Kaisen Zhao

Background: Local goat resources have unique meat quality and phenotypic advantages over cultivated breeds. Clarifying breed-specific metabolic differences in meat helps understand meat quality formation and resource utilization. Methods: the study used ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) technology to perform untargeted metabolomic analysis on the longissimus dorsi meat of Beichuan White goats (BCWG) and Tianfu goats (TMG). Results: A total of 452 differential metabolites were identified between the two breeds, including 100 lipids and lipid-like molecules, 74 organic acids and their derivatives, 12 nucleosides, nucleotides, and analogues, 204 organic compounds, and 62 unclassified metabolites. Among them, 132 metabolites exhibited higher abundance in Beichuan White goats and 320 metabolites showed significantly higher abundance in Tianfu goats. Metabolomic profiling revealed that differential metabolites of lipids and amino acids (e.g., valine and glutamate) might be correlated with interbreed disparities in meat sensory quality and flavor, as indicated by metabolomic profiling. BCWG displayed relatively higher abundances of nucleoside and nucleotide metabolites, which might hint at a possible link to variations in disease-resistance capacity. Among the 12 nucleoside and nucleotide differential metabolites, UDP-N-acetylglucosamine, 1-methyllinosine, 1-methylguanosine, 3-methylcytidine, and N-(2-Furanylmethyl) adenosine could serve as candidate molecular indicators for studying immune-related traits in goats. Conclusions: The study clarifies the breed-specific metabolic characteristics of the longissimus dorsi meat in BCWG and TMG at the metabolite level, provides novel molecular markers for chevon quality evaluation and immune trait selection, and lays a theoretical foundation for the rational development and utilization of local goat resources and improvement of cultivated meat goat breeds.

At present, it is common to feed calves with “Concentrate”, “Concentrate + hay” and TMR “Total Mixed Rations” feeding patterns in China, which achieved well feeding efficiency, but the three feeding patterns molecular regulation mechanism in actual production is still unclear. The study aimed to explore the most suitable feeding pattern for Chinese Holstein calves to improve the rumen fermentation function and growth performance of calves. In this regard, the interactions between rumen microorganisms and host metabolism were investigated. The rumen volume and weight of calves in the GF group were significantly higher than those in the GFF and TMR groups (p < 0.05), and the rumen pH of calves in the GF group was 6.47~6.79. Metagenomics analysis revealed that the rumen microbiome of GF and GFF calves had higher relative abundances of Methanobrevibacter, Methanosphaera, and Methanolacinia (p < 0.05). Prevotella multisaccharivorax was significantly more abundant in the rumen of GF calves (p < 0.05), indicating that GF group calves had a stronger ability to ferment sugars. Notably, in the pyruvate metabolic pathway, phosphoenolpyruvate carboxylase was significantly up-regulated in GF calves compared with the TMR group, and pyruvate-phosphate dikinase was significantly down-regulated. Metabolomic results showed that Ursodeoxycholic acid was significantly up-regulated in GF calves, and most of the differential metabolites were enriched in Bile secretion pathways. The association analysis study found that the microorganisms of Prevotella and Ruminococcaceae might cooperate with the host, which was helpful for the digestion and absorption of lipids and made the calves have better growth. The three feeding modes had similar effects, but the ‘GF’ feeding pattern was more beneficial to the individual growth and ruminal development regarding ruminal morphology, contents physiology and microorganisms. Furthermore, the synergistic effect of rumen microorganisms and the host could more effectively hydrolyze lipid substances and promote the absorption of lipids, which was of great significance to the growth of calves.

Obesity has become a major health problem worldwide, and increasing evidence supports the importance of microRNAs (miRNAs) in its pathogenesis. Recently, we found that miR-383-5p_1 is highly expressed in the perirenal fat of high-fat-fed rabbits, but it is not yet known whether miR-383-5p is involved in lipid metabolism. Here, we used transcriptome sequencing technology to screen 1642 known differentially expressed genes between miR-383-5p mimic groups and miR-383-5p negative control groups. Gene Ontology Resource (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were enriched in the pathway related to lipid metabolism, and glycine biosynthesis, the NOD receptor signal pathway and nonalcoholic fatty liver were significantly enriched. Afterwards, our research results indicated that miR-383-5p can promote the proliferation and differentiation of rabbit preadipocytes, and there is a direct targeting relationship with RAD51AP1. Mechanistically, miR-383-5p directly interacts with the lipid metabolism and participates in adipogenesis and lipid accumulation by targeting RAD51AP1. In conclusion, our data highlight a physiological role for miRNA in lipid metabolism and suggest the miR-383-5p/RAD51AP1 axis may represent a potential mechanism for controlling lipid accumulation in obesity.

At present, there is still room for research on the relationship between the vaginal microbiome and the reproductive health of dairy cows. In this study, high-throughput 16S rRNA sequencing technology was used to explore the differences of bacterial communities of dairy cows of different births, gain a deeper understanding of cow reproductive physiology, and maintain cow health. With the increase in parity, the number of vaginal flora decreased from 3511 to 469, but the number of species increased significantly, and Chao1 increased from 1226.41 ± 345.40 to 1467.76 ± 269.76. There was a significant difference in the number of vaginal microbiome functions between uncounted cows and calving cows. There was no significant difference in microbial diversity in calves. The relative abundance variation of vaginal microbiota in high-parity cows is less than that in low-parity cows. The amino acid metabolism of calves increased, the endocrine function of high-parity cows was enhanced, and the function of the vaginal microbiome increased after the first delivery, which gradually decreased with the increase in parity. This study also found that Methanobacteria and Caviibacter may be involved in amino acid metabolism and endocrine function, and they may play a key role in cow reproduction. This study provides an important theoretical basis for studying changes in vaginal microorganisms in dairy cows, improves the understanding of reproductive health and production performance, and provides a scientific basis for improving the reproductive management of dairy cows.

Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM–receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.

For many years, antibiotics in feed have been an effective and economical means to promote growth and disease resistance in livestock production. However, the rampant abuse of antibiotics has also brought very serious harm to human health and the environment. Therefore, the Chinese government promulgated laws and regulations on 1 July 2020, to prohibit the use of antibiotics in feed. To improve the effect of antibiotic-free feeding on China’s existing rabbit industry, we used the nontargeted metabolomics method to detect the differences between diarrhea rabbits (Dia) and normal rabbits (Con) on an antibiotic-free diet. A total of 1902 different metabolites were identified. A KEGG analysis showed that in the cecum, metabolites were mainly concentrated in bile secretion, antifolate resistance, aldosterone synthesis, and secretion pathways. The ileal metabolites were mainly concentrated in tyrosine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, steroid hormone biosynthesis, alanine, aspartate, and glutamate metabolism. The metabolites in the jejunum were mainly rich in panquinone and other terpenoid compound quinone biosynthesis, AMPK (adenosine 5′-monophosphate (AMP)-activated protein kinase) signal, inositol phosphate metabolism, and pentose phosphate pathway. After a deep excavation of the discovered differential metabolites and metabolic pathways with large differences between groups, it was found that these metabolic pathways mainly involved intestinal inflammation, intestinal barrier, and autophagy. The results showed that panquinone and other terpenoids could increase AMPK activity to promote cell metabolism and autophagy, thus trying to prevent inflammation and alleviate intestinal disease symptoms. In addition, we discussed the possible reasons for the changes in the levels of seven intestinal endogenous metabolites in rabbits in the diarrhea group. The possibility of improving diarrhea by adding amino acids to feed was discussed. In addition, the intermediate products produced by the pentose phosphate pathway and coenzyme Q had a positive effect on steroid hormone biosynthesis to combat intestinal inflammation.

Diarrhea symptoms appeared after antibiotics were banned from animal feed based on the law of the Chinese government in 2020. The colon and its contents were collected and analyzed from diarrheal and healthy rabbits using three omics analyses. The result of the microbial genomic analysis showed that the abundance of Bacteroidetes and Proteobacteria increased significantly (p-value < 0.01). Transcriptomes analysis showed that differentially expressed genes (DEGs) are abundant in the IL-17 signaling pathway and are highly expressed in the pro-inflammatory pathway. The metabolome analysis investigated differential metabolites (DMs) that were mainly enriched in tryptophan metabolism and bile secretion, which were closely related to the absorption and immune function of the colon. The results of correlation analysis showed that Bacteroidetes was positively correlated with 4-Morpholinobenzoic acid, and 4-Morpholinobenzoic acid could aggravate inflammation through its influence on the bile secretion pathway. The enriched DMs L-Tryptophan in the tryptophan metabolism pathway will lead to the functional disorder of inhibiting inflammation by affecting the protein digestion and absorption pathway. Thus, the colonic epithelial cells were damaged, affecting the function of the colon and leading to diarrhea in rabbits. Therefore, the study provided an idea for feed development and a theoretical basis for maintaining intestinal tract fitness in rabbits.

With the comprehensive prohibition of antibiotics in the feed industry in China, the incidence of diarrhea in rabbits increased, such as loss of appetite, vomiting, and excretion of atheromatous feces. In order to explore the pathological and the molecular mechanisms of the diarrhea in the rabbitry fed with antibiotic-free diet, we used microbial metagenomics, transcriptome, and non-targeted metabolomics sequencing. The results showed that the Firmicutes level was significantly decreased (p < 0.001) and the Proteobacteria level was significantly increased (p < 0.05). The functional enrichment of cecum revealed that most differentially expressed genes (DEGs) were expressed in immune, inflammatory, and metabolic processes. The enrichment of the cecal fecal metabolites focused on the bile secretion, antifolate resistance, and tryptophan metabolism pathways, which are mainly associated with inflammation. The results of correlation analysis showed that Fournierella was positively correlated with myricetin, ursolic acid, and furtherly might cause bile secretion and tryptophan metabolism disorder, aggravate intestinal inflammation, change intestinal permeability, and reduce host immunity, leading to diarrhea in rabbits. This study provides a theoretical basis for illustrating the reason for diarrhea and developing new feeds for the health of rabbits.