Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review

Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions

Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.

A review of genetic resources and trends of omics applications in donkey research: focus on China

Omics methodologies, such as genomics, transcriptomics, proteomics, metabolomics, lipidomics and microbiomics, have revolutionized biological research by allowing comprehensive molecular analysis in livestock animals. However, despite being widely used in various animal species, research on donkeys has been notably scarce. China, renowned for its rich history in donkey husbandry, plays a pivotal role in their conservation and utilization. China boasts 24 distinct donkey breeds, necessitating conservation efforts, especially for smaller breeds facing extinction threats. So far, omics approaches have been employed in studies of donkey milk and meat, shedding light on their composition and quality. Similarly, omics methods have been utilized to explore the molecular basis associated with donkey growth, meat production, and quality traits. Omics analysis has also unraveled the critical role of donkey microbiota in health and nutrition, with gut microbiome studies revealing associations with factors such as pregnancy, age, transportation stress, and altitude. Furthermore, omics applications have addressed donkey health issues, including infectious diseases and reproductive problems. In addition, these applications have also provided insights into the improvement of donkey reproductive efficiency research. In conclusion, omics methodologies are essential for advancing knowledge about donkeys, their genetic diversity, and their applications across various domains. However, omics research in donkeys is still in its infancy, and there is a need for continued research to enhance donkey breeding, production, and welfare in China and beyond.

Exploring the Spatial Variation in the Microbiota and Bile Acid Metabolism of the Compound Stomach in Intensively Farmed Yaks

Yaks are one of the important livestock on the Qinghai-Tibet Plateau, providing abundant dairy and meat products for the local people. The formation of these dairy and meat products mainly relies on the microbiota in their gastrointestinal tract, which digests and metabolizes plant feed. The yak's gastrointestinal microbiota is closely related to the health and production performance of the host, but the molecular mechanisms of diet-induced effects in intensively farmed yaks remain to be elucidated. In this study, 40 chyme samples were collected from the four stomach chambers of 10 intensively farmed yaks, and the bacterial diversity and bile acid changes in the rumen (SFRM), reticulum (SFRC), omasum (SFOM), and abomasum (SFAM) were systematically analyzed using 16S rRNA sequencing and bile acid metabolism. Our results showed that the gastrointestinal microbiota mainly distributes in the four-chambered stomach, with the highest microbial diversity in the reticulum. There is a highly negative correlation among the microbiota in the four chambers. The dominant bacterial phyla, Bacteroidota and Firmicutes, were identified, with Rikenellaceae_RC9_gut_group being the dominant genus, which potentially helps maintain short-chain fatty acid levels in the stomach. In contrast, the microbiome within the four stomach chambers synergistically and selectively altered the content and diversity of bile acid metabolites in response to intensive feeding. The results of this study provide new insights into the microbiota and bile acid metabolism functions in the rumen, reticulum, omasum, and abomasum of yaks. This can help uncover the role of gastrointestinal microbiota in yak growth and metabolic regulation, while also providing references for improving the production efficiency and health of ruminants.

Rumen Development of Tianhua Mutton Sheep Was Better than That of Gansu Alpine Fine Wool Sheep under Grazing Conditions

The purpose of this experiment was to investigate the differences in rumen tissue morphology, volatile fatty acid content, and rumen microflora between Tianhua mutton sheep and Gansu alpine fine wool sheep under the same grazing conditions. Twelve 30-day-old lambs were randomly selected from two different flocks in Duolong Village and grazed together for a period of 150 days. The rumen tissue was fixed with 4% paraformaldehyde and brought back to the laboratory for H&E staining, the volatile fatty acid content of the rumen contents was detected by gas chromatography, and the rumen flora structure was sequenced by full-length sequencing of the bacterial 16S rRNA gene using the PacBio sequencing platform. The acetic acid and total acid contents of the rumen contents of Tianhua mutton sheep were significantly higher than those of Gansu alpine fine wool sheep (p < 0.05). The rumen papillae height of Tianhua mutton sheep was significantly higher than that of Gansu alpine fine wool sheep (p < 0.05). The diversity and richness of the rumen flora of Tianhua mutton sheep were higher than those of Gansu alpine fine wool sheep, and Beta analysis showed that the microflora structure of the two fine wool sheep was significantly different. At the phylum level, Firmicutes and Bacteroidetes dominated the rumen flora of Tianhua mutton sheep and Gansu alpine fine wool sheep. At the genus level, the dominant strains were Christensenellaceae_R_7_group and Rikenellaceae_RC9_gut_group. LEfSe analysis showed that Prevotella was a highly abundant differential species in Tianhua mutton sheep and lachnospiraccac was a highly abundant differential species in Gansu alpine fine wool sheep. Finally, both the KEGG and COG databases showed that the enrichment of biometabolic pathways, such as replication and repair and translation, were significantly higher in Tianhua mutton sheep than in Gansu alpine fine wool sheep (p < 0.05). In general, there were some similarities between Tianhua mutton sheep and Gansu alpine fine wool sheep in the rumen tissue morphology, rumen fermentation ability, and rumen flora structure. However, Tianhua mutton sheep had a better performance in the rumen acetic acid content, rumen papillae height, and beneficial bacteria content. These differences may be one of the reasons why Tianhua mutton sheep are more suitable for growing in alpine pastoral areas than Gansu alpine fine wool sheep.

Analysis of Rumen Degradation Characteristics, Attached Microbial Community, and Cellulase Activity Changes of Garlic Skin and Artemisia argyi Stalk

The purpose of this study was to study the chemical composition, rumen degradation characteristics, surface attached microbial community and cellulase activity of garlic skin (GS) and Artemisia argyi stalk (AS), in order to explain their feeding value. Four 14-month-old healthy Min Dong male goats with permanent rumen fistula were selected as experimental animals. The rumen degradation characteristics of GS and AS were determined by using the nylon bag method, and the bacterial composition, cellulase activity and their relationship on the surface of the two groups were analyzed with high-throughput sequencing of 16S rRNA gene. The results showed that in GS and AS, the effective degradation rate (ED) values of dry matter (DM) were 42.53% and 37.12%, the ED values of crude protein (CP) were 37.19% and 43.38%, the ED values of neutral detergent fiber (NDF) were 36.83% and 36.23%, and the ED values of acid detergent fiber (ADF) were 33.81% and 34.77%. During rumen degradation, the richness and evenness of bacteria attached to the AS surface were higher. At the phylum level, Bacteroidetes and Firmicutes were always the main rumen bacteria in the two groups. At the genus level, fiber-degrading bacteria such as Prevotella, Treponema, and Ruminococcus showed higher levels in GS (p < 0.05). Compared with GS, the activity of β-glucosidase (BG enzyme), endo-β-1,4-glucanase (C1 enzyme), exo-β-1,4-glucanase (Cx enzyme) and neutral xylanase (NEX enzyme) attached to AS surface showed a higher trend. Correlation analysis showed that the relative abundance of Succinivibrio and Rikenellaceae_RC9_gut_group was positively correlated with the rumen degradability of nutrients in GS, and the relative abundance of Christensenellaceae R-7_group, Succinivibrio and Ruminococcus was positively correlated with the rumen degradability of nutrients in AS. The conclusion of this study shows that AS has more potential to become ruminant roughage than GS. In addition, this study also revealed the relationship between cellulase activity and bacteria, which provided new information for us to better analyze the effects of GS and AS on the rumen of ruminants and provided an important theoretical basis for the development and utilization of agricultural by-products.

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.