Oxidative stress is a risk factor for mammary health, resulting in decreased milk yield and milk quality. Application of exogenous bioactive compounds has been a research focus of antioxidation of animals in the mammary gland. Quercetin is a flavonoid extracted from vegetables, fruits and tea and has been shown to have a variety of biological activities, but the effect of quercetin on redox imbalance in mammary epithelial cells is unclear. In this study, cells of HC11, a mouse mammary epithelial cell line, were treated with quercetin, and the effects and molecular mechanisms of quercetin protection on hydrogen peroxide-induced oxidative stress were studied. Results showed that 20 μΜ quercetin attenuated hydrogen peroxide-induced lactate dehydrogenase release and reactive oxygen species (ROS) accumulation and alleviated the reduction of cell viability and antioxidant capacity. Quercetin significantly restored the activation of mitogen-activated protein kinase (MAPK) and nuclear factor E2-related factor 2 (Nrf2) pathways induced by hydrogen peroxide. Importantly, the inhibitors of p38 MAPK and extracellular regulated protein pathways affected the activation of Nrf2 pathway. All inhibitors of MAPK and Nrf2 pathways reduced the protective effects of quercetin on cell proliferation, the activity of catalase and the expression of glutamate-cysteine ligase modifier subunit. Meanwhile, the effects of quercetin on the production of ROS and expression of glutamate/cystine reverse transporter light chain were mainly dependent on Nrf2 pathway. In summary, the protective effect of quercetin in mammary epithelial cells was mediated via MAPK and Nrf2 pathways.

Initial microbial colonization plays an important role in neonatal gut health. However, studies on gut microbial composition at birth are challenging, due to the limited access to accurate sampling. Here, we characterized the jejunal and ileal bacterial composition (epimural and luminal) of neonatal calves within 30 minutes after birth, and compared it with maternal (birth canal and rectum) and birth environments. RNA-based quantification along with amplicon sequencing revealed the colonization of active, dense (1.1–9.4 × 108 16S rRNA copy/g of sample), and diverse bacteria in the calf small intestine at birth. Pseudomonadaceae and Propionibacteriaceae dominated epimural communities, while Propionibacteriaceae, Prevotellaceae, Ruminococcaceae, and Lachnospiraceae dominated luminal communities. The composition of calf gut bacteria at birth was significantly different from maternal bacteria, especially for beneficial bifidobacteria. The bacterial communities of calf body habitats were similar to those of the birth environment, which was again divergent from gut microbiota. This study suggests an establishment of small intestinal-specific microbiota from birth, which is considerably deviated from maternal microbiota. In corollary, we further propose that small intestinal microbiota colonization could be mainly modulated by host selection.

Gut microbiome changed dramatically during pregnancy and played important roles in metabolic status and reproductive endocrinology in mammals. However, investigating the functional microbiota and metabolites to improve the reproductive performance and understanding the host–microbiota interaction are still arduous tasks. This study aims to reveal the dominant strains and metabolites that improve the reproductive performance. We analyzed the fecal microbiota composition and metabolic status of higher yield Chinese pig breed Meishan (MS) sows and lower yield but widespread raised hybrid pig breed Landrace × Yorkshire (L × Y) sows on days 28 and 100 of gestation. Results showed that MS sows had higher litter sizes and steroid hormone level but lower short-chain fatty acid level in feces. Fecal metabolomic analysis revealed that MS sows showed a different metabolic status compared with L × Y sows both at early and late pregnancy, which enriched with phenylpropanoid biosynthesis, bile secretion, steroid hormone biosynthesis, and plant secondary metabolite biosynthesis. In addition, 16S rDNA and internal transcribed spacer sequencing indicated that MS sows showed different structures of microbiota community and exhibited an increased bacterial α-diversity but non-differential fungal α-diversity than L × Y sows. Moreover, we found that the litter sizes and bacteria including Sphaerochaeta, Solibacillus, Oscillospira, Escherichia–Shigella, Prevotellaceae_UCG-001, dgA-11_gut_group, and Bacteroides, as well as fungi including Penicillium, Fusarium, Microascus, Elutherascus, and Heydenia both have positive association to the significant metabolites at the early pregnancy. Our findings revealed significant correlation between reproductive performance and gut microbiome and provided microbial and metabolic perspective to improve litter sizes and steroid hormones of sows.

The rise of sequencing technologies has greatly contributed to our knowledge of the microbiota and its role in animal health and production. However, many members of the microbiota have historically been considered “unculturable.” Culturomics can be utilized to bring these fastidious microbes into cultivation and can be used in conjunction with culture-independent methods to study the microbiota in a more comprehensive manner. This review paper details culturomics’ role in revolutionizing human, swine, and bovine microbiota research and how its use has greatly increased the bacterial repertoire. Additionally, it describes how culturomics can be applied to develop microbiota-derived therapeutics, such as next-generation probiotics, and to study the role of the microbiota. Finally, this review provides potential methods and considerations for designing future culturomics studies.

The sophisticated relationship between the intake of dietary carbohydrates and host immunity is mediated in large part by the gut microbiota. This comprehensive review explores the multifaceted connections linking human gut microbiota with nondigestible carbohydrate metabolism and immune responses, highlighting the critical importance of this symbiotic relationship in maintaining overall host health. Understanding the mechanisms by which gut microbiota act as a bridge between carbohydrate intake and host immunity has significant implications for precision nutrition strategies and the development of therapeutic interventions.

The innate immune response is the host’s first line of defense, promptly activated upon pathogen invasion. Its precise and rapid activation relies on innate immune cells (IICs). Upon recognizing danger signals postinfection or injury, they release various innate immune effectors to eliminate invading pathogens or damaged cells, thus supporting the host’s immune homeostasis. Epigenetic modifications, by shaping chromatin structures, orchestrate specific gene transcription patterns to regulate the lineage development, differentiation, and activation of IICs. This intricate process ultimately contributes to effective pathogen clearance and IICs’ healthy development and differentiation. To thoroughly elucidate the epigenetic mechanisms underlying the development and differentiation of IICs, this review first introduces the fundamental concepts and latest advancements in this field. We then delve into how the immune microenvironment or other signaling molecules shape the epigenetic landscapes of distinct IIC subsets during their lineage development and differentiation. Furthermore, we summarize how different epigenetic modification profiles mediate specific transcriptional patterns, thereby influencing the lineage development, differentiation, and activation of IICs in response to infections or injuries. Finally, we discuss several unresolved critical issues from the perspective of targeting epigenetic modifications to modulate the innate immune response. In summary, this review aims to uncover the molecular mechanisms underlying the development, differentiation, and activation of IICs from an epigenetic perspective, providing theoretical foundations for scientific and medical researchers pursuing disease treatments.

We previously reported changes in gene expression in mammary tissue from non-inflamed mammary glands adjacent to an inflamed gland challenged with lipopolysaccharide (LPS). We determined if changes in the expression of selected genes in non-inflamed glands would be replicated in RNA isolated from milk fat. Cows were milked twice daily prior to experiment. Per cow, one mammary gland (QLPS) was randomly assigned to receive an intramammary infusion of 50 µg LPS immediately after morning milking on d-0. The ipsilateral (QI) and contralateral (QC) mammary glands adjacent to QLPS remained untreated. Quarter foremilk samples from all mammary glands were collected on d-1 and d-0 for milk composition and isolation of RNA for quantification of selected genes via quantitative polymerase chain reaction. Symptoms of clinical mastitis developed only in QLPS and were apparent within 3 h post-challenge. In QI and QC, lactose percentages were lower at 12 h post-challenge compared to d-1, but milk fat and protein contents were not different. For gene expression, 7 of 13 selected genes were differentially regulated in non-inflamed glands. In QI but not QC, LALBA expression was lower at 12 h post-challenge than on d-1. One gene of interest, LPIN1, was significantly upregulated in QI and QC but downregulated in QLPS at 12 h post-challenge. Five additional immune or stress-related genes were significantly upregulated in QLPS and, to a lesser but significant degree, in QI and QC compared to d-1. Notably, expression of two immune genes (NFKBIA, PTX3) was significantly greater in QI than QC despite QI having a numerically lower somatic cell count. Minor changes in the composition of milk secreted by non-inflamed mammary glands were linked to several immune and stress responses in those glands. Further, individual non-inflamed mammary glands responded differently depending on their position relative to the mastitic gland.

The rumen microbiome has attracted tremendous interest among microbiologists and ruminant nutritionists because of its crucial role in mediating feed digestion and fermentation and supplying most of the energy, nutrients, and precursors for producing ruminant products. The application of various omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics, have enabled unprecedented investigations into this ecosystem, shedding new light on its interactions with diet and animals and its relationships with key production traits. Despite the valuable insights these omics technologies provide, each has its unique utility and inherent limitations. Achieving a holistic characterization of the rumen microbiome and deciphering its causal relationship with diet and key animal production traits remain an ongoing endeavor. In this perspective review paper, we highlight the limitations of individual technologies and advocate for an integrated multi-omics approach and data analyses in studying the intricate relationships between diet, rumen microbes, and ruminant nutrition. This approach, termed “rumen microbiome nutriomics,” aims to comprehensively understand the rumen microbiome in the context of diets and animal productivity. Our emphasis lies in recognizing the necessity of integrated analysis across multiple data layers, encompassing data of diet, rumen microbiome features, animal genotypes, and production traits and identifying the causal relationship among them. We also call for collaborative efforts to develop a comprehensive rumen microbiome genome database, including prokaryotes, protozoa, fungi, and viruses. Furthermore, standardization of processes and analyses is crucial to address the variability observed in the literature, facilitating comparison of results among future studies and enabling robust data reanalysis through advanced data analytics.

Calorie restriction plays a role in reducing food intake and weight gain, and improving health and lifespan. We hypothesized that calorie restriction would affect body weight (BW), serum indices, gut microbiota, metabolites and short-chain fatty acids of finishing pigs. Castrated male (Landrace × Yorkshire) pigs (86.13 ± 3.50 kg) were randomly assigned into two groups indicated as control (Con) and calorie restriction (CR) (eight pigs/group), respectively. Pigs in the Con group consumed feed ad libitum, whereas pigs in the CR group were fed 70% of the amount of feed in the Con group. The trial lasted for 38 days. Blood and colonic contents were collected for serum parameters, and microbiota and metabolome analysis, respectively. Main effects were tested by Student’s t-test. We found that for finishing pigs, calorie restriction reduced the cumulative food intake, BW gain, serum total cholesterol, triglyceride, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, alanine aminotransferase and aspartate aminotransferase levels. Calorie restriction did not change the α and β diversity of intestinal microbiota. However, calorie restriction significantly increased the abundance of Romboutsia and unclassified_c_Bacilli, and significantly reduced the abundance of Lachnospiraceae_XPB1014_group, Candidatus_Saccharimonas, Escherichia-–Shigella and Gastranaerophilales. Calorie restriction also simultaneously changed the structure of intestinal metabolites and increased the concentration of isobutyric acid, isovaleric acid and valeric acid. In conclusion, calorie restriction may affect metabolism, reduce obesity and improve intestinal microbiota, which may be a healthy diet treatment that can reduce obesity and improve metabolism.

The gastrointestinal microbiota plays a crucial role in host nutrition and health. While culture-independent techniques have advanced microbial research, they often overlook low-abundance bacteria in the microbial community. Furthermore, empirical studies and mechanistic research rely on bacterial isolates obtained through culturing. The introduction of culturomics in 2012 significantly advanced culture-dependent techniques, contributing to microbial research. However, these methods remain labor-intensive, time-consuming, and costly, similar to traditional culture methods. This review provides an overview of the contributions of culturomics, summarizes procedures for optimizing sample and culture processes, and offers guidance on utilizing metagenomic data to enhance culturomics workflows. By collating and synthesizing these developments, this review aims to provide valuable insights into improving the practicality and productivity of culturomics for capturing gastrointestinal bacterial communities.

This experiment aimed to investigate the impacts of tributyrin (TB) dietary supplementation on serum biochemical indices and meat quality characteristics of longissimus thoracis et lumborum (LTL) muscle of lambs after weaning. Thirty healthy Small-Tailed Han female lambs (27.5 ± 4.1 kg; mean ± standard deviation) were randomly assigned to five treatments: basal diet (1) without TB, (2) with 0.5 g/kg TB, (3) with 1.0 g/kg TB, (4) with 2.0 g/kg TB or (5) with 4.0 g/kg TB. Each treatment consisted of six lambs, and the lambs were weaned on d 90 and were raised until d 165. Results showed that supplementing TB significantly promoted serum immunoglobulin concentrations of lambs such as immunoglobulins G, A and M. Besides, TB significantly increased muscle ether extract content, intermuscular fat length, pH value and redness but decreased lightness, drip loss and shear force. In addition, TB significantly elevated inosine-5ʹ-phosphate content and upregulated the relative expressions of genes related to lipid metabolism such as SREBP-1C, SCD, PPARγ, FAS and LPL. The mostly important, TB significantly enhanced essential amino acids (EAAs) and conjugated linoleic acids contents of the LTL muscle, despite it decreased total unsaturated fatty acids level. In conclusion, supplementing TB not only could promote the healthy status of weaned lambs via promoting serum immunity but also may improve nutritional quality of LTL muscle by improving EAA and conjugated linoleic acid contents.

The global challenge of methane emissions from enteric fermentation is critical, as it contributes significantly to atmospheric greenhouse gases and represents a loss of energy that could otherwise be utilized by ruminants. With the increasing demand for dairy and meat products, finding effective methods to reduce methane production is essential. This review explores the use of advanced meta-omics techniques – including metagenomics, metatranscriptomics, metaproteomics, and metabolomics – to deepen our understanding of ruminal methane production and identify potential strategies for its mitigation. These high-throughput technologies provide comprehensive insights into the rumen microbial communities and their metabolic functions by analyzing DNA, RNA, proteins, and metabolites directly from environmental samples. Metagenomics and metatranscriptomics offer a detailed view of microbial diversity and gene expression, while metaproteomics can identify specific enzymes and proteins directly involved in methane production pathways, revealing potential targets for mitigation strategies. Integrating these meta-omics approaches allows for a holistic understanding of the microbial processes that drive methane emissions, enabling the development of more precise interventions, such as tailored dietary modifications and the use of specific inhibitors. This review underscores the importance of a multi-omics strategy in characterizing microbial roles and interactions within the rumen, which is crucial for devising effective and sustainable methods to reduce methane emissions without compromising livestock productivity.

Milk fat is a high-value component of the U.S. dairy market. It is the major energy component of milk and is responsible for many organoleptic and technological characteristics of milk and dairy products. In addition, milk fat is unquestionably distinctive among all dietary fats that humans consume, as it is not only comprised of several hundred different fatty acids (FAs) but also contains a wide and unique array of bioactive lipids. Milk fat is dispersed in milk primarily in the form of fat globules. These cytoplasmic lipid droplets originate from mammary epithelial cells (MECs) and are secreted into the alveolar lumen surrounded by a membrane. Many advances in our knowledge of specific enzymes involved in milk lipid synthesis, the selectivity of the triacylglyceride (TAG) synthesis enzymes for specific FAs, the molecular mechanisms behind the uptake of long-chain FAs into the cells and the milk lipid secretion process have led to an improved understanding of the biology of milk fat synthesis. However, research to provide deeper insights into the mechanism of lipid synthesis in MECs is warranted and might lead to novel strategies to alter milk fat content and quality to benefit the dairy industry and meet dietary recommendations and consumer demands for foods that positively impact health. In this review, we aimed to provide a general overview of our current knowledge of the molecular aspects of milk lipid synthesis in MECs, from the uptake of blood-derived precursors to the intracellular formation of TAG-rich fat droplets secreted into milk as milk fat globules. We also highlight some current gaps in the knowledge that warrant further exploration. Given the importance of dairy food in the human diet, a better understanding of these processes could help develop novel strategies to alter milk fat composition in ways that benefit both human health and dairy producers.

Species of epiphytic microbiota are closely associated with the fermentation performance of natural forage silage. This study aimed to evaluate the dynamic microbial communities, fermentation parameters, and aerobic stability of Napier grass silage from the same variety and growth period but harvested from three different regions (NGP1, NGP2, and NGP3). After 60 days of ensiling, triplicate silos were opened for sampling and testing aerobic stability. The epiphytic microbiota with higher relative abundances in fresh Napier grass (NGP1, NGP2, and NGP3) were Weissella, Enterobacter, and Lactococcus, respectively. After 60 days of ensiling, NGP3 exhibited higher fermentation quality, indicated by higher lactic acid (LA) concentration and lower pH than that of NGP1 and NGP2. The NH3–N content of all treatments was lower than 100 g/kg total nitrogen. Compared with NGP1 and NGP2 silage, NGP3 silage exhibited a sharp rise in pH and LA consumption during air exposure. After 7 days of air exposure, NGP3 had higher ethanol concentrations and pH. Ruminiclostridium_5, Pediococcus, and Lactobacillus predominated in NGP1, NGP2, and NGP3 silages, respectively, whereas Candida and Monascus predominated in air-exposed NGP3 silage. The bacterial co-occurrence networks from fresh samples to ensiling and air exposure became more complex; however, NGP3 had a higher negative correlation with co-occurrence after air exposure. Different regions had significant effects on the fermentation patterns, bacterial communities, and aerobic stability of Napier grass silage. This was mainly due to variable epiphytic microbiota. Higher fermentation quality of Napier grass silage may also result in accelerated spoilage due to air exposure. Candida and Monascus were primarily responsible for the lower dry matter recovery and higher ethanol contents and air exposure spoilage of Napier grass silage.

Newborn calf diarrhea has led to widespread overuse of antibiotics. Therefore, it is crucial to find effective solutions for calf diarrhea. In this study, we aimed to evaluate the impact of the synthetic organic zinc-chelating-peptide glycine-glutamine-Zn (GQ-Zn) on the microbiota and metabolites in the gut of calves with diarrhea. The results showed that GQ-Zn alleviated diarrhea in calves. Additionally, 16S rDNA sequencing and metabolomic analysis revealed that GQ-Zn improved antioxidant capacity, relieved inflammation, altered the gut microbiota by decreasing the number of harmful bacteria Prevotella denticola, Fusobacterium necrophorum and influenced metabolomic profiles via the linoleic acid metabolic pathway in calves. In conclusion, GQ-Zn supplementation alleviated diarrhea through regulating the gut microbiota and metabolites in pre-weaning Holstein calves.

This study investigated the impact of diallyl disulfide (DADS) on oxidative stress induced by hydrogen peroxide (H2O2) in ovine rumen epithelial cells (RECs). Initially, the effects of DADS were evaluated on cellular reactive oxygen species (ROS) levels, antioxidant capacity in RECs were estimated. Then, RNA-seq analysis was conducted in DADS-treated and untreated cells to analyze the differential gene expression, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Finally, the effects of DADS on Kelch-like ECH associated protein 1/the nuclear factor erythroid 2-related factor 2 (Keap1/Nrf2) signaling pathway in RECs were evaluated. Results showed that DADS remarkably enhanced superoxide dismutase (SOD) activity and total antioxidant capacity (T-AOC) (P < 0.05) while reducing ROS and malonaldehyde production (P < 0.05) in H2O2-treated RECs. Transcriptomic analysis revealed that DADS might influence glutathione synthesis through cysteine and methionine metabolism, thereby affecting the transcription of genes involved in immunity and oxidative stress. The DADS treatment resulted in increased nuclear translocation of Nrf2 and upregulation of mRNA and protein levels of quinone oxidoreductase 1, heme oxygenase 1, and Nrf2. The Nrf2-specific inhibitor nullified the protective effects of DADS on malonaldehyde formation induced by H2O2 and decreased T-AOC and SOD activities. In conclusion, DADS demonstrated the ability to alleviate oxidative stress in RECs by promoting antioxidative capacity through the Keap1/Nrf2 signaling pathway.

Understanding the genetic basis of porcine mental health (PMH)-related traits in intensive pig farming systems may promote genetic improvement animal welfare enhancement. However, investigations on this topic have been limited to a retrospective focus, and phenotypes have been difficult to elucidate due to an unknown genetic basis. Intensively farmed pigs, such as those of the Duroc, Landrace, and Yorkshire breeds, have undergone prolonged selection pressure in intensive farming systems. This has potentially subjected genes related to mental health in these pigs to positive selection. To identify genes undergoing positive selection under intensive farming conditions, we employed multiple selection signature detection approaches. Specifically, we integrated disease gene annotations from three human gene–disease association databases (Disease, DisGeNET, and MalaCards) to pinpoint genes potentially associated with pig mental health, revealing a total of 254 candidate genes related to PMH. In-depth functional analyses revealed that candidate PMH genes were significantly overrepresented in signaling-related pathways (e.g., the dopaminergic synapse, neuroactive ligand‒receptor interaction, and calcium signaling pathways) or Gene Ontology terms (e.g., dendritic tree and synapse). These candidate PMH genes were expressed at high levels in the porcine brain regions such as the hippocampus, amygdala, and hypothalamus, and the cell type in which they were significantly enriched was neurons in the hippocampus. Moreover, they potentially affect pork meat quality traits. Our findings make a significant contribution to elucidating the genetic basis of PMH, facilitating genetic improvements for the welfare of pigs and establishing pigs as valuable animal models for gaining insights into human psychiatric disorders.

Rumen microbial biohydrogenation (RBH) is the major factor responsible for the bovine milk rich in saturated fatty acids (FAs). Here, we evaluated the effects of nutritional manipulation of ruminal propionogenesis and methanogenesis, two primary hydrogen sinks, on the RBH and milk FA profiles in vivo and in vitro using three propionogenesis enhancers (fumarate [FUM], biotin and monensin) and one methanogenesis inhibitor (N-[2-(nitrooxy)ethyl]-3-pyridinecarboxamide [NPD]). The in vivo results showed that inclusion of FUM in lactating dairy goat diet could protect dietary unsaturated FAs against RBH with increased proportions of C18:2n − 6 (by 33.5%), C18:3n − 3 (by 38.1%) and RBH intermediates (e.g. trans-10 C18:1 and trans-11 C18:1) in rumen contents. Additionally, FUM supplementation increased the milk Δ9 desaturase index (by 15.5%) with higher cis-9 monounsaturated FAs in the milk. As a result, FUM increased the proportions of polyunsaturated and monounsaturated FAs in the milk with lower atherogenicity index (by −15.3%) and thrombogenicity index (by −19.5%). Conversely, supplementing NPD increased RBH completeness (by 7.4%) with higher milk atherogenicity index (by 10.5%) and thrombogenicity index (by 8.7%). The adverse effects of NPD on the milk FA profiles can be eliminated when supplemented in combination with FUM. The metagenomic analyses showed that neither FUM nor NPD affect the rumen microbial α- or β-diversity at the strain or gene level. The in vitro study showed that the conversion rate of FUM to propionate was increased from 54.7% to 80.6% when FUM supplemented in combination with biotin and monensin, resulting a higher anti-RBH potential. Accordingly, manipulation of ruminal methanogenesis and propionogenesis can redirect hydrogen toward or away from RBH and thereby influence the milk FA profiles. FUM is a promising feed additive in ruminant not only to reduce the methane emissions as previously proved but also to improve the nutritional desirability of the milk FA profiles for human health.