Deciphering the Impact of Nutrient Composition and Tissue Structure on Rumen Microbiome Dynamics in Roughage Degradation

Background Ruminant animals, such as goats, depend on rumen microbial communities to degrade fibrous nutrients from roughages, facilitating their growth and development. This research delved into the dynamic shifts in surface-attached rumen microbes found in representative roughages (rice straw, bamboo shoot sheet, and alfalfa) and examined their degradation characteristics. Four 14-month-old Min Dong goats with rumen fistulas were used for the experiment, and the roughages were assessed at seven intervals (4 h, 12 h, 24 h, 36 h, 48 h, and 72 h). Using the 16S rRNA and metagenomics sequencing techniques to reveal the microbiome composition and their functions. Results Prevotella and Treponema were pinpointed as pivotal genera in roughage degradation. The nutritional composition and tissue structure of roughages affected microbial attachment, causing variations in nutrient degradation rates and the overall degradation process. Microbes related to dry matter (DM) and crude protein (CP) degradation were abundant in the early fermentation stages (4-12h) while decreased as time progressed. In contrast, microbes of fiber degradation increased gradually after 24-hour. Dominant in the goat rumen, Prevotella and Treponema are integral to roughage degradation, attributed to their multifaceted functional traits. Furthermore, the surface-attached microbes in the three roughages produced BG (β-Glucosidase), C1 (Endo-β-1,4-glucanase), Cx (Exo-β-1,4-glucanase), and NEX (Neutral xylanase) enzymes. The activity of these enzymes and their correlation with GHs (Glycoside Hydrolases) functional genes increased with the fiber content of the roughages. Conclusions These insights advance our understanding of microbial roles in ruminant nutrition and digestion. The interaction between microbial communities and rumen fermentation is pivotal to understanding the collaborative gene encoding by goat rumen microbiota being critical for fiber degradation.