Dataset of the rumen microbiota and epithelial transcriptomics and proteomics in goat affected by solid diets

Abstract

Although early solid diet supplementation is a common practice to improve the growth and development in goat kids, its biological mechanism how solid diet induces rumen microbiota and epithelial development is still unknow. In this study, rumen fermentation parameters, 16S rRNA sequencing for rumen content and epithelial microbiota, transcriptomics and proteomics of epithelium were determined to classify the effects of solid diet supplementation. Here, we classified the changes of goat phenotypes (i.e., growth performance, rumen fermentation and development) and linked them to the changes of rumen microbiota, transcriptome and expressed proteins. The mechanism of solid diet improving rumen development was elucidated preliminarily. Moreover, different roles between the rumen content and epithelial microbiota were identified. Thess datasets expands our understanding of the association between the early diet intervention and rumen development, providing the useful information how nutrient strategy affects rumen function and subsequently improves the host growth. The generated data provides insights in the importance of rumen niche microbiota and microbe-host interactions, which benefits future studies.

Fig. 1

Overview of the experimental workflows. The goat kids were assigned into three treatments (milk replacer only (MRO), milk replacer supplemented concentrate (MRC) and milk replacer supplemented concentrate plus alfalfa pellets (MCA)) on 20 days of age. At the end of animal feeding trial (60 days of age), goat kids were slaughtered for rumen sample collection. After the rumen was weighted, rumen content and epithelial microbial samples were collected for 16S rRNA sequencing. The rumen epitheliums were collected for transcriptomics, proteomics, and morphology measurements.

Fig. 2

Next-generation sequencing of the rumen content and epithelial microbiota in goat kids. (A) Beta diversity of the rumen content and epithelial microbiota based on Bray–Curtis. One point represents one sample. (B) Rumen microbial composition at the genus level. Each column represents a sample, and each bar represents one bacterium. MROC, MRCC and MCAC represent content samples in animals that received MRO, MRC and MCA diets, while MROE, MRCE and MCAE represent the epithelial microbiota from the three diets, respectively. The MRO treatment was fed only milk replacer, the MRC treatment was fed milk replacer with concentrate and the MCA treatment was fed milk replacer with concentrate plus alfalfa.

Fig. 3

Gene expression stacked bar plot of each epithelial sample. LF1-LF6, LF7-LF12 and LF13-LF17 belong to MRO, MRC and MCA treatments, respectively. MRO = milk replacer, MRC = milk replacer + concentrate, MCA = milk replacer + concentrate + alfalfa.

Fig. 4

Quantification repeat analysis of the rumen epithelial proteomics. X-axis is the deviation between the protein ratio of the repetitive samples. Y-axis is the quantified protein amount at the corresponding range.

Fig. 5

Bar plot of the Gene Ontology Analysis using proteomics. The bar chart shows the distribution of corresponding GO terms. Different colors represent different GO categories.