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 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.

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.

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.

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.

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.

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.