In vitro metabolic signaling in two intestinal bacterial isolates: glutamate-driven transcriptional and functional reprogramming in Clostridium butyricum and Bacteroides thetaiotaomicron
Aug 2026· Msphere· Vol 11· 0 citations· 78 references
Medicine
TL;DR
Analysis of strain-specific transcriptomic and metabolic responses of Clostridium butyricum and Bacteroides thetaiotaomicron grown in pure anaerobic culture with 0.1% MSG suggested that MSG's physiological effects may depend on which bacterial groups dominate an individual’s microbiome.
Abstract
ABSTRACT Monosodium glutamate (MSG; L-glutamate monosodium salt) is among the most widely used flavor enhancers, yet its molecular effects on gut microbial physiology remain poorly understood. Here, we examined the strain-specific transcriptomic and metabolic responses of Clostridium butyricum and Bacteroides thetaiotaomicron grown in pure anaerobic culture with 0.1% (wt/vol) MSG. Although MSG exposure was not associated with major changes in total bacterial biomass dynamics, both species showed a temporal functional reprogramming. In C. butyricum, MSG rapidly intensified metabolic activity to capitalize on exogenous glutamate by activating central carbon metabolism, redox-balancing pathways, and the GABA shunt, thereby collectively enhancing butyrate synthesis, a metabolite associated with gut barrier integrity, energy regulation, and anti-inflammatory signaling. On the other hand, B. thetaiotaomicron adopted a conservative, homeostatic response, suppressing glycan utilization and central carbon and energy metabolism, and maintaining stable SCFA production through controlled regulation that buffered against abrupt dietary perturbations. Overall, MSG functioned as a potent metabolic signal, triggering distinct adaptive strategies in two dominant gut bacteria. IMPORTANCE The impact of monosodium glutamate (MSG) as a highly consumed food additive on the gut microbiome is often overlooked, and community-level analyses reveal little change, masking distinct phenotypic responses of individual strains. By combining gene expression and metabolite profiling using two key human gut bacteria, we show that MSG is sensed as a metabolic signal. A butyrate-producing gut bacterium increases energy metabolism and butyrate production, and a fiber-degrading gut bacterium transiently moderates metabolism to maintain stable fermentation products. These differences suggest that MSG's physiological effects may depend on which bacterial groups dominate an individual’s microbiome. The impact of monosodium glutamate (MSG) as a highly consumed food additive on the gut microbiome is often overlooked, and community-level analyses reveal little change, masking distinct phenotypic responses of individual strains. By combining gene expression and metabolite profiling using two key human gut bacteria, we show that MSG is sensed as a metabolic signal. A butyrate-producing gut bacterium increases energy metabolism and butyrate production, and a fiber-degrading gut bacterium transiently moderates metabolism to maintain stable fermentation products. These differences suggest that MSG's physiological effects may depend on which bacterial groups dominate an individual’s microbiome.
Pseudomonas aeruginosa (PA) uses its quorum-sensing molecule 2’-aminoacetophenone (2-AA) to modulate host mitochondrial activity. This study investigates how 2-AA—driven host metabolic reprogramming contributes to macrophage dysfunction and supports bacterial persistence.
We used biochemical and molecular assays to show that 2-AA induced host lactate augmentation. Immunoprecipitation identified proteins involved in histone lactylation (Kla), while CUT&RUN and transcriptomics studies deciphered gene regulation and molecular anergy.
Mechanistically, 2-AA disrupts the ESRRA—PPARGC1α regulatory axis, leading to the downregulation of the mitochondrial pyruvate carrier (MPC1). This impairment affects pyruvate transport into mitochondria, rewiring cellular metabolism to a glycolytic state, leading to increased lactate dehydrogenase A (LDHA) activity, elevated and sustained lactate levels in PA-infected immune cells and host tissues, and Kla. Genome-wide profiling of H3 lysine 18 lactylation (H3K18la) demonstrated distinct chromatin modification at regulatory regions, indicating novel epigenetic regulation by lactylation. The 2-AA-mediated H3K18la involves the GTP-specific succinyl-CoA synthetase (GTPSCS) and its interaction with histone lactyl-transferases CREB-binding protein (CBP) and p300. In agreement with H3k18la signatures, transcriptomic profiling of wild-type PA and its 2-AA-deficient mutant revealed regulatory pathways modulating immune and metabolic responses. Functionally, enhanced H3K18la favors a tolerogenic macrophage phenotype that supports intracellular bacterial survival. Conversely, inhibiting lactate accumulation or blocking 2-AA synthesis diminishes H3K18la and enhances bacterial clearance.
Collectively, these findings uncover a previously unrecognized QS-regulated metabolic—epigenetic axis through which PA manipulates host immunity, highlighting lactate metabolism as a potential therapeutic target for combating chronic Pseudomonas infections.
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Innate Immune Responses and Host Defense: Molecular Mechanisms (INM)
Arijit Chakraborty, Arijit Chakraborty, Shifu Aggarwal et al.· Journal of Immunology· 0 citations
ABSTRACT Alkaline environments disrupt ammonia excretion and challenge nitrogen metabolism in aquatic invertebrates, but the underlying cellular mechanisms remain unclear. To elucidate the adaptive mechanisms of crustaceans in highly alkaline environments, the responses of Macrobrachium hainanense to acute carbonate alkalinity stress are characterized using single‐cell RNA sequencing. High alkalinity inhibits normal ammonia excretion, leading to ammonia accumulation in the hemolymph, gill injury, mitochondrial dysfunction, and elevated oxidative stress. Marked heterogeneous remodeling occurs across distinct cell populations; pillar cells, nephrocytes, and semi‐granulocytes play primary roles in nitrogen metabolic regulation, acid‐base homeostasis, and immune defense, respectively. Further analyses identify glutamate dehydrogenase (GDH) as a key regulator of alkalinity adaptation. Inhibition of GDH significantly reduces alkaline tolerance, exacerbating tissue damage and metabolic disturbances while impairing ATP maintenance and inducing mitochondrial dysfunction under alkaline stress. Furthermore, GDH suppression inhibits urea metabolism while enhancing purine catabolism, indicating an adaptive shift in nitrogen metabolic strategy. This study provides a single‐cell resolution of crustacean alkalinity adaptation and identifies GDH‐mediated metabolic remodeling as a determinant of the environmental stress response. These findings offer theoretical insights into the regulatory mechanisms underlying stress adaptation in invertebrates.
Yiting Jin, Zhimin Lv, Chao Bian et al.· Advancement of science· 0 citations
S-Adenosylmethionine (SAM) is a high-value biomolecule with critical applications in nutraceuticals, pharmaceuticals, and health supplements. However, the detailed metabolic mechanism by which sodium citrate promotes SAM production in Pichia pastoris has not yet been elucidated. Here, a comprehensive time-series transcriptomic analysis revealed that sodium citrate profoundly influences gene expression across multiple pathways. Sodium citrate supplementation redirects carbon flux toward oxidative energy metabolism by upregulating amino acid biosynthesis, translation, and glycolysis. Crucially, the transcriptional upregulation of argininosuccinate synthase (ARG1) and argininosuccinate lyase (ARG4) was identified as a key node driving fumarate-mediated TCA cycle anaplerosis and ATP supply. This foundational analysis led to the identification of ARG4 as a key metabolic engineering target. Overexpression of ARG4 significantly improved SAM production, achieving a 56.46% increase in shake flasks and 9.06 g/L SAM (a 22.10% improvement) in 500 mL fermenters compared to control strains. Integrated physiological and metabolic flux analysis (MFA) demonstrated that ARG4 overexpression redirects metabolic flow, channeling energy substrates toward SAM synthesis, effectively maintaining cellular respiratory metabolism and alleviating energy limitations in the late fermentation phase. This work establishes a novel strategy for enhancing product synthesis by restructuring energy allocation rather than merely increasing overall energy supply.
Muconic acid is a versatile platform chemical that can be biologically produced from lignocellulosic substrates, including from lignin-related aromatic compounds. Pseudomonas putida has been previously engineered to convert lignin-related aromatic compounds to muconate at quantitative molar yields. This high atom efficiency requires a supplemental carbon and energy source to support bacterial growth, and central carbon metabolic efficiency and its interaction with aromatic catabolism are underexplored. Here, we applied proteomics, metabolomics, and 13C-fluxomics to quantitatively compare central carbon and energy metabolism in wild-type P. putida KT2440 and a muconate-producing strain, P. putida CJ781. During cultivation on glucose and 4-hydroxybenzoate, CJ781 showed increased glucose uptake, reconfigured central fluxes, and increased extracellular leakage of aliphatic acids relative to wild type. These altered fluxes supported a 3-fold higher ATP pool, in excess of demand. Pyruvate and acetate secretion in CJ781 was mitigated by debottlenecking TCA-cycle entry via citrate synthase overexpression. Furthermore, tuned expression of the catechol dioxygenase and protocatechuate decarboxylase enabled the production of 36.3 g L-1 muconate at 1.1 g L-1 h-1. Overall, this work reveals how P. putida redirects carbon and energy fluxes to support aromatic bioconversion for improved bioproduction from renewable feedstocks.
R. Wilkes, P. Suthers, A. Borchert et al.· bioRxiv· 3 citations
Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia exposed to 42 °C for 6 h and then allowed to recover at 28 °C for 2 h (HPJZ42-R). Metabolomic and transcriptomic profiles separated clearly between the two conditions, indicating broad post-heat recovery-associated molecular remodeling. Most differential metabolites were lower in HPJZ42-R, whereas a smaller subset accumulated, suggesting selective metabolic reorganization rather than generalized activation. Transcriptome analysis identified extensive gene-expression remodeling, with 1081 upregulated and 1878 downregulated genes in the HPJZ28 versus HPJZ42-R comparison. Pathway-level analyses implicated central carbon metabolism, lipid metabolism, amino acid metabolism, peroxisome-related processes, and calcium signaling. Because the sampling design included a recovery period and a single post-stress time point, integrated gene–metabolite correlations are interpreted as exploratory associations rather than evidence of direct regulatory coupling. These results provide species-level multi-omics evidence for the post-heat recovery state of O. raphanipes and identify candidate pathways for future functional and physiological validation.
Yangyang Peng, Jianhao Wang, Ling-Jun Xu et al.· Journal of Fungi· 0 citations
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