United States Department of Agriculture (USDA) - Agricultural Research Service, Dairy Forage Research Center, Madison, WI, USA.
Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
Sci Rep. 2024 Jul 23;14(1):16914. doi: 10.1038/s41598-024-65685-y.
Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus, Lachnospira, and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.
早期生活中对瘤胃微生物生态系统的操纵可能会影响瘤胃发酵，并提高奶牛的生产性能。本实验的目的是评估向奶牛犊牛瘤胃上皮组织（RE）和瘤胃上皮黏膜微生物组（REM）中投喂三种不同类型微生物接种物对其的影响。为此，15 头荷斯坦公牛犊牛在出生时被纳入研究，并在 3 至 6 周龄时每周口服接受三种不同的瘤胃内接种物处理。接种物是通过对从瘤胃瘘管泌乳奶牛采集的瘤胃液进行灭菌（对照；ARF）、差速离心处理以创建细菌富集接种物（BE）或通过重量分离创建原生动物富集接种物（PE）制备的。犊牛在 0 至 7 周龄期间每天 3 次接受 2.5 L 巴氏消毒废奶，9 周龄时接受膨化育成料直至安乐死，此时从每个处理组中随机选择的 4 头犊牛采集 RE 组织进行转录组和微生物黏膜组分析。与 ARF 相比，BE 组中有 9 个基因在 RE 中上调，PE 组中有 92 个基因上调，而 BE 和 PE 之间，BE 组中有 13 个基因上调，PE 组中有 114 个基因上调。基因本体论分析确定了在 PE 和 ARF 之间的生物过程类别中富集的 GO 术语，而 BE 和 ARF 之间没有富集。RE 功能特征显示了与 BE 和 ARF 相关的不同 KEGG 途径，而 PE 则没有特定的 KEGG 途径。我们观察到 ARF 中 RE 微生物组的 alpha 多样性指数较低（观察到的属和 Chao1（p<0.05））。有 5 个微生物属与宿主基因表达的变化呈显著相关：Roseburia（25 个基因）、Entamoeba（两个基因）；Anaerosinus、Lachnospira 和 Succiniclasticum 分别与一个基因相关。sPLS-DA 分析表明，尽管在分类和功能微生物谱上存在不同的分布，但处理之间的 RE 微生物群落存在差异。共表达差异网络分析表明，BE 和 PE 都对酰基辅酶 A 合成、VI 型分泌和甲烷生成相关的 KEGG 模块的丰度有影响，而 PE 对与章鱼碱生物合成和 D-木糖转运相关的 KEGGs 有显著影响。我们的研究表明，在生命早期使用不同的微生物接种物进行人工接种不仅会改变 RE 转录组，还会影响 REM 及其功能。
