The complex structure of lignocellulose, one of the most abundant renewable resources on earth, makes biodegradation challenging. Ruminant gastrointestinal microbiota achieves efficient lignocellulose degradation through a highly synergistic ecosystem, which provides an important research model for sustainable energy development and high value-added chemical production. This review systematically summarizes the key mechanisms of lignocellulose degradation by ruminant gastrointestinal microorganisms, focusing on the synergistic roles of rumen and hindgut (including cecum, colon, and rectum) microorganisms in cellulose, hemicellulose, and lignin degradation. The study focuses on the functional differentiation and cooperation patterns of bacteria, fungi and protozoa in lignocellulose decomposition, and summarizes the roles of carbohydrate-active enzymes (CAZymes) and their new discoveries under the histological techniques. In addition, this manuscript explores the potential application of gastrointestinal tract (GIT) microbial degradation mechanisms in improving the utilization of straw-based feeds. In the future, by revealing the mechanism of microbe-host synergy and integrating multi-omics technologies, the study of ruminant gastrointestinal microbial ecosystems will provide new solutions to promote the efficient utilization of lignocellulose and alleviate the global energy crisis.

Milk is rich in a variety of essential nutrients, including fats, proteins, and trace elements that are important for human health. In particular, milk fat has an alleviating effect on diseases such as heart disease and diabetes. Fatty acids, the basic units of milk fat, play an important role in many biological reactions in the body, including the involvement of glycerophospholipids and sphingolipids in the formation of cell membranes. However, milk fat synthesis is a complex biological process involving multiple organs and tissues, and how to improve milk fat of dairy cows has been a hot research issue in the industry. There exists a close relationship between milk fat synthesis, genes, and microbial functions, as a result of the organic integration between the different tissues of the cow’s organism and the external environment. This review paper aims (1) to highlight the synthesis and regulation of milk fat by the first and second genomes (gastrointestinal microbial genome) and (2) to discuss the effects of ruminal microorganisms and host metabolites on milk fat synthesis. Through exploring the interactions between the first and second genomes, and discovering the relationship between microbial and host metabolite in the milk fat synthesis pathway, it may become a new direction for future research on the mechanism of milk fat synthesis in dairy cows.

As a semi-wild breed, Gayals have a strong fiber degradation capacity, which is unique to the microbial structure and function of their rumen. In this study, the unique rumen microbial composition and function of Gayals were investigated by metagenomic sequencing, with the Yunnan yellow cattle as the control. We compared the differences in rumen micro-organisms between Gayals and the Yunnan Yellow cattle, and the results showed that there were differences in bacteria, archaea and fungi between Gayals and the Yunnan Yellow cattle, while no significant abundance changes were observed in the protozoa. In addition, the ratio of Firmicutes to Bacteroidetes (1.06) in Gayals was higher than that of the Yunnan Yellow cattle (0.66). Three enzymes (PTA, ACH and FTHFS) related to the acetate production pathway and five enzymes (BHBD, THL, PTB, BK and BCACT) involved in butyric acid production were annotated in this study. The CAZymes search results showed that the abundance of GH5, GH26, GH94, CBM11 and CBM63 in Gayals was higher than in the Yunnan Yellow cattle (p < 0.05). Furthermore, this research constructed a model of rumen micro-organisms degrading fibers according to the characteristics and differences in the rumen microbiota structures and functions of the two breeds. This study expands our knowledge of the rumen microbiota and the mechanisms of fiber degradation in Gayals.

Beef flavor is affected by muscle metabolites and their related regulatory genes, and the molecular regulatory mechanisms vary among different beef breeds. To provide some new ways to improve meat quality and cattle breed improvement, 24-month-old Gayal (n = 8) and yellow cattle (n = 8) were selected for comparison in this study. The result revealed that the longissimus dorsi muscle fiber diameter, protein content and a-value of Gayal were significantly higher than that of yellow cattle, but the fat content was lower than that of yellow cattle. Furthermore, Gayal meat contained notably higher levels of polyunsaturated fatty acids (PUFA) and n-3PUFA than that of yellow cattle, and also had better levels of flavor amino acids (FAAs) and sweet amino acids (SAAs), which contribute to the flavor of beef. Through comprehensive analysis of transcriptomics and metabolomics, we detected a total of 109 markedly different metabolites (DEMs) and 1,677 differentially expressed genes (DEGs) in the pectoral muscles of the two breeds. Further analysis indicated that amino acid and lipid metabolism might be the key factors contributing to the differences in meat quality and flavor between Gayal and yellow cattle, involving metabolites such as L-2-aminobutyric acid, L-glutamic acid, L-glutamine, L-serine, betaine, pantothenic acid, and taurine. Through correlation analysis, we identified genes highly associated with flavor amino acids (GSTM3, GSTT2), muscle development (FGF10, EIF4EBP1, PPP2R2C), and lipid metabolism (CYP4A22, ACOX3, PLIN1, ADH6, CNDP1, LPAR3, BRCA1, ADIPOQ, FABP3) related essential regulatory genes and constructed a gene-metabolite interaction network for meat quality and flavor formation in Gayal. In summary, it was shown that significant differences in muscle metabolites between Gayal and yellow cattle, especially in amino acid and lipid metabolism, may be the major reason for the differences in quality and flavor between the two types of beef. This study provides a theoretical basis for further exploring the molecular regulatory mechanisms of the differences in beef quality and flavor between Gayal and yellow cattle, and provides a reference for the development and genetic breeding of high-quality cattle breeds.

Consumers are increasing their daily demand for beef and are becoming more discerning about its nutritional quality and flavor. The present objective was to evaluate how the ration energy content (combined net energy, Nemf) impacts the slaughter performance, carcass characteristics, and meat qualities of Honghe yellow cattle raised in confinement. Fifteen male Honghe yellow cattle were divided into three groups based on a one-way design: a low-energy group (LEG, 3.72 MJ/kg), a medium-energy group (MEG, 4.52 MJ/kg), and a high-energy group (HEG, 5.32 MJ/kg). After a period of 70 days on these treatments, the animals were slaughtered and their slaughter performance was determined, and the longissimus dorsi muscle (LD) and biceps femoris (BF) muscles were gathered to evaluate meat quality and composition. Increasing the dietary energy concentration led to marked improvements (p < 0.05) in the live weight before slaughter (LWBS), weight of carcass, backfat thickness, and loin muscle area. HEG also improved the yield of high-grade commercial cuts (13.47% vs. 10.39%) (p < 0.05). However, meat quality traits were not affected by treatment except for shear force, which was affected by dietary energy. A significant improvement (p < 0.05) in the intramuscular fat (IMF) content was observed in the HEG. Little effect on the amino acid profile was observed (p > 0.05), except for a tendency (p = 0.06) to increase the histidine concentration in the BF muscle. Increasing dietary energy also reduced C22:6n-3 and saturated fatty acids (SFAs) and enhanced C18:1 cis-9 and monounsaturated fatty acids (MUFAs, p < 0.05). Those results revealed that increasing energy levels of diets could enhance slaughter traits and affect the meat quality and fatty acid composition of different muscle tissues of Honghe yellow cattle. These results contribute to the theoretical foundation to formulate nutritional standards and design feed formulas for the Honghe yellow cattle.

The present study was conducted to analyze the correlation between the milk fat content of Binglangjiang buffaloes and their microbial and host metabolites. The 10 buffaloes with the highest milk fat content (HF, 5.60 ± 0.61%) and the 10 with the lowest milk fat content (LF, 1.49 ± 0.13%) were selected. Their rumen fluid and plasma were collected for rumen microbiota and metabolome analysis. The results showed that the rumen bacteria abundance of Synergistota, Quinella, Selenomonas, and Fretibacterium was significantly higher in the HF buffaloes. The abundance of 14 rumen fungi, including Candida, Talaromyces, Cyrenella, and Stilbella, was significantly higher in the HF buffaloes. The analysis of the metabolites in the rumen and plasma showed that several metabolites differed between the HF and LF buffaloes. A total of 68 and 42 differential metabolites were identified in the rumen and plasma, respectively. By clustering these differential metabolites, most of those clustered in the HF group were lipid and lipid-like molecules such as secoeremopetasitolide B, lucidenic acid J LysoPE (0:0/18:2 (9Z, 12Z)), and 5-tetradecenoic acid. Spearman’s rank correlations showed that Quinella, Fretibacterium, Selenomonas, Cyrenella, and Stilbella were significantly positively correlated with the metabolites of the lipids and lipid-like molecules in the rumen and plasma. The results suggest that rumen microbiota such as Quinella, Fretibacterium, Selenomonas, and Cyrenella may regulate milk fat synthesis by influencing the lipid metabolites in the rumen and plasma. In addition, the combined analysis of the rumen microbiota and host metabolites may provide a fundamental understanding of the role of the microbiota and host in regulating milk fat synthesis.