The rumen microbiota is essential to substrate digestion and fermentation of nutrients, which has a direct impact on animal sustainability and productivity. It is further known that diet composition has an impact on rumen microbial communities, while the proportional roles of feed types and rumen fraction type (solid vs. liquid) to the diversity of bacterial communities in sheep kept indoors are still lacking. This study examined the impact of rumen sample fractions (solid vs. liquid) and diet composition (single vs. mixed) on the diversity and structure of the sheep’s rumen bacterial community. Eight adult sheep were used in two different feeding groups: mixed feeding (hay, straw, and silage) and single feeding (orchard grass silage only). The solid and liquid fractions of the rumen were separated after 21 days of feeding. The V4 region of the 16 S rRNA gene was sequenced using the Illumina MiSeq platform after microbial DNA was extracted from both fractions. The SILVA database was used to assign amplicon sequence variants (ASVs) for bioinformatic analysis, which was carried out using QIIME2. Using R, analyses of differential abundance, beta diversity, and alpha diversity were performed. While microbial richness stayed consistent across diets ( P = 0.065), mixed feeding increased species richness compared to single feeding ( P = 0.0076. On the other hand, the rumen sample fraction had a greater impact on microbial community structure: liquid fractions were dominated by taxa linked to fermentation of soluble carbohydrates, while solid fractions showed greater richness ( P = 0.012) and were enriched with bacteria associated with fibre ( P < 0.001). Significant compositional differences between solid and liquid fractions were found via beta-diversity analysis (PERMANOVA, R ² = 0.553, P < 0.001), but remained similar across the feeding regimens ( R ² = 0.139, P = 0.099). The phyla Bacteroidota (54.82%) and Bacillota (19.17%) dominated the rumen microbiota in all samples, with Prevotella being the most prevalent genus (18.74%). Dietary differences in volatile fatty acid profiles were negligible, suggesting functional redundancy in spite of taxonomic changes in the rumen bacterial community. Under the conditions examined, this study shows that the rumen sample fraction (solid vs. liquid) is a more important determinant of the composition of the microbial community than the effects of diet composition. Microbial richness is increased by mixed feeding, while different and functionally complementary bacterial communities are present in solid and liquid rumen fractions. These results emphasize how crucial it is to include both rumen sample fractions in microbiome research and offer insightful information for the improvement of feeding practices or sudden dietary changes meant to enhance nutrient utilization in sheep under indoor conditions.
Barsila et al. (Fri,) studied this question.