Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted P < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response (P < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera (P < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 (LYZ2), fatty acid binding protein 5 (FABP5), and fucosyltransferase (FUT1). Specifically, the profound increase in expression of LYZ2 in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.

中文翻译：

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人工添加外源瘤胃内容物的奶牛回肠宿主转录组和微生物转录组的变化。

早期发展功能正常的胃肠道（GIT）对于奶牛的健康和终生生产力至关重要。早期微生物定植在新生牛的GIT发育中的作用以及相关的分子变化仍然未知，特别是对于小肠而言。在这项研究中，我们在小牛的早期阶段，从出生开始到8周断奶过渡，对外源瘤胃液进行了人工加药。本研究包括六头犊牛。在8周龄时，收集来自回肠的组织，并使用RNA测序对其进行宿主转录组和微生物元转录组分析。共有333个基因显示出显着的差异表达（DE）（倍数变化≥2;调整的P＜0.1，平均读数计数≥10）。基因本体分析表明，这些DE基因主要与与宿主免疫反应有关的过程有关（P <0.0001）。宿主基因表达与微生物属丰度之间的关联分析确定了57个基因与回肠微生物属具有显着相关性（P <0.0001）。其中，三个基因与六个微生物属显着相关：溶菌酶2（LYZ2），脂肪酸结合蛋白5（FABP5）和岩藻糖基转移酶（FUT1）。具体而言，LYZ2表达的大幅增加接受治疗的牛犊中的α-氨基丁酸暗示了宿主的抗菌活性和先天反应的启动。尽管样本量相对较小，但这项研究揭示了早期引入微生物对犊牛小肠的潜在影响。