The unique flavors of fermented foods significantly influence consumer purchasing choices, prompting widespread scientific interest in the flavor development process. Fermented rice and wheat foods are known for their unique flavors and they occupy an important place in the global diet. Many of these are produced on an industrial scale using starter cultures, whereas others rely on spontaneous fermentation, homemade production, or traditional activities. Microorganisms are key in shaping the sensory properties of fermented products through different metabolic pathways, thus earning the title \"the essence of fermentation.\" Therefore, this study systematically summarizes the key microbial communities and their interactions that contribute positively to iconic fermented rice and wheat foods, such as steamed bread, bread, Mifen, and rice wine. This study revealed the mechanism by which these core microbial communities affect flavor and revealed the strategies of core microorganisms and related enzymes to enhance flavor during fermentation.

Lactic acid bacteria are commonly used in plant-based fermentation to reduce off-flavor and improve sensory characteristics. However, there have been few studies on Latilactobacillus sakei for plant-based yogurt fermentation and, particularly, its metabolic features at the genomic level remain unclear. This study aims to analyze the fermentation characteristics of the L. sakei DCF0720 strain and compare genetics and metabolic relations. For this, DCF0720 was used to ferment the black soybean milk and conduct the physicochemical analysis and sensory test. The genomic and metabolic analyses were performed by complete genome sequencing and 500 MHz 1H NMR, respectively. As a result, DCF0720 exhibited enhanced fermentation performance and sensory evaluations at 37 °C compared to 30 °C, which is generally recognized as the optimal growth temperature for most L. sakei strains. It also produced flavor enhancing volatile compounds such as acetoin and hydroxyacetone, possessing all three key genes for acetoin biosynthesis. DCF0720 lacks 2,3-butanediol dehydrogenase, which leads to the inhibition of acetoin production. DCF0720 possesses a complete pathway to utilize primary black soybean carbon sources such as sucrose, raffinose, and stachyose. DCF0720 also possesses genes for the GH28 family, including the key enzymes in the hydrolysis of pectin substances, which means eliminating the main soybean nonstarch polysaccharides. This study demonstrates that DCF0720 is a suitable starter for plant-based yogurt fermentation, providing a better understanding of fermentation conditions with genetic and metabolic features for black soybean yogurt. Various carbon source utilization abilities with depth metabolic pathway analysis provide that DCF0720 can be employed to develop enhanced starter cultures for black soybean yogurt and diverse plant-based yogurts.

Colon cancer is on the rise in younger adults. Despite multimodal treatment strategies, clinical outcomes in advanced stage colon cancer patients remain poor. Neoadjuvant/adjuvant chemotherapy efficacy is limited due to chemoresistance, toxicity, and negative side effects. Overwhelming evidence supporting the small-molecule metabolites derived from breakdown of food or microbial sources confer an extensive array of host benefits, including chemo-preventive role in colon cancer. Our previous study indicated that the introduction of glyoxylate (Glx), an intermediate product of microbial or plant metabolism, exerts a cytotoxic effect in colon cancer cells. This study was designed to evaluate the effects of Glx on colon cancer with molecular insights. For this, we established an AOM/DSS-induced colitis associated colon cancer model in mice. Supplementation of Glx in vivo reduced colitis associated tumor growth and altered the metabolic characteristics of tumor tissue in mice without initiating any severe liver or renal toxicity. More specifically, intake of glyoxylate accumulated glycine in the colon tissue by elevation of alanine-glyoxylate transferase (AGXT) activity. Glycine accumulation increased intracellular Ca2+ concentration via glycine receptor activation and dysregulation of Ca2+ homeostasis lead to induction of apoptosis that resulted in arresting tumor growth. Interestingly, elevation of AGXT activity or Glx related specific metabolic pathway provides better survival in colon cancer patients. Collectively, our exclusive findings support the exploration of Glx either as a preventive molecule or its inclusion in the treatment regimens for colon cancer.

UNASSIGNED: Diabetic retinopathy (DR) is one of the common chronic complications of diabetes mellitus, which has developed into the leading cause of irreversible visual impairment in adults worldwide. Compound Qilian tablets (CQLT) is a traditional Chinese medicine (TCM) developed for treating DR, but its mechanism is still unclear. This study explored the mechanism of action of CQLT in treating DR through metabolomics and intestinal microbiota.
UNASSIGNED: Histopathologic examination of the pancreas and retina of Zucker diabetic fatty (ZDF) rats and immunohistochemistry were used to determine the expression levels of retinal nerve damage indicators ionized calcium binding adaptor molecule-1 (Iba-1) and glial fibrillary acidic protein (GFAP). Rat fecal samples were tested by LC-MS metabolomics to search for potential biomarkers and metabolic pathways for CQLT treatment of DR. Characteristic nucleic acid sequences of rat intestinal microbiota from each group were revealed using 16S rDNA technology to explore key microbes and related pathways for CQLT treatment of DR. At the same time, we investigated the effect of CQLT on the gluconeogenic pathway.
UNASSIGNED: After CQLT intervention, islet cell status was improved, Iba-1 and GFAP expression were significantly decreased, and abnormal retinal microvascular proliferation and exudation were ameliorated. Metabolomics results showed that CQLT reversed 20 differential metabolites that were abnormally altered in DR rats. Intestinal microbiota analysis showed that treatment with CQLT improved the abundance and diversity of intestinal flora. Functional annotation of metabolites and intestinal flora revealed that glycolysis/gluconeogenesis, alanine, aspartate and glutamate metabolism, starch and sucrose metabolism were the main pathways for CQLT in treating DR. According to the results of correlation analysis, there were significant correlations between Iba-1, GFAP, and intestinal microbiota and metabolites affected by CQLT. In addition, we found that CQLT effectively inhibited the gluconeogenesis process in diabetic mice.
UNASSIGNED: In conclusion, CQLT could potentially reshape intestinal microbiota composition and regulate metabolite profiles to protect retinal morphology and function, thereby ameliorating the progression of DR.

The increasing production of industrial solid waste requires better disposal solutions. Porous hollow microspheres (PHM) are small inorganic materials with high surface area and adsorption capacity, but their potential for use in anaerobic digestion (AD) has not been explored. With PHM as additive, the effects of different industrial solid wastes (waste glass, steel slag, and fly ash) with different loadings (2 %-8 %), respectively, on the AD of corn straw were investigated in this study. The results showed that PHM could supplement trace elements and promote biofilm formation, which effectively shortened the lag period (25.00-60.87 %) and increased the methane yield (4.75 %-16.28 %). The 2 % PHM loading based on steel slag gave the highest methane yield (300.16 NmL/g VSadd). Microbial and PICRUSt2 analyses indicated that PHM enriched hydrolytic and acidogenic bacteria, increased the abundance of methanogenesis-related enzyme genes. This study provides a theoretical basis for the comprehensive utilization of coupled industrial and agricultural wastes.

Atrazine is one of the most used herbicides, posing non-neglectable threats to ecosystem and human health. This work studied the performance and mechanisms of surface-modified biochar in accelerating atrazine biodegradation by exploring the changes in atrazine metabolites, bacterial communities and atrazine degradation-related genes. Among different types of biochar, nano-hydroxyapatite modified biochar achieved the highest degradation efficiency (85.13 %), mainly attributing to the increasing pH, soil organic matter, soil humus, and some enriched indigenous bacterial families of Bradyrhizobiaceae, Rhodospirillaceae, Methylophilaceae, Micrococcaceae, and Xanthobacteraceae. The abundance of 4 key atrazine degradation-related genes (atzA, atzB, atzC and triA) increased after biochar amendment, boosting both dechlorination and dealkylation pathways in atrazine metabolism. Our findings evidenced that biochar amendment could accelerate atrazine biodegradation by altering soil physicochemical properties, microbial composition and atrazine degradation pathways, providing clues for improving atrazine biodegradation performance at contaminated sites.

Pesticide residues in soil, especially multiple herbicide residues, cause a series of adverse effects on soil properties and microorganisms. In this work, the degradation of three herbicides and the effect on bacterial communities under combined pollution was investigated. The experimental results showed that the half-lives of acetochlor and prometryn significantly altered under combined exposure (5.02-11.17 d) as compared with those of individual exposure (4.70-6.87 d) in soil, suggesting that there was an antagonistic effect between the degradation of acetochlor and prometryn in soil. No remarkable variation in the degradation rate of atrazine with half-lives of 6.21-6.85 d was observed in different treatments, indicating that the degradation of atrazine was stable. 16S rRNA high-throughput sequencing results showed that the antagonistic effect of acetochlor and prometryn on the degradation rate under combined pollution was related to variation of the Sphingomonas and Nocardioide. Furthermore, the potential metabolic pathways of the three herbicides in soil were proposed and a new metabolite of acetochlor was preliminarily identified. The results of this work provide a guideline for the risk evaluation of combined pollution of the three herbicides with respect to their ecological effects in soil.

Hyperlipidemia is a lipid metabolism disorder that refers to increased levels of total triglycerides (TGs), cholesterol (TC), and low-density lipoprotein-cholesterol (LDL-C) and decreased levels of high-density lipoprotein-cholesterol (HDL-C). It is a major public health issue with increased prevalence and incidence worldwide. The ability to identify individuals at risk of this disorder before symptoms manifest will facilitate timely intervention and management to avert potential complications. This can be achieved by employing metabolomics as an early detection method for the diagnostic biomarkers of hyperlipidemia. Metabolomics is an analytical approach used to detect and quantify metabolites. This provides the ability to explain the metabolic processes involved in the development and progression of certain diseases. In recent years, interest in the use of metabolomics to identify disease biomarkers has increased, and several biomarkers have been discovered, such as docosahexaenoic acid, glycocholic acid, citric acid, betaine, and carnitine. This review discusses the primary metabolic alterations in the context of hyperlipidemia. Furthermore, we provide an overview of recent studies on the application of metabolomics to the assessment of the efficacy of traditional herbal products and common lipid-lowering medications.

UNASSIGNED: Inflammatory bowel disease (IBD) is a common chronic inflammatory bowel disease characterized by diarrhea and abdominal pain. Recently human metabolites have been found to help explain the underlying biological mechanisms of diseases of the intestinal system, so we aimed to assess the causal relationship between human blood metabolites and susceptibility to IBD subtypes.
UNASSIGNED: We selected a genome-wide association study (GWAS) of 275 metabolites as the exposure factor, and the GWAS dataset of 10 IBD subtypes as the outcome, followed by univariate and multivariate analyses using a two-sample Mendelian randomization study (MR) to study the causal relationship between exposure and outcome, respectively. A series of sensitivity analyses were also performed to ensure the robustness of the results.
UNASSIGNED: A total of 107 metabolites were found to be causally associated on univariate analysis after correcting for false discovery rate (FDR), and a total of 9 metabolites were found to be significantly causally associated on subsequent multivariate and sensitivity analyses. In addition we found causal associations between 7 metabolite pathways and 6 IBD subtypes.
UNASSIGNED: Our study confirms that blood metabolites and certain metabolic pathways are causally associated with the development of IBD subtypes and their parenteral manifestations. The exploration of the mechanisms of novel blood metabolites on IBD may provide new therapeutic ideas for IBD patients.

Vitamins, as indispensable organic compounds in life activities, demonstrate a complex and refined metabolic network in organisms. This network involves the coordination of multiple enzymes and the integration of various metabolic pathways. Despite the achievements in metabolic engineering and catalytic mechanism research, the lack of studies regarding detailed enzymatic properties for a large number of key enzymes limits the enhancement of vitamin production efficiency and hinders the in-depth understanding and optimization of vitamin synthesis mechanisms. Such limitations not only restrict the industrial application of vitamins but also impede the development of related bio-technologies. This study comprehensively reviews the research progress in the enzymes involved in vitamin biosynthesis and details the current status of research on the enzymes of 13 vitamin synthesis pathways, including their catalytic mechanisms, kinetic properties, and applications in biology. In addition, this study compares the properties of enzymes involved in vitamin metabolic pathways and the glycolysis pathway, and reveals the characteristics of catalytic efficiency and substrate affinity of enzymes in vitamin synthesis pathways. Furthermore, this study discusses the potential and prospects of applying deep learning methods to the research on properties of enzymes associated with vitamin biosynthesis, giving new insights into the production and optimization of vitamins.