Short-term shifts in bovine rumen community structure (bacteria, archea, protozoa, and fungi) resulting from each separate forage and feedstuff addition were measured using unique operational taxonomic units (OTU)s contained in terminal-restriction fragment length polymorphism (T-RFLP) profiles. The Tukey Vacuum Cleaner Analysis (TVCA) model of bacteria accounted for 66.3% of the treatment variance and OTUs clustered into 3 distinct groupings. The model developed for TVCA analysis of archaea accounted for 76.6% of the treatment variance and OTUs clustered into 2 distinct groupings. The TVCA treatment variance of protozoa accounted for 75.8% and OTUs clustered into 3 distinct groupings. Additions of various forages and feedstuffs did not result in shifts in fungal community structure in the short-term experiment. Our results demonstrate that the rumen ecology using initial T-RFLP profiles in vitro of bacteria, archaea, and protozoa and a TVCA analysis can identify pattern groupings of forages and feedstuffs. Groupings of forages and feedstuffs can help refine supplementation for improved nutritional management of ruminants.