Rumen bacterial communities continue to shift five weeks after switching diets from conserved forage to pasture

Abstract Text:

Bacterial community structure is known to shift as a result of diet changes, but it is not known how long it takes for the bacterial populations to stabalize. The objective of this study was to characterize the weekly dynamics of rumen bacterial community composition of cows transitioning from an indoor diet, comprising of conserved forage (CF), to a pasture. Five lactating Holstein dairy cows, maintained on a CF diet during the winter season, were switched to a pasture and followed for five weeks. Individual rumen digesta samples were collected via esophageal intubation on weeks -1, 1, 2, 3, 4, and 5 relative to the diet switch. Microbial DNA was extracted and the V1-V3 region of the 16S rRNA gene was amplified. Sequence reads were obtained using Illumina MiSeq (v. 3) and sequences were analyzed using MOTHUR (v. 1.36.1). Bacterial densities (log₁₀ 16S rRNA gene copies/mL rumen digesta) were quantified by real-time PCR. Data were analyzed using a repeated measures ANOVA in SAS (v. 9.4). By week 3 on pasture, bacterial densities in rumen digesta were higher when compared to CF (8.9 vs. 9.4, 9.4, and 9.5 log₁₀ copies/mL, for weeks -1, 3, 4, and 5 respectively; P<0.01). Bacteroidetes was the predominant phylum, accounting for 48-81% of total bacteria, followed by Firmicutes (16-47%) and TM7 (0-4%). Prevotella, was the predominant genus of the Bacteroidetes phylum. By week 5 on pasture, a higher abundance was observed of both bacteria of the phylum Bacteroidetes (75.3%) and Prevotella species (72.7%) when compared to CF (65.4% and 58.3% for Bacteroidetes and Prevotella, respectively; P<0.05). The genus Ruminococcus was more abundant during weeks 1 and 2 post diet switch (3.4% for both weeks), when compared to 2.0% on week -1 of CF (P<0.01). Similarly, bacteria in the family Lachnospiraceae were more abundant during weeks 1 and 2 (8.4 and 8.2%) and then became less abundant by week 5 of cows grazing pasture (3.1%) when compared to week -1 of cows on a CF diet (5.4%; P<0.05). Butyrivibrio species were more abundant on week 4 after the diet switch (3.6 vs. 1.7% for week 4 of pasture and week -1 of CF, respectively; P<0.05), then, on week 5, returned to an abundance similar to CF (1.5%). In conclusion, rumen bacterial communities are highly dynamic after a diet switch and did not stabilize within 5 weeks of cows grazing pasture.

Keywords: Illumina MiSeq, bacterial diversity, dairy cow