DNA methylation is one of the main epigenetic phenomena affecting gene expression. It is an important mechanism for the development of embryo, growth and health of animals. As a key nutritional factor limiting the synthesis of protein, methionine serves as the precursor of S-adenosylmethionine (SAM) in the hepatic one-carbon metabolism. The dietary fluctuation of methionine content can alter the levels of metabolic substrates in one-carbon metabolism, e.g., the SAM, S-adenosylhomocysteine (SAH), and change the expression of genes related to the growth and health of animals by DNA methylation reactions. The ratio of SAM to SAH is called 'methylation index' but it should be carefully explained because the complexity of methylation reaction. Alterations of methylation in a specific cytosine-guanine (CpG) site, rather than the whole promoter region, might be enough to change gene expression. Aberrant methionine cycle may provoke molecular changes of one-carbon metabolism that results in deregulation of cellular hemostasis and health problems. The importance of DNA methylation has been underscored but the mechanisms of methionine affecting DNA methylation are poorly understood. Nutritional epigenomics provides a promising insight into the targeting epigenetic changes in animals from a nutritional standpoint, which will deepen and expand our understanding of genes, molecules, tissues, and animals in which methionine alteration influences DNA methylation and gene expression.

Garlic extracts have been reported to be effective in reducing methanogenesis. Related mechanisms are not well illustrated, however, and most studies have been conducted in vitro. This study investigates the effects of supplementary allicin (AL) in sheep diet on in vivo digestibility, rumen fermentation, and shifts of microbial flora. Two experiments were conducted using Dorper × thin-tailed Han crossbred ewes. In experiment 1, eighteen ewes (60.0 ± 1.73 kg BW) were randomly assigned for 29 days to either of two dietary treatments: a basal diet or the basal diet supplemented with 2.0 g AL/head·day to investigate supplementary AL on nutrient digestibility and methane emissions. In experiment 2, six ewes (65.2 ± 2.0 kg BW) with ruminal canulas were assigned to the same two dietary treatments as in experiment 1 for 42 days to investigate supplementary AL on ruminal fermentation and microbial flora. The methane emissions were determined using an open-circuit respirometry system and microbial assessment was done by qPCR of 16S rRNA genes. Supplementary AL increased the apparent digestibility of organic matter (P < 0.001), nitrogen (P = 0.006), neutral detergent fiber (P < 0.001), and acid detergent fiber (P = 0.002). Fecal nitrogen output was reduced (P = 0.001) but urinary nitrogen output was unaffected (P = 0.691), while nitrogen retention (P = 0.077) and nitrogen retention/nitrogen intake (P = 0.077) tended to increase. Supplementary AL decreased methane emissions scaled to metabolic bodyweight by 5.95 % (P = 0.007) and to digestible organic matter intake by 8.36 % (P = 0.009). Ruminal pH was unaffected (P = 0.601) while ammonia decreased (P = 0.024) and total volatile fatty acids increased (P = 0.024) in response to supplementary AL. Supplementary AL decreased the population of methanogens (P = 0.001) and tended to decrease that of protozoans (P = 0.097), but increased the populations of F. succinogenes (P < 0.001), R. flavefaciens (P = 0.001), and B. fibrisolvens (P = 0.001). Supplementation of AL at 2.0 g/head·day effectively enhanced OM, N, NDF, and ADF digestibility and reduced daily methane emissions (L/kg BW0.75) in ewes, probably by decreasing the population of ruminal protozoans and methanogens.

It is well known that phenotype of animals may be modified by the nutritional modulations through epigenetic mechanisms. As a key and central component of epigenetic network, DNA methylation is labile in response to nutritional influences. Alterations in DNA methylation profiles can lead to changes in gene expression, resulting in diverse phenotypes with the potential for decreased growth and health. Here, I reviewed the biological process of DNA methylation that results in the addition of methyl groups to DNA; the possible ways including methyl donors, DNA methyltransferase (DNMT) activity and other cofactors, the critical periods including prenatal, postnatal and dietary transition periods, and tissue specific of epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals.

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.

Summary: Early gut microbial colonization is important for postnatal metabolic and immune development. However, little is known about the effects of different feeding modes (suckling versus bottle‐feeding) or microbial sources on this process in farm animals. We found that suckled and bottle‐fed newborn lambs had their own distinct gut microbiota. Results from 16S rRNA gene sequencing and qPCR showed that, compared with suckling, bottle feeding significantly increased the abundances of Escherichia/Shigella , Butyricicoccus , and Clostridium XlVa, while significantly decreased the abundance of Clostridium XI. The higher levels of Escherichia/Shigella in bottle‐fed lambs suggest that artificial feeding may increase the number of potential pathogens and delay the establishment of the anaerobic environment and anaerobic microbes. Feeding modes also affected the direct transmission of bacteria from the mother and the environment to newborns. The SourceTracker analysis estimated that the early gut microbes of suckled lambs were mainly derived from the mother's teats (43%) and ambient air (28%); whereas those of bottle‐fed lambs were dominated by bacteria from the mother's vagina (46%), ambient air (31%), and the sheep pen floor (12%). These findings advance our understanding of gut microbiota in early life and may help design techniques to improve gut microbiota and health.

Under current breeding conditions, multiple stressors are important challenges facing animal husbandry in achieving animal wellbeing. For many years, the use of antibiotics has been a social concern in the livestock industry. With the implementation of the non-antibiotics policy, there is an urgent need to find relevant technologies and products to replace antibiotics and to solve the problem of disease prevention during animal growth. Phytogenic extracts have the unique advantages of being natural and extensive sources, having a low residue, and being pollution-free and renewable. They can relieve the various stresses, including oxidative stress, on animals and even control their inflammation by regulating the signaling pathways of proinflammatory cytokines, improving animal immunity, and improving the structure of microorganisms in the gastrointestinal tract, thereby becoming the priority choice for improving animal health. In this study, we reviewed the types of antioxidants commonly used in the livestock industry and their applicable effects on ruminants, as well as the recent research progress on their potential mechanisms of action. This review may provide a reference for further research and for the application of other phytogenic extracts and the elucidation of their precise mechanisms of action.