Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya.
Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya.
PLoS One. 2023 Jan 13;18(1):e0274371. doi: 10.1371/journal.pone.0274371. eCollection 2023.
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
本研究旨在探讨不同粗饲料和精饲料比例对杂交奶牛瘤胃和粪便微生物组成及其相关功能基因的影响。我们还探索了粪便样本作为瘤胃液样本的替代物。将 6 头杂交奶牛分别饲养在 3 种不同的日粮中，在 3 个连续的 10 天周期内逐渐增加精饲料量并减少粗饲料量。每个周期结束后，分别采集个体瘤胃液和粪便样本，通过高通量宏基因组测序进行分析。比较了 3 种日粮和粪便及瘤胃液样本之间所有动物的平均相对丰度。结果表明，日粮的改变显著影响了几种瘤胃和粪便微生物的 OTU。在瘤胃中，增加日粮中的精饲料会导致变形菌门的丰度增加，而减少厚壁菌门和拟杆菌门的比例。相反，粪便样本中微生物组成的变化与日粮的改变模式不一致。微生物功能途径分类表明，碳水化合物代谢和蛋白质代谢途径是微生物主要功能。评估日粮对这些微生物预测功能作用的影响表明，高比例的精饲料会导致碳水化合物代谢的中心增加，相应地减少蛋白质的合成。此外，我们还发现了与日粮变化相关的几种微生物应激反应。拟杆菌属和梭菌属是这些微生物功能的主要宿主。因此，粗饲料与精饲料的比例对瘤胃样本中的微生物组成和微生物功能基因的影响大于粪便样本。因此，我们没有建立瘤胃和粪便宏基因组图谱之间的显著关系，而且同一动物的瘤胃和粪便微生物之间的相关性也不如不同动物之间的相关性高。
