Whole transcriptome analysis of RNA expression profiles reveals the potential regulating action of long noncoding RNA in lactating cows fed a high concentrate diet

Effects of High-Grain Diet on Performance, Ruminal Fermentation, and Rumen Microbial Flora of Lactating Holstein Dairy Cows

The objectives of the current study were to evaluate the fluctuations in production performance, rumen fermentation, and microbial community in lactating dairy cows fed a high-grain diet (HG). In this study, 16 healthy Holstein lactating dairy cattle with similar milk yields of 16.80 ± 4.30 kg/d, days in milk 171.44 ± 23.25 days, and parity 2.2 ± 1.5 times were selected and randomly allocated into two groups. One group was fed a low-grain diet (LG; 40% concentrate, DM basis; n = 8), and the other group was fed a high-grain diet (HG; 60% concentrate, DM basis; n = 8). The experiment lasted 6 weeks, including 1 week for adaptation. The experimental results showed that the milk fat content in the milk of lactating cows in the HG group was significantly reduced (p < 0.05), and the milk urea nitrogen (MUN) content showed an increasing trend (0.05 < p < 0.10) compared with the LG group. Compared with the LG group, rumen fluid pH was significantly decreased after feeding a high-grain diet, and contents of total volatile fatty acids (TVFA), acetate, propionate, and butyrate were significantly increased (p < 0.05). The acetate/propionate significantly decreased (p < 0.05). HG group significantly increased the abundance of Prevotella and Bacteroides in rumen fluid while significantly reducing the abundance of Methanobrevibacter and Lachnospiraceae ND3007_group (p < 0.05). Microorganisms with LDA scores > 2 were defined as unique, with the bacterial genus Anaerorhabdus_furcosa_group identified as a biomarker for the LG group, and the unique bacterial genus in the HG group were Prevotella, Stenotrophomonas, and Xanthomonadaceae. The prediction results of microbial function showed that a total of 18 KEGG differential pathways were generated between the two treatment groups, mainly manifested in metabolic pathways, signal transduction, and the immune system. In conclusion, the HG group promoted rumen fermentation by altering the microbial composition of lactating cows. Our findings provide a theoretical basis for the rational use of high-grain diets to achieve high yields in intensive dairy farming.

Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves

Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM-receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.

Weighted Gene Co-expression Network Analysis Identifies Specific Modules and Hub Genes Related to Subacute Ruminal Acidosis

Weighted gene co-expression network analysis (WGCNA) was used to understand the pathogenesis of subacute ruminal acidosis (SARA) and identify potential genes related to the disease. Microarray data from dataset GSE143765, which included 22 cows with and nine cows without SARA, were downloaded from the NCBI Gene Expression Omnibus (GEO). Results of WGCNA identified highly correlated modules of sample genes, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses allowed further biological insights into SARA-related modules. The protein-protein interaction (PPI) network, modules from the PPI network, and cistron annotation enrichment of modules were also analyzed. A total of 14,590 DEGs were used for the WGCNA. Construction of a protein-protein network identified DCXR, MMP15, and MMP17 as hub genes. Functional annotation showed that DCXR mainly exhibited L-xylulose reductase (NADP+) activity, glucose metabolic process, xylulose metabolic process, and carbonyl reductase (NADPH) activity, which are involved in the pentose and glucuronate interconversion pathways. MMP15 and MMP17 mainly have a collagen catabolic process. Overall, the results of this study aid the clarification of the biological and metabolic processes associated with SARA at the molecular level. The data highlight potential mechanisms for the future development of intervention strategies to reduce or alleviate the risk of SARA.