Rumen fraction type (solid vs. liquid) modulates diet-driven patterns of bacterial diversity and composition in sheep.
4 affiliations
- 1Agriculture and Forestry University, Faculty of Animal Science, Veterinary Science and Fisheries, Bharatpur Metropolitan City, Rampur, Chitwan, 00977, Nepal. [email protected].
- 2Integrated Field Science Center, Graduate School of Agricultural Science, Tohoku University, Naruko-onsen 232-3, Yomogita Osaki, 04 989-6711, Japan.
- 3Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Ikenodai 2, Tsukuba, Ibaraki, 305-0901, Japan.
- 4Agriculture and Forestry University, Centre for Biotechnology, Bharatpur Metropolitan City, Rampur, Chitwan, 00977, Nepal.
Abstract
Background
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.Methods
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.Results
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, R² = 0.553, P < 0.001), but remained similar across the feeding regimens (R² = 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.Conclusion
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.
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BibTeX
@article{barsila2026rumen,
title = {{Rumen fraction type (solid vs. liquid) modulates diet-driven patterns of bacterial diversity and composition in sheep.}},
author = {S R Barsila and Y Gotoh and S Takizawa and Y Fukuda and H Kakihara and Wang T Pakhrin and S Ogura},
journal = {BMC microbiology},
year = {2026},
month = jul,
doi = {10.1186/s12866-026-05438-1},
url = {https://europepmc.org/article/MED/42958040},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Rumen fraction type (solid vs. liquid) modulates diet-driven patterns of bacterial diversity and composition in sheep.
AU - S R Barsila
AU - Y Gotoh
AU - S Takizawa
AU - Y Fukuda
AU - H Kakihara
AU - Wang T Pakhrin
AU - S Ogura
PY - 2026
DA - 2026/07/24
JO - BMC microbiology
DO - 10.1186/s12866-026-05438-1
UR - https://europepmc.org/article/MED/42958040
AB - Background 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.Methods 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.Results 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, R² = 0.553, P < 0.001), but remained similar across the feeding regimens (R² = 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.Conclusion 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.
SN - 1471-2180
ER -