Supporting data for "Deterministic Succession Patterns in the Rumen and Fecal Microbiome Associated with Metabolic Shifts in Pertiparturient Dairy Cattle"

Metabolic disorders in periparturient ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of periparturient dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the periparturient period.<br> In a longitudinal study of 91 periparturient cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By employing enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as <i>Succiniclasticum</i> and <i>Bifidobacterium</i>, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin level). Mediation analysis suggested that specific gut microbes (e.g., <i>Prevotella sp900315525</i> in the rumen and <i>Alistipes sp015059845</i> in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.<br> Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in periparturient dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of periparturient dairy cows. These findings provide valuable insights for developing health management strategies for periparturient ruminants.