Effects of Different Feeding Regimes on Rumen Microbial Composition, Functional Potential, and Fermentation Characteristics of Longdong Goats (Capra hircus)

The rumen microbiota plays a key role in nutrient fermentation and short-chain fatty acid (SCFA) production in ruminants. However, the impacts of different feeding regimes on rumen microbial composition, functional potential, and metabolic outputs remain unclear. In this study, rumen fluid samples were collected from 12 Longdong goats (Capra hircus), which were divided into four groups based on feeding regime and coat color: housed white goats (n = 3), housed black goats (n = 3), grazing white goats (n = 3), and grazing black goats (n = 3). Samples were analyzed using high-throughput sequencing combined with functional annotation (KEGG and CAZy) and targeted SCFA profiling. Distinct differences in microbial community composition were observed primarily between feeding regimes, with enrichment of taxa related to carbohydrate degradation and fermentation. Functional analyses revealed significant shifts in metabolic pathways, particularly those associated with carbohydrate metabolism, energy production, and glycan biosynthesis. Several glycoside hydrolase and glycosyltransferase families showed differential abundances across groups. Consistently, SCFA concentrations varied significantly among feeding regimes. Correlation analyses further demonstrated strong associations between key microbial taxa, functional pathways, and specific SCFAs. Overall, these results indicate that feeding regime, rather than coat color, plays a dominant role in shaping rumen microbial structure, functional capacity, and fermentation characteristics, providing insights into microbial mechanisms underlying rumen metabolism and informing feeding strategy optimization.