Temporal profiling of rumen and hindgut microbiota revealed enterotypes affecting the microbial interactions and assembly in the gut of dairy cows

It has been reported that rumen microbiota affects the cattle's milk-yield productivity, but the gut microbiota's contribution to the individualized performance and its associated mechanism have not been well defined. In this study, microbiota of 222 rumen and hindgut respective samples collected from 74 cows throughout the prepartum, postpartum, and peak-lactation periods were assessed using 16S rRNA gene amplicon analysis and were evaluated whether they affected inter-individual microbial interactions, assembly, functions, and contributed to host milk production and serum parameters. Prevotella-dominated (R-Prevot, n = 27) and Butyrivibrio-dominated (R-Butyri, n = 47) enterotypes were identified for rumen microbiota, and Prevotellaceae_UCG-003-dominated (H-Prevot, n = 33) and Paeniclostridium-dominated (H-Paenic, n = 41) enterotypes were identified for fecal microbiota. Positive cohesion (cooperative behaviour) was higher, while negative cohesion (competitive behavior) was lower in R-Prevot compared to R-Butyri enterotype throughout the three lactation periods. For H-Prevot enterotype, positive cohesion was higher at prepartum and peak-lactation, but lower at postpartum; and negative cohesion was lower at prepartum and postpartum with no difference detected at peak-lactation. Both deterministic and stochastic processes contributed to the rumen and hindgut microbiota assembly process with the proportion of dispersal limitation process being higher in R-Butyri than in R-Prevot, as well as in H-Prevot than in H-Paenic enterotype at peak-lactation. Additionally, the cows with R-Prevot/H-Prevot enterotypes (n = 15) had higher milk yield and lower serum non-esterified fatty acid concentration than the cows with R-Butyri/H-Paenic enterotypes (n = 29) during lactation. These findings provide evidence that enterotype could affect microbial interactions and assembly processes, as well as the cows' productivity.