BACKGROUND

Diurnal oscillations have been reported on ruminal prokaryotes, but the daily rhythmicity of eukaryotes remains unknown. This study investigated diurnal oscillations of ruminal prokaryotes and eukaryotes under three different feeding managements and rumen fluid transplantation conditions, aiming to elucidate the regulatory mechanisms influencing the dynamic shifts of rumen microbiome through the daily feeding cycle.

RESULTS

Quantification and profiling of the microbiota of 288 rumen samples collected from lactating dairy cows (n = 12) every 6-h over 48-h feeding cycles under ad libitum, restricted feeding at daytime and nighttime, respectively, revealed the rhythmicity in the population and abundance of ruminal bacteria, archaea, and protozoa. Under restricted-feeding regimes, 61.99% bacterial genera including Prevotella and Ruminococcus, and 7.19% archaeal species including Methanosphaera sp. ISO3-F5, and 66.93% protozoa genera including Entodinium and Isotricha showed feeding-time-influenced changes in circadian rhythms. However, 4.76% bacterial genera such as Prevotellaceae_UCG-001, and 0.29% archaeal species such as group 12 sp. ISO4-H5 exhibited non-feeding-time affected circadian rhythm pattern shifts. Further analysis of 176 rumen fluid samples collected after rumen fluid transplantation showed the proportion of bacterial, archaeal, and protozoal taxa displayed consistent (including Anaeroplasma and Fibrobacter), inconsistent (including Bacteroidales_UCG-001 and NK4A214_group), gain (including Prevotella and Succinivibrio), and loss (including Butyrivibrio and Mycoplasma) of circadian rhythms over the 48-h to 7-day period after transplantation. Similar circadian patterns were found among feed intake, ruminal volatile fatty acid concentrations, bacterial functions such as glycolysis/gluconeogenesis, and deterministic assembly processes of bacterial communities. However, different circadian patterns (12-h shifts) were observed for rumination time, ruminal pH, ammonia nitrogen concentration, and bacterial functions such as chemotaxis, nitrogen metabolism, and deterministic assembly processes of archaeal communities. Additionally, cross-lagged effects were observed between the relative abundance of microbial taxa and rumen fermentation parameters, which could affect feed intake, rumination time, microbial population/diversity, and microbial interactions. Video Abstract CONCLUSIONS: The classified feeding-time responsive, multi-factor responsive, consistent, and inconsistent circadian rhythm of microbial taxa underscore the driven factors behind the daily dynamics of rumen microbes, which also filled the gaps for targeting specific microbial taxa for better animal production.