The feeding regime of early, supplementary solid diet improved rumen development and production in goat kids. However, the signature microbiota responsible for linking dietary regimes to rumen function shifts are still unclear. This work analyzed the rumen microbiome and functions affected by an early solid diet regime using a combination of machine learning algorithms. Volatile fatty acids (i.e., acetate, propionate and butyrate) fermented by microbes were found to increase significantly in the supplementary solid diet groups. Predominant genera were found to alter significantly from unclassified Sphingobacteriaceae (non-supplementary group) to Prevotella (supplementary solid diet groups). Random Forest classification model revealed signature microbiota for solid diet that positively correlated with macronutrient intake, and linearly increased with volatile fatty acid production. Bacteria associated with carbohydrate and protein metabolism were also identified. Utilization of a Fish Taco analysis portrayed a set of intersecting core species contributed to rumen function shifts by the solid diet regime. The core community structures consisted of the specific, signature microbiota and the manipulation of their symbiotic partners are manipulated by extra nutrients from concentrate and/or forage, and then produce more volatile fatty acids to promote rumen development and functions eventually host development. Our study provides mechanisms of the microbiome governed by a solid diet regime early in life, and highlights the signature microbiota involved in animal health and production.

Supplying sufficient nutrients, such as dietary energy and protein, has a great effect on the growth and rumen development of ruminants. This study was conducted to evaluate the effects of dietary energy and protein levels on growth performance, microbial diversity, and structural and physiological properties of the rumen in weaned lambs. A total of 64 two-month-old Hu lambs were randomly allotted to 2 × 2 factorial arrangements with four replicates and with four lambs (half male and half female) in each replicate. The first factor was two levels of dietary metabolizable energy (ME) density (ME = 10.9 MJ/Kg or 8.6 MJ/Kg), and the second factor was two levels of dietary crude protein (CP) content (CP = 15.7% or 11.8%). The trial lasted for 60 days. A low dietary energy level restrained the growth performance of lambs (p < 0.05). The ruminal concentration of acetate and the ratio of acetate to propionate increased but the propionate concentration decreased significantly with the low energy diet. However, the rumen morphology was not affected by the diet energy and protein levels. Moreover, a low energy diet increased ruminal bacterial diversity but reduced the abundance of the phylum Proteobacteria (p < 0.05) and genus Succinivibrionaceae_uncultured (p < 0.05), which was associated with the change in ruminal fermentation phenotypes. By indicator species analysis, we found three indicator OTUs in the high energy group (Succinivibrionaceae_uncultured, Veillonellaceae_unclassified and Veillonellaceae_uncultured (p < 0.01)) and two indicator OTUs in the low energy group (Bacteroidales_norank and Lachnospiraceae_uncultured (p < 0.01)). In conclusion, these findings added new dimensions to our understanding of the diet effect on rumen microbial community and fermentation response, and are of great significance for establishing the optimal nutrient supply strategy for lambs.

The overuse and misuse of antibiotics in the livestock and poultry industry has led to the development of multi-drug resistance in animal pathogens, and antibiotic resistance genes (ARGs) in bacteria transfer from animals to humans through the consumption of animal products, posing a serious threat to human health. Therefore, the use of antibiotics in livestock production has been strictly controlled. As a result, bacteriophages have attracted increasing research interest as antibiotic alternatives, since they are natural invaders of bacteria. Numerous studies have shown that dietary bacteriophage supplementation could regulate intestinal microbial composition, enhance mucosal immunity and the physical barrier function of the intestinal tract, and play an important role in maintaining intestinal microecological stability and normal body development of animals. The effect of bacteriophages used in animals is influenced by factors such as species, dose, and duration. However, as a category of mobile genetic elements, the high frequency of gene exchange of bacteriophages also poses risks of transmitting ARGs among bacteria. Hence, we summarized the mechanism and efficacy of bacteriophage therapy, and highlighted the feasibility and challenges of bacteriophage utilization in farm animal production, aiming to provide a reference for the safe and effective application of bacteriophages as an antibiotic alternative in livestock and poultry.

It is well known that solid diet supplementation in early life can significantly promote rumen development and metabolic function in young ruminants. However, the changes in the expressed proteome and related metabolism in rumen epithelium in response to a supplemented solid diet remain unclear. In this study, rumen epithelial tissue from goats in three diet regimes including milk replacer only (MRO), milk replacer supplemented concentrate (MRC), and milk replacer supplemented concentrate plus alfalfa pellets (MCA) were collected for measurement of the expression of epithelial proteins using proteomic technology (six per group). The results showed that solid diet significantly improved the growth performance of goats, enhanced the ability of rumen fermentation, and promoted the development of epithelial papilla (p < 0.05). Proteome analysis revealed the distinct difference in the expressed protein in the MRC and MCA group compared with the MRO group (42 upregulated proteins and 79 downregulated proteins in MRC; 38 upregulated proteins and 73 downregulated proteins in MCA). Functional analysis showed that solid diet supplementation activated a variety of molecular functions in the epithelium, including protein binding, ATP binding, structural constituent of muscle, etc., in the MRC and MCA groups. Meanwhile, the expression of proteins related to fatty acid metabolism, the PPAR signaling pathway, valine, leucine, and isoleucine degradation, and butanoate metabolism were upregulated, being stimulated by solid feed. In contrast, the proteins associated with carbohydrate digestion and absorption and glycosaminoglycan degradation were downregulated. In addition, the protein expression of enzymes involved in ketone body synthesis in the rumen was generally activated, which was caused by solid feed. In summary, solid feed promoted the development of rumen epithelium by changing the expression of proteins related to fatty acid metabolism, energy synthesis, and signal transduction. The ketone body synthesis pathway might be the most important activated pathway, and provides energy for rumen development.

The performance of dairy cows is closely tied to the metabolic state, and this performance varies depending on the number of times the cows have given birth. However, there is still a lack of research on the relationship between the metabolic state of Holstein cows and the performance of lactation across multiple parities. In this study, biochemical analyses and metabolomics studies were performed on the serum and milk from Holstein cows of parities 1–4 (H1, N = 10; H2, N = 7; H3, N = 9; H4, N = 9) in mid-lactation (DIM of 141 ± 4 days) to investigate the link between performance and metabolic changes. The results of the milk quality analysis showed that the lactose levels were highest in H1 (p = 0.036). The total protein content in the serum increased with increasing parity (p = 0.013). Additionally, the lipase activity was found to be lowest in H1 (p = 0.022). There was no difference in the composition of the hydrolyzed amino acids in the milk among H1 to H4. However, the free amino acids histidine and glutamate in the serum were lowest in H1 and highest in H3 (p < 0.001), while glycine was higher in H4 (p = 0.031). The metabolomics analysis revealed that 53 and 118 differential metabolites were identified in the milk and serum, respectively. The differential metabolites in the cows’ milk were classified into seven categories based on KEGG. Most of the differential metabolites in the cows’ milk were found to be more abundant in H1, and these metabolites were enriched in two impact pathways. The differential metabolites in the serum could be classified into nine categories and enriched in six metabolic pathways. A total of six shared metabolites were identified in the serum and milk, among which cholesterol and citric acid were closely related to amino acid metabolism in the serum. These findings indicate a significant influence of blood metabolites on the energy and amino acid metabolism during the milk production process in the Holstein cows across 1–4 lactations, and that an in-depth understanding of the metabolic changes that occur in Holstein cows during different lactations is essential for precision farming, and that it is worthwhile to further investigate these key metabolites that have an impact through controlled experiments.