Supplementary file 1_Lyophilized rumen fluid from goats fed different roughage-based diets: fermentation characteristics, microbial communities, and post-reconstitution in vitro fermentation performance.docx

CSP was significantly enriched in the bacterial genera norank_f__F082, Rikenellaceae_RC9_gut_group, norank_f__Bacteroidales_BS11_gut_group, norank_f__[Eubacterium]_coprostanoligenes_group, Ruminococcus, Monoglobus, norank_f__UCG-010, and Candidatus Saccharimonas; the fungal genera Orpinomyces, unclassified_f__Neocallimastigaceae, Cyllamyces, Caecomyces, Pecoramyces, Anaeromyces, Joblinomyces, and Alternaria; and the methanogen genera Methanobrevibacter and Methanolacinia.

Cross-domain correlation analysis showed predominantly positive associations among genera enriched within the same roughage-source group and negative associations between AHP- and CSP-enriched genera. Compared with their substrate-free controls, AH and CS showed increased gas production, bacterial crude protein (BCP), total volatile fatty acids (TVFA), acetate, propionate, and butyrate, and decreased pH (p < 0.05). CS showed higher pH, acetate, isovalerate, TVFA, and A/P, whereas AH showed higher gas production, butyrate, and valerate (p < 0.01).</p>Discussion<p>Overall, the roughage source in the donor diets influenced the fermentation characteristics and microbial composition of lyophilized rumen fluid.

After reconstitution, both inocula fermented exogenous substrate and exhibited different fermentation profiles, supporting their potential as storable inocula for standardization in RFT.</p>