Metabolomics Work Flow and Analytics in Systems Biology

Metabolomics-Driven Insights into Biomarkers for Poor Ovarian Response: A Narrative Review

Poor ovarian response (POR) remains a significant challenge in the field of assisted reproductive technology (ART), as the quantity and quality of oocytes retrieved directly influence embryo implantation, clinical pregnancy, and live birth rates. Metabolomics has become a valuable tool for elucidating the molecular mechanisms underlying diminished ovarian reserve (DOR) and POR. This review aims to synthesize findings from metabolomic studies examining metabolite expression patterns in serum and follicular fluid samples from women with POR. A literature search was performed using the Medline/PubMed and Scopus databases, employing keywords related to metabolomics and POR. In total, nine studies met the inclusion criteria for this review. These studies identified several metabolites with differential expression in serum and follicular fluid samples between women with normal ovarian response and those with POR. Although the metabolomic profiles varied significantly among studies, consistent alterations in prostaglandin related metabolites were observed in two of the nine studies reviewed. These findings suggest that, pending further validation, these metabolites may serve as potential biomarkers for ovarian response. Metabolomics has significantly advanced our understanding of the mechanisms underlying ovarian function and holds promise for identifying effective biomarkers that could improve the prediction and management of POR.

Recent findings on metabolomics and the microbiome of oral bacteria involved in dental caries and periodontal disease

Periodontal disease is characterized by bacterial toxins within the oral biofilm surrounding the teeth, leading to gingivitis and the gradual dissolution of the alveolar bone, which supports the teeth. Notably, symptoms in the early stages of the disease are often absent. Similarly, dental caries occurs when oral bacteria metabolize dietary sugars, producing acids that dissolve tooth enamel and dentin. These bacteria are commonly present in the oral cavity of most individuals. Metabolomics, a relatively recent addition to the "omics" research landscape, involves the comprehensive analysis of metabolites in vivo to elucidate pathological mechanisms and accelerate drug discovery. Meanwhile, the term "microbiome" refers to the collection of microorganisms within a specific environmental niche or their collective genomes. The human microbiome plays a critical role in health and disease, influencing a wide array of physiological and pathological processes. Recent advances in microbiome research have identified numerous bacteria implicated in dental caries and periodontal disease. Additionally, studies have uncovered various pathogenic factors associated with these microorganisms. This review focuses on recent findings in metabolomics and the microbiome, specifically targeting oral bacteria linked to dental caries and periodontal disease. We acknowledge the limitation of relying exclusively on the MEDLINE database via PubMed, while excluding other sources such as gray literature, conference proceedings, and clinical practice guidelines.

Effects of Different Drying Methods on Amino Acid Metabolite Content and Quality of Ophiocordyceps sinensis by LC-MS/MS Combined with Multivariate Statistical Methods

Ophiocordyceps sinensis, a medicinal fungus utilized in traditional Chinese medicine, exhibits a range of biological activities and pharmacological functions. In this study, we determined the amino acid composition of 94 amino acids in Ophiocordyceps sinensis using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fresh samples of Ophiocordyceps sinensis were analyzed under three different drying methods: vacuum freeze drying (DG), oven drying (HG), and air drying (YG). This investigation aims to assess the effects of these drying methods on the content and quality of amino acid metabolites in Ophiocordyceps sinensis. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were employed for sample classification and the identification of differentially accumulated metabolites (DAMs). The results revealed the detection of 79 amino acid metabolites, which included elevated levels of oxidized L-glutamic acid, L-glutamic acid, and glutathione. Differential amino acid metabolites that met the criteria of fold change (|FC|) ≥ 2, p-value (p) ≤ 0.5, and variable importance in projection (VIP) ≥ 1 were analyzed. Significant differences in 48 amino acid metabolites between the groups were primarily related to protein synthesis. According to the KEGG analysis, all three comparison samples exhibited significant enrichment in several pathways. These pathways included the interaction of neuroactive ligands with receptors, the metabolism of cysteine and methionine, and the biosynthesis of plant hormones. The variations in amino acid metabolite levels observed across the three drying methods may be attributed to the degradation of proteins or amino acid metabolites, influenced by several factors, including temperature, enzyme activity, and moisture content. Additionally, Maillard and oxidative reactions involving substances such as amino acids, sugars, and oxygen may also play a significant role. This study demonstrates that various drying methods significantly influence the amino acid metabolite content of Ophiocordyceps sinensis. Therefore, the selection of drying methods should be tailored to meet specific requirements. This research provides important insights into the metabolite composition of Ophiocordyceps sinensis under different drying techniques, thereby contributing to a more comprehensive understanding of its nutritional and therapeutic properties.

Pan-Omics in Sheep: Unveiling Genetic Landscapes

Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.

Arecoline-Induced Hepatotoxicity in Rats: Screening of Abnormal Metabolic Markers and Potential Mechanisms

Arecoline is a pyridine alkaloid derived from areca nut in the Arecaceae family. It has extensive medicinal activity, such as analgesic, anti-inflammatory, and anti-allergic. However, the toxicity of Arecoline limits its application. Most current studies on its toxicity mainly focus on immunotoxicity, carcinogenesis, and cancer promotion. However, there are few systematic studies on its hepatotoxicity and mechanisms. Therefore, this research explored the mechanism of hepatotoxicity induced by Arecoline in rats and analyzed endogenous metabolite changes in rat plasma by combining network toxicology with metabolomics. The differential metabolites after Arecoline exposure, such as D-Lysine, N4-Acetylaminobutanal, and L-Arginine, were obtained by metabolomics study, and these differential metabolites were involved in the regulation of lipid metabolism, amino acid metabolism, and vitamin metabolism. Based on the strategy of network toxicology, Arecoline can affect the HIF-1 signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, and other concerning pathways by regulating critical targets, such as ALB, CASP3, EGFR, and MMP9. Integration of metabolomics and network toxicology results were further analyzed, and it was concluded that Arecoline may induce hepatotoxicity by mediating oxidative stress, inflammatory response, energy and lipid metabolism, and cell apoptosis.

Exploring the roles of microorganisms and metabolites in the 30-year aging process of the dried pericarps of Citrus reticulata 'Chachi' based on high-throughput sequencing and comparative metabolomics

GuangChenpi (GCP), the dried pericarps of Citrus reticulata 'Chachi', has been consumed daily as a food and dietary supplement in China for centuries. Its health benefits are generally recognized to be dependent on storage time. However, the specific roles of microorganisms and metabolites during long-term storage are still unclear. In this study, comparative metabolomics and high-throughput sequencing techniques were used to investigate the effects of co-existing microorganisms on the metabolites in GCP stored from 1 to 30 years. In total, 386 metabolites were identified and characterized. Most compounds were flavonoids (37%), followed by phenolic acids (20%). Seventeen differentially upregulated metabolites were identified as potential key metabolites in GCP, and 8 of them were screened out as key active ingredients by Venn diagram comparative analyses and verified by network pharmacology and molecular docking. In addition, long-term storage could promote the accumulation of secondary metabolites. Regarding the GCP microbiota, Xeromyces dominated the whole 30-year aging process.Moreover, Spearman correlation analysis indicated that Bacillus thuringiensis and Xeromyces bisporus, the dominant bacterial and fungal species, were strongly associated with the key active metabolites. Our results suggested that the change of active ingredients caused by the dominant microbial is one of the mechanisms affecting the GCP aging process. Our study provides novel functional insights and research perspectives on microorganism-associated metabolite changes that may improve the GCP aging process.

Untargeted metabolomic analysis of metabolites related to body dysmorphic disorder (BDD)

Body dysmorphic disorder (BDD) is a disorder associated with depression and eating disorders. It often arises from minor defects in appearance or an individual imagining that he or she is defective. However, the mechanisms causing BDD remain unclear, and its pathogenesis and adjuvant treatment methods still need to be explored. Here, we employed a liquid chromatography-mass spectrometry (LC-MS)-based metabolomics approach to identify key metabolic differences in BDD versus healthy patients. We obtained plasma samples from two independent cohorts (including eight BDD patients and eight healthy control patients). Raw data were analyzed using Compound Discoverer to determine peak alignment, retention time correction, and extraction of peak areas. Metabolite structure identification was also obtained using Compound Discoverer by of accurate mass matching (< 10 ppm) and secondary spectral matching queries of compound databases. Next, multidimensional statistical analyses were performed using the ropls R package. These analyses included: unsupervised principal component analysis, supervised partial Least-Squares Discriminant Analysis, and orthogonal partial Least-Squares Discriminant Analysis. We then identified the most promising metabolic signatures associated with BDD across all metabolomic datasets. Principal component analysis showed changes in small-molecule metabolites in patients, and we also found significant differences in metabolite abundance between the BDD and normal groups. Our findings suggest that the occurrence of BDD may be related to metabolites participating in the following KEGG pathways: ABC transporters, purine metabolism, glycine, serine and threonine metabolism, pyrimidine, pyrimidine metabolism, biosynthesis of 12-, 14-, and 16-membered macrolides, microbial metabolism in diverse environments, biosynthesis of secondary metabolites, and caffeine and insect hormone biosynthesis.