Carbohydrate Metabolic Pathways Research Articles

Dynamics of Fermentation Parameters and Bacterial Community in Rumen of Calves During Dietary Protein Oscillation

Dietary crude protein concentration oscillation can improve the nitrogen utilization efficiency of ruminants. However, little is known about the dynamic changes in microbiota and fermentation in the rumen of calves during the oscillation period. In this study, six calves were fed an oscillating diet at 2-day intervals, including a high-protein diet (HP) and a low-protein diet (LP). The rumen fermentation parameters, plasma urea-N concentration, and rumen bacterial diversity were characterized throughout the oscillation period. The concentrations of volatile fatty acids, NH3-N, and plasma urea-N in rumen changed significantly with an oscillating diet. The abundance of Prevotella_1, Selenomonadales, Succiniclasticum, Clostridiales, Ruminococcaceae, Lachnospiraceae, and Rikenellaceae_RC9_gut_group showed significant changes with diet. Prevotella_1 was positively correlated, and Lachnospiraceae_AC2044_group and Saccharofermentans were negatively correlated with NH3-N. The abundance of Amino Acid Metabolism, Metabolism of Other Amino Acids, and Glycan Biosynthesis and Metabolism pathways, annotated by bacterial functional genes, decreased when the diet changed from HP to LP. The abundance of the Carbohydrate Metabolism pathway increased after the two dietary changes. In conclusion, the plasma urea-N concentration was not as sensitive and quick to adapt to diet changes as the rumen fermentation parameters. Rumen bacteria were responsible for increasing the nitrogen utilization efficiency of calves fed an oscillating diet.

Detrimental effects of glyphosate on muscle metabolism in grass carp (Ctenopharyngodon idellus)

Glyphosate, a commonly used herbicide, has been associated with environmental pollution and potential health risks to aquatic organisms. This study investigated the effects of glyphosate on the muscle metabolism of grass carp (Ctenopharyngodon idellus) following exposure to environmentally relevant concentrations. Over a 14-day exposure period to varying glyphosate levels, significant disruptions were observed in antioxidant capacity and muscle health. These disruptions were evidenced by reductions in total antioxidant capacity (T-AOC), increases in malondialdehyde (MDA) levels, and decreases in activities of glutathione peroxidase (GSH-PX) and catalase (CAT). Furthermore, exposure to glyphosate resulted in a reduction of vitamin E content and an elevation of hormonal levels, suggesting the potential for endocrine disruption. Metabolomics analysis identified 605 distinct metabolites, with notable alterations in amino acid, carbohydrate, and nucleotide metabolism pathways. Specifically, arginine and glutathione metabolisms were severely impacted, with decreases in key amino acids such as glycine and glutathione at higher glyphosate concentrations. Nucleotide metabolism, particularly purine synthesis, was also significantly affected, with reduced levels of deoxyguanosine and other purine-related compounds. The study further investigated the origins of these differential metabolites using the MetOrigin platform, suggesting a potential involvement of the intestinal microbiota in the metabolic response to glyphosate. These findings highlight the multifaceted adverse effects of glyphosate on fish muscle, including oxidative stress and metabolic dysregulation, which may contribute to diminished muscle quality and health risks for aquatic organisms.

Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.

Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre-TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients.

Effects of Shaofu Zhuyu decoction on intestinal flora and fibrosis in a mouse model of endometriosis

Shaofu Zhuyu decoction has been widely used to treat gynecological diseases; however, its mechanism of action in endometriosis remains unclear. We analyzed Shaofu Zhuyu decoction’s chemical composition using ultra-high performance liquid chromatography-mass spectrometry. In an endometriosis mouse model, ectopic lesions weight measurements and hematoxylin and eosin staining were used to assess the therapeutic efficacy of Shaofu Zhuyu decoction. Effects on intestinal microflora were analyzed using 16S ribosomal ribonucleic acid sequencing, and impacts on focal fibrosis were analyzed using Masson’s trichrome staining. Moreover, fibrosis- and metabolism-related proteins were assessed using immunohistochemistry and enzyme-linked immunosorbent assay. The study identified 157 chemical constituents within Shaofu Zhuyu decoction. Shaofu Zhuyu decoction treatment in mice with endometriosis resulted in a reduction in ectopic lesions weight (P<0.05) and delayed disease progression. Moreover, it improved the diversity and abundance of intestinal flora, and decreased the expression of Lachnospiraceae (P<0.05), Rikenellaceae (P<0.01), Ruminococcaceae (P<0.01), Lachnoclostridium (P<0.05), and unclassified_f__Ruminococcaceae (P<0.05). Kyoto Encyclopedia of Genes and Genomes analysis revealed enrichment in carbohydrate, amino acid, and lipid metabolism pathways. Masson’s trichrome staining revealed that compared to the untreated group, the Shaofu Zhuyu decoction group exhibited significantly reduced collagen deposition areas (P<0.001), lower TGF-β1 (P<0.001), COL1A1 (P<0.05), and α-SMA (P<0.01) expression in ectopic lesions, along with increased serum adiponectin (P<0.05), decreased serum leptin (P<0.05), TGF-β1 (P<0.001), and CTGF (P<0.05). Shaofu Zhuyu decoction regulates the intestinal flora of mice with endometriosis while also reducing fibrosis at the lesion site. These findings highlight novel mechanisms for its efficacy in alleviating endometriosis.

Colonization profiles of gut microbiota in goat kids from neonatal to weaning period.

Understanding the colonization and change patterns of gut microbiota is pivotal for comprehending host health. As a newly cultured breed, the studies on the gut microbiota of Tianfu goats remain limited. This study aimed to address this gap by analyzing the microbial composition and colonization patterns of fecal samples collected from goat kids from birth to weaning. Fecal samples were collected on days 0, 7, 14, 21, 28, 35, 42, 49, 53, 55, 57, and 64, and the changes and colonization patterns of microorganisms were analyzed through high-throughput 16S rRNA sequencing. The results showed that the abundance of fecal microbiota in goat kids gradually increased over time, followed by a decrease after weaning and stabilization, with reduced individual differences. The colonization of fecal microorganisms mainly presented three different stages: days 0-14, days 21-49, and days 53-64. During the suckling period, the relative abundance of Proteobacteria (72.34%) was the highest, followed by Firmicutes (21.66%). From 21 days old, the microbiota in goat kids gradually to be diverse, with Lachnospiraceae and Ruminococcaceae being dominant. During post-weaning, Ruminococcaceae (30.98-33.34%) was becoming prominence which helpful for cellulose decomposition. LEfSe analyzed three important time points (d0 vs. d7, d7 vs. d14, d49 vs. d53, LDA score > 4 and p < 0.05), 53 microbial communities with stage differences were identified. Functional prediction using PICRUSt revealed that differential microbial communities are mainly related to carbohydrate and amino acid metabolism pathways. Overall, this study addresses the intricate relationship between ages, diets, and microbiota compositions in Tianfu goat kids, and also offering insights into microorganisms-host interactions.

Regulatory network analysis reveals gene-metabolite relationships in pear fruit treated with methyl jasmonate

The economic value of pear is determined by its intrinsic qualities, which are influenced by metabolites produced during the ripening process. Methyl jasmonate (MeJA), a hormone, plays an important role in plant metabolism. To date, few studies have investigated the molecular mechanism underlying the changes in metabolic pathways related to the internal quality of pear fruit after MeJA treatment. In this study, ultrahigh-performance liquid chromatography‒Q Exactive Orbitrap mass spectrometry (UHPLC‒QE‒MS) was used to determine the changes in metabolite contents in pear after MeJA treatment. MeJA treatment primarily activated carbohydrate metabolism and amino acid metabolism pathways. Through combined analysis of UHPLC‒QE‒MS data and whole-transcriptome data, the abovementioned pathways and each metabolite were analysed separately, and competitive endogenous RNA (ceRNA) and microRNA–transcription factor–target (miRNA–TF–target) regulatory networks were constructed. The core nodes of three genes (PEA, Pbr022732.1; GAA, Pbr035655.1; and miR8033-x) and two genes (SDS, Pbr031708.1; and novel-m6796-3p) were associated with the carbohydrate metabolism and amino acid metabolism pathways, respectively. The core mRNA nodes TCONS_00048038 and Pbr019584.1, the core miRNA node miR4993-x, the core lncRNA node TCONS_0004356, the core circRNA node novel_circ_001967 and the core transcription factor node TSO1 (Pbr025407.1) were identified via separate metabolite analyses. These findings elucidate the changes in metabolites related to fruit quality in ‘Nanguo’ pear and the relationships between the metabolites and genes, reveal the molecular mechanism underlying the response of MeJA treatment in pear fruit, and provide a theoretical basis for improving the internal quality of ‘Nanguo’ pear.

Preliminary Metabolomics Study Suggests Favorable Metabolic Changes in the Plasma of Breast Cancer Patients after Surgery and Adjuvant Treatment.

Background/Objectives: The management of early breast cancer (BC) includes surgery, followed by adjuvant radiotherapy, chemotherapy, hormone therapy, or immunotherapy. However, the influence of these interventions in metabolic reprogramming remains unknown. This study explored alterations in the plasma metabolome of BC patients following distinct treatments to deepen our understanding of BC pathophysiology, outcomes, and the identification of potential biomarkers. Methods: We included 52 women diagnosed with BC and candidates for surgery as primary oncological treatment. Blood samples were collected at diagnosis, two weeks post-surgery, and one month post-radiotherapy. Plasma samples from 49 healthy women served as controls. Targeted metabolomics assessed 74 metabolites spanning carbohydrates, amino acids, lipids, nucleotide pathways, energy metabolism, and xenobiotic biodegradation. Results: Before treatment, the BC patients exhibited notable changes in carbohydrate, nucleotide, lipid, and amino acid metabolism. We noticed a gradual restoration of specific metabolite levels (hypoxanthine, 3-phosphoglyceric acid, xylonic acid, and maltose) throughout different treatments, suggesting a normalization of the nucleotide and carbohydrate metabolic pathways. Moreover, we observed increased dodecanoic acid concentrations, a metabolite associated with cancer protection. These variations distinguished patients from controls with high specificity and sensitivity. Conclusions: Our preliminary study suggests that oncological treatments modify the metabolism of patients towards a favorable profile with a decrease in the pathways that favor cell proliferation and an increase in the levels of anticancer molecules. These findings emphasize the pivotal role of metabolomics in recognizing the biological pathways influenced by each cancer treatment and the resulting metabolic consequences. Furthermore, it aids in identifying potential biomarkers for disease onset and progression.

Metabolomic and Physiological Analyses Reveal the Effects of Different Storage Conditions on Sinojackia xylocarpa Hu Seeds.

Sinojackia xylocarpa Hu is a deciduous tree in the Styracaceae family, and it is classified as a Class II endangered plant in China. Seed storage technology is an effective means of conserving germplasm resources, but the effects of different storage conditions on the quality and associated metabolism of S. xylocarpa seeds remain unclear. This study analyzed the physiological and metabolic characteristics of S. xylocarpa seeds under four storage conditions. Our findings demonstrate that reducing seed moisture content and storage temperature effectively prolongs storage life. Seeds stored under that condition exhibited higher internal nutrient levels, lower endogenous abscisic acid (ABA) hormone levels, and elevated gibberellic acid (GA3) levels. Additionally, 335 metabolites were identified under four different storage conditions. The analysis indicates that S. xylocarpa seeds extend seed longevity and maintain cellular structural stability mainly by regulating the changes in metabolites related to lipid, amino acid, carbohydrate, and carotenoid metabolic pathways under the storage conditions of a low temperature and low seed moisture. These findings provide new insights at the physiological and metabolic levels into how these storage conditions extend seed longevity while also offering effective storage strategies for preserving the germplasm resources of S. xylocarpa.

Unveiling responses and mechanisms of spice crop chive exposure to three typical pesticides using metabolomics combined with transcriptomics, physiology and biochemistry

Pesticides are frequently used to control target pests in the production of spice crops such as chives (Allium ascalonicum). However, little information is available on the responses and underlying mechanisms of pesticide exposure in this crop. Our findings revealed that the uptake, transportation, and subcellular distribution of three typical pesticides—the fungicide pyraclostrobin (PAL), insecticide acetamiprid (ATP), and herbicide pendimethalin (PND) in chives, as well as their physiological, biochemical, metabolic, and transcriptomic responses—were dependent on pesticide properties, especially hydrophobicity. The distribution of PAL and PND in chives decreased in the order root > stem > leaf, but the distribution order of ATP was the opposite. The proportion of PAL and PND in the solid phase of the root cells gradually increased, but ATP mainly existed in the cell-soluble component, indicating that the latter had an upward translocation ability and thus mainly accumulated in the leaves. Malondialdehyde levels in chive leaves were not significantly affected by exposure to these pesticides; however, the activities of superoxide dismutase (SOD) and catalase (CAT) in chive leaves increased significantly. Moreover, these pesticides exhibited critical differences in chive responses through the interaction of metabolites and regulation of differentially expressed genes. PAL dramatically influenced five carbohydrate metabolic pathways (34.35 %), disturbing the starch-to-sucrose balance. ATP strongly affected five amino acid (AC) metabolic pathways (33.38 %), enhancing four free amino acid levels. PND notably affected eight fatty acid (FA) metabolic pathways (25.38 %), increasing two unsaturated and decreasing one saturated FA. Simultaneously, PND, ATP, and PND accumulated in the chives could be detoxified through metabolic pathways mediated by cytochrome P450 (P450) and glycosyltransferase (GT)/glutathione S-transferase (GST), producing phase I (7, 4, and 5) and II (11, 13, and 10) metabolites, respectively. This study provides important molecular insights into the responses and underlying mechanisms of spice crop exposure to pesticides.

93 Ruminal archaea and bacteria metatranscriptomic responses to supplementation in steers fed low-quality forage

Abstract Forage comprises the majority of beef cattle diets globally, and its quality can vary. Supplementation presents a significant opportunity to improve the efficiency of production. Supplementation has been shown to increase ruminally available nitrogen, improve forage utilization, and reduce livestock methane (CH4) emissions. However, corresponding effects of supplementation on gene expression of rumen microbiota, in particular metabolic pathways involved in methanogenesis, have yet to be studied. This study aimed to evaluate the effect of supplement composition before and after feeding on rumen archaeal and bacterial gene expression in steers consuming a low-quality forage diet. Ruminal samples were collected from five ruminally cannulated Angus steers [body weight (BW) = 375 ± 45 kg] used in a 4 × 4 Latin square fed a basal diet of King Ranch Bluestem Hay (3.5% CP, 73% NDF), and one of four isonitrogenous (130 mg N/kg BW) supplements. Steers provided the two most divergent supplements (2% starch, 43% CP; 56% starch, 21% CP) were used for metatranscriptomic analysis. Rumen fluid samples were collected via rumen cannula 0 and 4 h post-feeding. Total RNA was extracted and sequenced. Differentially expressed genes (DEGs) were identified and functionally annotated. Pathway enrichment analysis was completed to determine enriched pathways (broad metabolic pathways) and modules (specific metabolic reactions). Only main effects are presented in this abstract. Archaeal hydrogenotrophic and methylotrophic methanogenesis reactions and tryptophan biosynthesis reactions were upregulated in the 2% starch supplement (P &amp;lt; 0.05). The 2% starch supplement resulted in fewer bacterial total upregulated carbohydrate-active enzymes compared with the 56% starch supplement (957 vs. 1,695 DEGs, respectively; P &amp;lt; 0.05), and an increased proportion of cellulose and hemicellulose-specific enzymes (35 vs. 29%, respectively; P &amp;lt; 0.05). The 56% starch supplement resulted in upregulation of the bacterial 3-Hydroxypropionate bi-cycle reaction (P &amp;lt; 0.05). Collection time exerted a larger effect than supplement composition on both archaeal and bacterial gene expression, with 83% and 63% of DEGs associated with time, respectively (P &amp;lt; 0.05). Archaeal hydrogenotrophic methanogenesis and carbon metabolism were upregulated 4 h post-feeding. In addition, 1,704 bacterial carbohydrate-active enzymes were upregulated 4 h post-feeding, as compared with 975 upregulated at 0 h (P &amp;lt; 0.05). However, these differences in DEGs did not correlate with significantly enriched pathways of bacterial carbohydrate metabolism. These findings demonstrate improvements to low-quality forage utilization, through CP and starch supplementation, can be correlated to relevant changes in gene expression of rumen microbiota. Furthermore, they demonstrate that supplementation influences the expression of methanogenesis reactions, suggesting an opportunity to affect CH4 production. Additional studies quantifying forage utilization, rumen microbiota gene expression and CH4 production are needed to further optimize supplementation strategies for improved efficiency of beef production whilst maintaining or reducing its carbon footprint.

Unraveling the toxicity mechanisms of nanoplastics with various surface modifications on Skeletonema costatum: Cellular and molecular perspectives

Nanoplastics are ubiquitous in marine environments, exhibiting high bioavailability and potential toxicity to marine organisms. However, the impacts of nanoplastics with various surface modifications on marine microalgae remain largely unexplored. This study explored the toxicity mechanisms of two nanoplastic types-polystyrene (PS) and polymethyl methacrylate (PMMA)-with distinct surface modifications on Skeletonema costatum at cellular and molecular levels. Results showed that nanoplastics significantly impaired the growth of microalgae, particularly PS-NH2, which caused the most pronounced growth inhibition, reaching 56.99 % after a 96-h exposure at 50 mg/L. Transcriptomic profiling revealed that nanoplastics disrupted the expression of genes predominantly involved in ribosome biogenesis, aminoacyl-tRNA biosynthesis, amino acid metabolism, and carbohydrate metabolism pathways. The integrated biochemical and transcriptomic evidence highlighted that PS-NH2 nanoplastics had the most adverse impact on microalgae, affecting fundamental pathways such as ribosome biogenesis, energy metabolism, photosynthesis, and oxidative stress. Our findings underscore the influence of surface-modified nanoplastics on algal growth and contribute new understanding to the toxicity mechanisms of these nanoplastics in marine microalgae, offering critical information for assessing the risks of emerging pollutants.

Mechanisms of ROS-mediated interactions between Bacillus aryabhattai LAD and maize roots to promote plant growth

BackgroundPlant growth-promoting rhizobacteria (PGPR), as a group of environmentally friendly bacteria growing in the rhizosphere of plants, play an important role in plant growth and development and resistance to environmental stresses. However, their limited understanding has led to the fact that their large-scale use in agriculture is still scarce, and the mechanisms by which beneficial bacteria are selected by plants and how they interact with them are still unclear.MethodIn this study, we investigated the interaction between the auxin-producing strain Bacillus aryabhattai LAD and maize roots, and performed transcriptomic and metabolomic analyses of Bacillus aryabhattai LAD after treatment with maize root secretions(RS).ResultsOur results show that there is a feedback effect between the plant immune system and bacterial auxin. Bacteria activate the immune response of plant roots to produce reactive oxygen species(ROS), which in turn stimulates bacteria to synthesize IAA, and the synthesized IAA further promotes plant growth. Under the condition of co-culture with LAD, the main root length, seedling length, root surface area and root volume of maize increased by 197%, 107%, 89% and 75%, respectively. In addition, the results of transcriptome metabolome analysis showed that LAD was significantly enriched in amino acid metabolism, carbohydrate metabolism and lipid metabolism pathways after RS treatment, including 93 differentially expressed genes and 45 differentially accumulated metabolites.ConclusionOur findings not only provide a relevant model for exploring the effects of plant-soil microbial interactions on plant defense functions and thereby promoting plant growth, but also lay a solid foundation for the future large-scale use of PGPR in agriculture for sustainable agricultural development.

Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations.

Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach to reveal that the gut microbiome of the Ju/'hoansi hunter-gatherers, one of the most remote KhoeSan groups, exhibit a higher diversity and richness, with an abundance of microbial species lost in the western population. The Ju/'hoansi microbiome showed enhanced global transcription and enrichment of complex carbohydrate metabolic and energy generation pathways. The Ju/'hoansi also show high abundance of short-chain fatty acids that are associated with health and optimal immune function. In contrast, these pathways and their respective species were found in low abundance or completely absent in Western populations. Amino acid and fatty acid metabolism pathways were observed prevalent in the Western population, associated with biomarkers of chronic inflammation. Our study provides the first in-depth multi-omic characterization of the Ju/'hoansi microbiome, revealing uncharacterized species and functional pathways that are associated with health.

Metabolic Characteristics of Gut Microbiota and Insomnia: Evidence from a Mendelian Randomization Analysis.

Insomnia is a common sleep disorder that significantly impacts individuals' sleep quality and daily life. Recent studies have suggested that gut microbiota may influence sleep through various metabolic pathways. This study aims to explore the causal relationships between the abundance of gut microbiota metabolic pathways and insomnia using Mendelian randomization (MR) analysis. This two-sample MR study used genetic data from the OpenGWAS database (205 gut bacterial pathway abundance) and the FinnGen database (insomnia-related data). We identified single nucleotide polymorphisms (SNPs) associated with gut bacterial pathway abundance as instrumental variables (IVs) and ensured their validity through stringent selection criteria and quality control measures. The primary analysis employed the inverse variance-weighted (IVW) method, supplemented by other MR methods, to estimate causal effects. The MR analysis revealed significant positive causal effects of specific carbohydrate, amino acid, and nucleotide metabolism pathways on insomnia. Key pathways, such as gluconeogenesis pathway (GLUCONEO.PWY) and TCA cycle VII acetate producers (PWY.7254), showed positive associations with insomnia (B > 0, p < 0.05). Conversely, pathways like hexitol fermentation to lactate, formate, ethanol and acetate pathway (P461.PWY) exhibited negative causal effects (B < 0, p < 0.05). Multivariable MR analysis confirmed the independent causal effects of these pathways (p < 0.05). Sensitivity analyses indicated no significant pleiotropy or heterogeneity, ensuring the robustness of the results. This study identifies specific gut microbiota metabolic pathways that play critical roles in the development of insomnia. These findings provide new insights into the biological mechanisms underlying insomnia and suggest potential targets for therapeutic interventions. Future research should further validate these causal relationships and explore how modulating gut microbiota or its metabolic products can effectively improve insomnia symptoms, leading to more personalized and precise treatment strategies.

Asiaticoside ameliorates type 2 diabetes mellitus in rats by modulating carbohydrate metabolism and regulating insulin signaling

Objective: To evaluate the effect of asiaticoside on streptozotocin (STZ) and nicotinamide (NAD)-induced carbohydrate metabolism abnormalities and deregulated insulin signaling pathways in rats. Methods: Asiaticoside (50 and 100 mg/kg body weight) was administered to STZ-NAD-induced diabetic rats for 45 days, and its effects on hyperglycaemic, carbohydrate metabolic, and insulin signaling pathway markers were examined. Results: Asiaticoside increased insulin production, lowered blood glucose levels, and enhanced glycolysis by improving hexokinase activity and suppressing glucose-6-phosphatase and fructose-1,6-bisphosphatase activities. Abnormalities in glycogen metabolism were mitigated by increasing glycogen synthase activity and gluconeogenesis was decreased by decreasing glycogen phosphorylase activity. Furthermore, asiaticoside upregulated the mRNA expressions of IRS-1, IRS-2, and GLUT4 in STZ-NAD-induced diabetic rats and restored the beta cell morphology to normal. Conclusions: Asiaticoside has the potential to ameliorate type 2 diabetes by improving glycolysis, gluconeogenesis, and insulin signaling pathways.

Characterizing flavor development in low-salt Chinese horse bean-chili paste through integrated metabolomics and metagenomics

This study utilized metabolomics and metagenomics to investigate the microbial composition and functions in low- and high-salt Chinese horse bean-chili pastes (CHCPs). The results showed that 25 key metabolites were identified to distinguish the flavor attributes between the two samples. Leuconostoc was identified as the dominant microbiota in low-salt CHCP, while Pantoea prevailed in the high-salt CHCP. Compared to traditional high-salt fermentation, low-salt and inoculated fermentation promoted the increase in the relative abundances of Companionlactobacillus, Levilactobacillus, Tetragenococcus, Zygosaccharomyces and Wickerhamiella as well as the enrichment of carbohydrate and amino acid metabolic pathways, which contributed to the enhancement of characteristic flavor compounds. Further metabolic pathway reconstruction elucidated 21 potential microbial genera associated with the formation of key metabolites, such as Leuconostoc, Levilactobacillus, Pantoea, and Pectobacterium. This study may provide insights for optimizing the fermentation process and improving the flavor quality of low-salt CHCP and similar fermentation products. KeywordsLow-salt fermentationHight-salt fermentationChinese horse-bean chili pasteFlavor formationMetabolomicsMetagenomics

Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.)

BackgroundThe yield of major crops is generally limited by sink capacity and source strength. Cucumber is a typical raffinose family oligosaccharides (RFOs)–transporting crop. Non-coding RNAs and alternative polyadenylation (APA) play important roles in the regulation of growth process in plants. However, their roles on the sink‒source regulation have not been demonstrated in RFOs–translocating species.ResultsHere, whole–transcriptome sequencing was applied to compare the leaves of cucumber under different sink strength, that is, no fruit-carrying leaves (NFNLs) and fruit-carrying leaves (FNLs) at 12th node from the bottom. The results show that 1101 differentially expressed (DE) mRNAs, 79 DE long non–coding RNAs (lncRNAs) and 23 DE miRNAs were identified, which were enriched in photosynthesis, energy production and conversion, plant hormone signal transduction, starch and carbohydrate metabolism and protein synthesis pathways. Potential co–expression networks like, DE lncRNAs–DE mRNAs/ DE miRNAs–DE mRNAs, and competing endogenous RNA (ceRNA) regulation models (DE lncRNAs–DE miRNAs–DE mRNAs) associated with sink‒source allocation, were constructed. Furthermore, 37 and 48 DE genes, which enriched in MAPK signaling and plant hormone signal transduction pathway, exist differentially APA, and SPS (CsaV3_2G033300), GBSS1 (CsaV3_5G001560), ERS1 (CsaV3_7G029600), PNO1 (CsaV3_3G003950) and Myb (CsaV3_3G022290) may be regulated by both ncRNAs and APA between FNLs and NFNLs, speculating that ncRNAs and APA are involved in the regulation of gene expression of cucumber sink‒source carbon partitioning.ConclusionsThese results reveal a comprehensive network among mRNAs, ncRNAs, and APA in cucumber sink–source relationships. Our findings also provide valuable information for further research on the molecular mechanism of ncRNA and APA to enhance cucumber yield.

Commonalities and Specificities in Wheat (Triticum aestivum L.) Responses to Aluminum Toxicity and Low Phosphorus Revealed by Transcriptomics and Targeted Metabolomics.

Aluminum (Al) toxicity and low phosphorus availability (LP) are the top two co-existing edaphic constraints limiting agriculture productivity in acid soils. Plants have evolved versatile mechanisms to cope with the two stresses alone or simultaneously. However, the specific and common molecular mechanisms, especially those involving flavonoids and carbohydrate metabolism, remain unclear. Laboratory studies were conducted on two wheat genotypes-Fielder (Al-tolerant and P-efficient) and Ardito (Al-sensitive and P-inefficient)-exposed to 50 μM Al and 2 μM Pi (LP) in hydroponic solutions. After 4 days of stress, wheat roots were analyzed using transcriptomics and targeted metabolomics techniques. In Fielder, a total of 2296 differentially expressed genes (DEGs) were identified under Al stress, with 1535 upregulated and 761 downregulated, and 3029 DEGs were identified under LP stress, with 1591 upregulated and 1438 downregulated. Similarly, 4404 DEGs were identified in Ardito under Al stress, with 3191 upregulated and 1213 downregulated, and 1430 DEGs were identified under LP stress, with 1176 upregulated and 254 downregulated. GO annotation analysis results showed that 4079 DEGs were annotated to the metabolic processes term. These DEGs were significantly enriched in the phenylpropanoid, flavonoid, flavone and flavonol biosynthesis, and carbohydrate metabolism pathways by performing the KEGG enrichment analysis. The targeted metabolome analysis detected 19 flavonoids and 15 carbohydrate components in Fielder and Ardito under Al and LP stresses. In Fielder, more responsive genes and metabolites were involved in flavonoid metabolism under LP than Al stress, whereas the opposite trend was observed in Ardito. In the carbohydrate metabolism pathway, the gene and metabolite expression levels were higher in Fielder than in Ardito. The combined transcriptome and metabolome analysis revealed differences in flavonoid- and carbohydrate-related genes and metabolites between Fielder and Ardito under Al and LP stresses, which may contribute to Fielder's higher resistance to Al and LP. The results of this study lay a foundation for pyramiding genes and breeding multi-resistant varieties.

Genomic and phenotypic analysis unveiling the carbohydrate metabolic characteristics of Leuconostoc citreum SH12 in plant-based fermentation

Leuconostoc citreum has been widely utilized for industrial fermentation. Previously, we found Leuc. citreum SH12 as a starter culture, exhibited superior fermentation characteristics in plant-based food, but its genomic, evolutionary and carbohydrate metabolic features remained unclear. This study aimed to reveal the metabolic characteristics of Leuc. citreum SH12 in response to various carbon sources by genomic and phenotypic analysis. By multiple sequencing technology, we assembled the 1.84 Mb complete genome of Leuc. citreum SH12 and identified 193 carbohydrate metabolism genes involved in the KEGG annotation, including 59 carbohydrate-active enzymes (CAZymes) genes. Comparative genome analysis indicated that Leuc. citreum SH12 had carbohydrate metabolism pathways similar to other Leuc. citreum, but it had 27 specific genes annotated as ABC transporters and hypothetical proteins, probably representing great resilience to the environment. The reconstruction of carbohydrate metabolic pathways and carbon utilization tests showed that Leuc. citreum SH12 could metabolize glucose, sucrose, fructose and maltose well, followed by xylose, arabinose, mannose and cellobiose, but could not utilize galactose, lactose, raffinose and stachyose. Soymilk fermentation test indicated that the strain could produce mannitol, and water-soluble and water-insoluble α-glucans. This study provided insights into a deeper understanding of the genomic and carbohydrate metabolic characteristics of Leuc. citreum SH12, and implied its potential application in plant-based fermented food.

Multi-Omics analysis reveals the important role of indole-3-acetic acid homeostasis in male fertility of cotton

Auxin (Indole-3-acetic acid, IAA) is essential for anther development and male fertility, but little is known about its homeostasis in developing anthers due to its complex and diverse synthesis pathways. Here, we employed transcriptomic, targeted metabolomic, and amino acid analyses on a wild type (WT) cotton (Gossypium hirsutum) line SD98–6 and its nearly-isogenic male sterile (MS) line SD98–6A, to delve into the relationship between IAA and anther fertility. In WT anthers, IAA homeostasis was achieved mainly through self-synthesis, conjugate hydrolysis, and polar transport, and accumulation of IAA exhibited an inverted "U" pattern with the highest content observed at the tetrad stage. In MS anthers, no IAA accumulation was observed after the meiosis stage and the IAA content remained constantly low, mainly due to reduction of the substrates (phenylalanine and tryptophan) for IAA synthesis, and significantly decreased expression of the genes involved in IAA synthesis. Meanwhile, carbohydrate metabolism pathways directly contributing to IAA synthesis and synthesis of amino acids were malfunctional in MS anthers based on the expression profile of the metabolic genes and content measurement. These results provide valuable insights into the IAA homeostasis in cotton anthers and imply that genes related to IAA homeostasis are potential targets for development of IAA-sensitive male sterile cotton lines.