Diurnal shifts of rumen fermentation and microbial profiles revealed circadian rhythms of rumen bacteria, methanogens, and protozoa under high-grain and high-forage diets

In this study, we investigated how the composition and population of rumen microbiota shifted in response to diurnal oscillations under 2 different diets (high grain vs high forage). Five multiparous Holstein dairy cows with similar body weight, days in milk, and parity were enrolled in this study. The cows were fed high-grain (HG) diet for 21 d and then shifted to high-forage (HF) diet in the next 21 d (7-d washout and 14-d experimental period). During the experimental period, dry matter intake (DMI) and rumination activity were recorded, and rumen fluid was collected 8 times post-feeding every 6 h during the last 2 d of each dietary feeding period. The rumen microbial (bacterial, archaeal, and protozoal) population and composition were assessed using quantitative PCR and amplicon sequencing respectively. The daily dynamic of measurements was assessed using cosinor model. The associations between microbial taxa and rumen fermentation profiles were assessed using linear mixed model, in which the cows were termed as random intercept effects. Daily rhythmicity was observed for DMI, rumination activity, and rumen fermentation profiles under both diets. Additionally, rumination time, rumen pH, and acetate/propionate ratio had a higher mesor (the average level of diurnal fluctuations) under HF diet than in HG diet. The amplitude (the distance between the peak and mesor) of DMI, rumen pH, ammonia nitrogen, and total volatile acid concentration were higher under HG diet than in HF diet. Although no significant diurnal oscillation was observed in rumen microbial population, the relative abundance of 14 bacterial genera, one protozoal genus, and 2 archaeal species had significant diurnal oscillations under both HF and HG diets. Among them, the bacterial genera Ruminococcus and Colidextribacter had time at peak of rhythm within 0 to12 h after feeding, which were also negatively associated with the rumen acetate/propionate ratio. The bacterial genus Rikenellaceae_RC9_gut_group had time at peak of rhythm within 12 to 24 h after feeding, which was also positively associated with the rumen acetate/propionate ratio. Our study illustrated the daily dynamic on the rumen microbiota population and composition under different diets, and also identified the feeding-responsive rumen microbiota, highlighting a more targeted approach is needed to manipulate rumen microbiota.