BackgroundRumen microbiota drive fermentation and contribute to variation in feed efficiency among ruminants, yet the underlying host–microbe mechanisms remain poorly understood. This study explores how rumen microbes shape feed conversion efficiency (FCR) through integrated interactions with multiple host organs.ResultsWe applied a multi-omics strategy—combining rumen metagenomics and host multi-organ transcriptomics—in Hu sheep with divergent FCR. From a uniform cohort of 150 weaned male Hu lambs, 13 low-FCR (LFCR) and 13 high-FCR (HFCR) individuals were selected for integrated analyses. LFCR sheep exhibited greater growth performance and higher ruminal propionate concentrations compared with HFCR animals. The ruminal microbiomes were enriched in Saccharofermentans and Succinivibrionaceae_UBA2804, and showed functional convergence on amino acid biosynthesis, central carbon metabolism, and propionate-oriented fermentation in LFCR sheep. Carbohydrate-active enzyme profiles indicated that LFCR animals favored fiber- and starch-associated modules (GH126, CBM27, EPS-GT), whereas HFCR animals were enriched in host-glycan and uronic acid–degrading families (CE14, GH89, PL15). Hydrogen metabolism highlighted a clear dichotomy: LFCR animals redirected H₂ toward propionate and sulfate reduction, while HFCR animals retained greater butyrate-producing and methanogenic capacity. Transcriptomic profiling across rumen epithelium, liver, and muscle identified tissue-specific regulatory modules. Only the liver showed strong enrichment of carbohydrate metabolism, with a complete glycogen turnover and glucose export system (GYS2, PYGL, PGM2, G6PC1) and pathways linking microbial short-chain fatty acids to gluconeogenesis. In contrast, muscle efficiency modules were dominated by contractile and cytoskeletal genes (e.g., MYL2, TNNC1, TPM3), reflecting optimized energy expenditure rather than substrate metabolism. No efficiency-associated modules were detected in the rumen epithelium, consistent with its role in propionate absorption rather than metabolism.ConclusionsThe rumen microbiota of LFCR sheep possess highly efficient capacities for volatile fatty acid and amino acid synthesis, thereby enhancing energy utilization at its source. The resulting propionate further promotes hepatic gluconeogenesis, directly supplying energy for muscle cell growth and ultimately improving FCR. Thus, co-metabolism between rumen microbiota and the liver provides energy for muscle cell growth and is a key determinant of improved feed efficiency.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40104-025-01333-3.

Microbial valorisation of PET-derived terephthalic acid by Rhizopus arrhizus: towards plastic waste biotransformation.

Metabolic control analysis is used to understand regulation of metabolism and identify bottlenecks to be overcome in metabolic engineering for desired products. Its application has been hampered by the need for either parameterized models or carefully titrated experiments. In this study, we use thermodynamically feasible, sampled parameters to overcome this limitation. We use metabolic control analysis to explore central carbon metabolism of Saccharomyces cerevisiae growing in continuous culture under different nutrient limitations. Furthermore, we demonstrate shifts in flux control patterns in response to the different growth conditions and show how our results for specific reactions agree with the literature. Key advantages of the proposed framework include the incorporation of allosteric effectors, the use of omics data from a single steady-state time point and the computational efficiency; in all cases, 100 feasible models were sampled in less than 20min on a laptop. The model and framework are freely available for researchers to use on their own data: https://github.com/biosustain/GRASP.git.

Does algal trophic mode affect the removal of norfloxacin? Insights from Tetradesmus obliquus.

Propionic acid is a common food preservative, but many microbes, including the important biocontrol agent Bacillus thuringiensis , can metabolize it via the 2-methylcitrate cycle. However, the accumulation of cycle intermediates, such as 2-methylcitrate, can be toxic, and the overall physiological effects of this toxicity on B. thuringiensis are unclear. In this study, we investigated the toxic effects of 2-methylcitrate on B. thuringiensis and its corresponding cellular responses by characterizing the prpD deletion mutant Δ prpD , which lacks the 2-methylcitrate dehydratase. We found that the accumulation of 2-methylcitrate in the Δ prpD mutant led to a sharp decline in biomass, extensive cell lysis and death during the stationary phase. Comparative transcriptomic analysis revealed that this toxicity is associated with severe overall metabolic imbalance, characterized by a significant transcriptional dichotomy: concerted downregulation of nearly all glycolytic pathway genes and simultaneous upregulation of TCA cycle genes. This transcriptional decoupling of central carbon metabolism is the root cause of the observed lethal phenotype. Furthermore, we identified and characterized an internal promoter located within the prp operon that specifically drives prpD expression. This internal promoter rapidly and efficiently clears toxic intermediates, representing a complex regulatory adaptation mechanism to combat the harmful effects of propionic acid metabolism. Our findings provide a comprehensive transcriptional view of the toxicity of 2-methylcitrate and reveal a unique bacterial metabolic detoxification strategy, highlighting the value of PrpD as a potential anti-bacterial target.

To elucidate the species-specific regulatory mechanisms of hydroxyacyl-CoA dehydrogenase alpha subunit (HADHA) in ruminant liver metabolism and to decipher the consequent metabolic-transcriptional network dysregulation using an integrated multiomics approach in a dairy cow hepatocyte model. A loss-of-function study was conducted using transfecting primary hepatocytes isolated from dairy cows with HADHA-targeting small interfering RNA (n = 6). LC-MS+GC-MS metabolomics and transcriptomics were integrated and analyzed via orthogonal partial least squares-discriminant analysis, differential and enrichment analysis, and multiomics network analysis. HADHA knockdown induced profound metabolic reprogramming, identifying 692 differentially abundant metabolites and 736 differentially expressed genes. Key dysregulated metabolomic pathways included upregulation of forkhead box O signaling, tricarboxylic acid cycle, and butanoate metabolism and downregulation of glycolysis/gluconeogenesis and ATP-binding cassette transporters. This was evidenced by suppression of primary bile acids and accumulation of glyceroneogenesis markers. Transcriptomic analysis revealed downregulation of insulin response and nuclear factor κ B signaling and upregulation of phosphatidylinositol and phosphatidylinositol 3-kinase-protein kinase B signaling. Multiomics integration confirmed disruption in core pathways, including arginine and proline metabolism, nicotinate and nicotinamide metabolism, and cAMP signaling. This study provides a comprehensive map of the HADHA-mediated regulatory network in the ruminant hepatocytes. Its depletion directly suppresses fatty acid oxidation and bile acid synthesis and rewires central carbon and lipid metabolism, leading to a state of metabolic imbalance. The elucidated mechanisms establish a foundational basis for future research aimed at developing nutritional or genetic strategies to improve metabolic health in the dairy industry.

Nutrient metabolism is a basic biochemical paradigm to which cells draw energy and produce biosynthetic precursors, as well as maintain homeostasis. At the molecular scale, the integrative processing of carbohydrates, lipids, and proteins are regulated by highly regulated enzymatic systems that dynamically react to cellular energy requirements, nutrient levels and physiological conditions. This review presents the existing knowledge of the molecular biochemistry in nutrient metabolism, with the focus being on the integrated character of metabolic pathways, as opposed to the reactions occurring in isolation. The process of carbohydrate metabolism is a fast and flexible energy source by glycolysis, gluconeogenesis, and pentose phosphate pathway which connects the production of ATP and the maintenance of redox homeostasis with anabolic needs. The long-term energy storage and structural components in lipid metabolism are based on fatty acid production, 2-oxidation as well as complex lipid remodeling and they are the centre of focus in the membrane dynamics as well as signaling processes. Protein metabolism provides functional macromolecules as well as metabolic intermediates, which the catabolism of amino acids connects to the relationships of central carbon metabolism and nitrogen homeostasis. In addition to the classics of pathway descriptions, this review identifies the regulatory processes that provide the flexibility of their metabolic reactions, such as allosteric enzyme regulation, post-translational changes, and intracellular compartmentalization. The interaction between carbohydrate, lipid and protein metabolism allows the cells to quickly adjust to changes in nutrient levels without compromising the metabolic effectiveness. These molecular processes are critical in explaining the biochemical basis of growth and development and disease because metabolic dysregulation causes many pathological conditions. The article offers a conceptual framework of future studies aimed at optimizing metabolism, therapeutic intervention, and system-level metabolic engineering by offering a single and sequential description of how nutrient metabolism works on the molecular level.

Acetate esters, synthesized by alcohol acyltransferase (AATases) encoded primarily by the ATF1 gene, are pivotal for the desirable fruity aroma in fermented foods. However, the role and regulatory impact of ATF1 in solid-state fermented meat remain largely unexplored. This study engineered Saccharomyces cerevisiae by knocking out and overexpressing ATF1 to investigate its influence on flavor formation in a sour meat model system. Compared to the wild-type strain, ATF1 overexpression (SCpA group) increased ethyl acetate content by 70.15% and uniquely produced significant levels of isoamyl acetate. Conversely, ATF1 deletion (SCdA group) led to a 61.23% reduction in ethyl acetate. Transcriptomic analysis revealed that ATF1 overexpression triggered a systemic metabolic shift, not only activating the final esterification step but also upregulating key genes in central carbon metabolism (SUC2, ICL1), amino acid biosynthesis, and precursor supply pathways (ACS2, ADH1). This synergistic regulation redirected metabolic flux towards the accumulation of both alcohol and acyl-CoA precursors, thereby amplifying acetate ester synthesis. Our findings demonstrate that ATF1 is a critical engineering target for flavor enhancement in fermented meats and uncover a broader metabolic network it influences, providing a robust strategy for the targeted modulation of food flavor profiles.

ABSTRACT Soybean ( Glycine max ) is a globally important crop, yet its productivity is highly susceptible to drought stress, particularly in rainfed systems. To better understand the biochemical basis of drought tolerance, this study employed pathway‐based metabolomics to characterize differentially expressed metabolites between drought‐tolerant and susceptible soybean genotypes and to identify underlying mechanisms. Metabolite profiles of leaves collected from both watered and drought‐stressed conditions were analyzed using liquid chromatography–mass spectrometry. Discriminant metabolites were identified through multivariate statistical analysis and pathway mapping. Principal component analysis revealed distinct metabolic variation primarily under drought stress, indicating that drought‐tolerant genotypes engage in active metabolic reprogramming in response to water deficit. Overall, the metabolic responses of drought‐tolerant genotypes were less pronounced than those of susceptible ones, suggesting a more selectively managed allocation of metabolic resources in the tolerant genotypes. Pathway analysis indicated that tolerant genotypes selectively enhanced specific primary and secondary metabolic processes, including central carbon metabolism, shikimate pathway–associated metabolites, and specific amino acid pools, while also displaying divergent allocation within phenylpropanoid (secondary metabolism) and branched‐chain amino acid pathways (primary metabolism). Both tolerant and susceptible cultivars exhibited shared drought responses, including hormonal activation, lipid remodeling, accumulation of phenylpropanoid intermediates, and osmoprotective amino acids. This study demonstrates that drought adaptation arises from the interplay between conserved biochemical adjustments and genotype‐specific reprogramming in primary and secondary metabolism, providing metabolite‐level insights that can guide future large‐scale field studies aimed at selecting genotypes for drought tolerance using biomarkers.

Abstract Hypoxia and cold temperatures are major limiting factors for animals reared at high altitudes. Previous adaptation studies have primarily focused on genetic and genomic aspects, while the mechanisms by which the gut microbiome contributes to this adaptation are still not fully understood. We used ruminants as both naturally adapted (yaks) and non‐adapted (Holstein cows) models to investigate the role of gut microbiome in high‐altitude adaptation by applying multi‐omics approaches. First, 20 yaks and 20 Holstein cows that had been reared at approximately 4000 m altitude since birth were fed the same diet for 44 days prior to sampling to eliminate the short‐term effects of nutrition and altitude adaptation. The yak rumen microbiome showed significant enrichment in carbon metabolism, particularly central carbon metabolism pathways, such as glycolysis/gluconeogenesis, pyruvate metabolism, and the pentose phosphate pathway, whereas that of Holstein cows was enriched in starch, sucrose, pentose, and glucuronate interconversions. Compared with those of Holstein cows kept at high altitudes for their entire life, the yak rumen epithelial cells, as determined by single‐nucleus RNA sequencing, exhibited higher elevated scores for ketone body biosynthesis and fatty acid beta‐oxidation. Second, mixed rumen fluid was transplanted from 10 yaks to 10 Holstein cows. Holstein cows then showed better milk production performance. A progressive decline in carbon metabolism activity from 6 h to 7 and 28 days post‐transplantation was verified. In conclusion, the rumen microbiome and host epithelial function appear to support high‐altitude adaptation by improving the energy supply of the host.

Xylitol, a valuable five-carbon sugar alcohol widely used in the food and pharmaceutical industries, can be biosynthesized through the reduction of xylose by engineered Saccharomyces cerevisiae. A major challenge in producing xylitol from lignocellulosic feedstocks is the sensitivity of yeast to multiple inhibitors generated during biomass pretreatment. Developing robust microbial cell factories with enhanced tolerance to these inhibitors is therefore essential for efficient and sustainable xylitol production. In this study, we employed comparative transcriptomic analysis to investigate the response mechanisms of two xylitol-producing S. cerevisiae strains, CXAU and TX2022, to vanillin and PCS-L (liquid hydrolysate from pretreated corn stover). Under vanillin stress, CXAU exhibited downregulation of glycolysis, the pentose phosphate pathway (PPP), and the tricarboxylic acid (TCA) cycle, accompanied by upregulation of amino acid and ergosterol biosynthesis. In contrast, TX2022 showed repression of central carbon metabolism, oxidative phosphorylation, and heme and thiamine synthesis, while enhancing amino acid synthesis and glutathione (GSH) regeneration. Under PCS-L exposure, CXAU experienced severe metabolic disruption but prioritized improving the fidelity of protein translation. Meanwhile, TX2022 upregulated amino acid and ergosterol synthesis, purine metabolism, and ribosome biogenesis, while downregulating oxidative phosphorylation and peroxisomal functions. Based on transcriptomic insights, 11 candidate genes potentially involved in stress tolerance were identified and individually overexpressed. Overexpression of SIP18 or CTT1 significantly enhanced tolerance to both vanillin and complex inhibitors. Additionally, overexpression of AAD4 or AAD6 improved vanillin tolerance, whereas SPI1 or GRE1 overexpression conferred increased resistance to the complex inhibitors. Notably, the engineered strain TX2022-SIP18 achieved high-level xylitol production of 43.50g/L (yield: 0.961g/g xylose) in concentrated hydrolysate from pretreated corn cob containing high concentrations of inhibitors. This study provides the first experimental evidence that SIP18, AAD4, AAD6, SPI1, CTT1, and GRE1 contribute to inhibitor tolerance of S. cerevisiae, highlighting their potential as targets for engineering robust industrial strains for sustainable lignocellulosic xylitol production.

Gene co-expression networks are commonly used to identify functionally related genes, but they often suffer from spurious associations and fail to capture genes with restricted, context-specific responses. To address these limitations, we constructed YeastCoDEGNet, a global co-differential expression network in Saccharomyces cerevisiae, by reanalyzing microarray data from 143 carefully curated experiments comprising 425 comparisons. In this network, gene connections are defined by shared context-specific responses, enabling the identification of distinct topological groups enriched in either essential or nonessential genes, often associated with metabolic or nonmetabolic biological processes, respectively. We further characterized each gene by its responsiveness, essentiality, and number of co-differentially expressed partners, uncovering positional clustering of these features across chromosomal locations. To explore higher-order functional organization, we built a cross-pathway coordination network based on context-specific responses between pathway pairs, revealing modules of functionally related pathways. This network not only recovered well-known associations but also identified novel links, with particularly strong coordination observed among pathways involved in central carbon metabolism, amino acid and antioxidant processes, protein synthesis, trafficking, degradation, and gene regulation. By capturing context-specific gene expression dynamics, YeastCoDEGNet provides a powerful framework for studying how genes and pathways adapt to genetic and environmental perturbations.

Targeting DHODH reveals a metabolic vulnerability in AR-positive and AR-negative prostate cancer cells via pyrimidine synthesis and metabolic crosstalk with the TCA and urea cycles

IntroductionJinfu’an Decoction (JFAD), a traditional Chinese medicine, is used to treat lung cancer and has shown significant anti-tumor effects in clinical and experimental studies. This study integrates metabolomics and gut microbiota analysis to elucidate JFAD’s anti-tumor mechanisms.MethodsA suspension of A549-luc cells, approximately 1 × 106 in number, was injected subcutaneously into the right axilla of mice to establish a tumor-bearing nude mouse model. Mice were randomly assigned to four groups: model group (MG), low-dose JFAD (JFAD-L), medium-dose JFAD (JFAD-M), and high-dose JFAD (JFAD-H), receiving treatments via gavage for 21 days. Additionally, three nude mice formed the normal group (NG), receiving no treatment. Changes in gut microbiota and serum metabolites were assessed using 16S rRNA gene sequencing and UHPLC-QE-MS non-targeted metabolomics.ResultsJFAD may help restore the balance of intestinal flora in mice with lung cancer to a more normalized state. Our findings indicate that JFAD increases the abundance of Bacteroidia and decreases the presence of Firmicutes and Clostridia, thereby altering intestinal bacterial composition. Primary metabolic pathways associated with significant differences include nicotinate and nicotinamide metabolism, glycine, serine and threonine metabolism, and pyrimidine metabolism. A key differential metabolite identified was succinic acid, part of the central carbon metabolism pathway in cancer. Succinic acid showed a negative correlation with gut microbiota families Tannerellaceae and Campylobacterota. In the MG group, essential amino acid levels were markedly diminished but were significantly elevated after JFAD-M intervention. KEGG pathway analysis identified these amino acids as being linked to the PI3K/AKT and mTOR signaling pathways.DiscussionJFAD regulates the homeostasis of intestinal flora and influences amino acid and succinic acid metabolism through various pathways. These mechanisms could serve as potential targets for JFAD in inhibiting lung cancer invasion and metastasis.

Non-alcoholic fatty liver disease (NAFLD) is a growing global health burden with limited therapeutic options. This study investigated the protective effects of mulberry leaf glutelin (UDG) on NAFLD using free fatty acid-induced HepG2 cells and a high-fat diet (HFD) mouse model. UDG inhibited pancreatic lipase and cholesterol esterase activities in vitro, promoted fecal lipid excretion, and reduced triglyceride and cholesterol accumulation in cells and liver tissue. In vivo, UDG administration significantly alleviated HFD-induced weight gain, dyslipidemia, hepatic steatosis, and liver injury (p < 0.05). Serum biochemical analyses showed improvements in ALT, AST, lipid profiles, and lipopolysaccharide levels, accompanied by decreased expression of inflammatory cytokines (IL-6, IL-1β, TNF-α) and suppression of the TLR4/MyD88/NF-κB signaling pathway. Furthermore, untargeted serum metabolomics revealed that UDG markedly regulated metabolic profiles, with enrichment in pathways related to bile acid metabolism, amino acid metabolism, and central carbon metabolism. Notably, metabolites such as cholic acid and chenodeoxycholic acid were negatively correlated with NAFLD indicators and restored by UDG intervention. These findings show that UDG exerts lipid-lowering, hepatoprotective, and anti-inflammatory effects against NAFLD, potentially through modulation of bile acid biosynthesis and serum metabolic pathways. This study highlights mulberry leaf glutelin as a promising plant protein source with functional food potential for NAFLD prevention and management.

Metabolism of p-chloro-m-xylenol by a newly isolated marine bacterium Rhodococcus ruber SJ-1: Cellular responses and detoxification mechanisms.

Mycobacterium tuberculosis (Mtb) employs a highly adaptable network of metabolic pathways that are pivotal for its survival and pathogenesis within the host during both exponential growth and persistent infection phases. Central carbon metabolism in Mtb exhibits remarkable flexibility, enabling the bacterium to utilize diverse carbon sources efficiently. In the absence of glucose, Mtb preferentially metabolizes fatty acids as primary carbon substrates. This metabolic shift is supported by the glyoxylate shunt and methyl citrate cycle, which replenish tricarboxylic acid (TCA) cycle intermediates essential for energy production and biosynthesis. Key enzymes such as isocitrate lyase (icl) and methylcitrate lyase (mcl) facilitate the catabolism of fatty acids and maintain TCA cycle functionality, thereby sustaining bacterial growth under nutrient-limited conditions. Further enhancing metabolic adaptability, Mtb modulates central carbon metabolism through lysine acetylation, a posttranslational modification that regulates enzyme activity, particularly within fatty acid metabolic pathways. This regulatory mechanism allows Mtb to fine-tune its metabolic responses and optimize carbon utilization in response to fluctuating environmental nutrient availability.Nitrogen metabolism in Mtb is equally versatile, characterized by the capacity to utilize a variety of nitrogen sources. Amino acids such as glutamine, glutamate, aspartate, and asparagine serve as superior nitrogen donors compared to inorganic ammonium (NH₄+), reflecting Mtb's adaptation to the nutrient milieu of the host, where these amino acids are abundant. Alanine dehydrogenase (ald) exemplifies the complexity of nitrogen metabolism by functioning dually in alanine utilization and ammonium assimilation. Mtb exhibits limited homeostatic control over certain intracellular amino acid pools and demonstrates the ability to co-metabolize multiple nitrogen sources simultaneously, underscoring the dynamic nature of its nitrogen metabolic network.Sulfur metabolism plays a critical role in maintaining redox balance and supporting Mtb virulence. The sulfate assimilation pathway is central to the biosynthesis of sulfur-containing metabolites such as cysteine (Cys), which serves as a precursor for low molecular weight thiols, including mycothiol (MSH) and ergothioneine (EGT). These thiols are essential antioxidants that protect Mtb from oxidative stress encountered within host macrophages. The trans-sulfuration pathway, which converts methionine (Met) to cysteine, links methylation processes to antioxidant metabolism, further contributing to sulfur homeostasis. Sulfotransferases (Stfs) utilize 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfate donor to catalyze the sulfation of lipids and other molecules, thereby influencing Mtb's virulence and survival mechanisms. Overall, Mtb's carbon, nitrogen, and sulfur metabolic pathways are intricately interconnected, with each influencing the others to create a robust and flexible metabolic network. This metabolic integration is fundamental to Mtb's ability to thrive within the hostile environment of the host. A comprehensive understanding of these pathways is critical for identifying novel therapeutic targets aimed at disrupting Mtb's metabolic adaptability and pathogenicity. Despite the challenges posed by Mtb's metabolic resilience, ongoing research into its metabolic mechanisms continues to provide valuable insights that will inform the development of innovative antituberculosis therapies.

GLUT3 coordinates mitochondrial respiration and metabolic reprogramming in ERα-positive breast cancer.

δ-MnO2-modified peanut shell biochar and humic acid promoted Mn(IV) reduction-driven ammonium oxidation with Cr(VI) removal.

Metabolic engineering of Escherichia coli for highly efficient N-acetylneuraminic acid production.