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PubMedDate not supplied

Quantitative prediction of biodegradability, metabolite distribution and toxicity of stable metabolites.

An evaluation of the capability of organic chemicals to mineralize is an important factor to consider when assessing their fate in the environment. Microbial degradation can convert a toxic chemical into an innocuous one, and vice versa, or alter the toxicity of a chemical. Moreover, primary biodegradation can convert chemicals into stable products that can be difficult to mineralize. In this paper, we present some new results obtained on the basis of a recently developed probabilistic approach to modeling biodegradation based on microbial transformation pathways. The metabolic transformations and their hierarchy were calibrated by making use of the ready biodegradability data from the MITI-I test and expert knowledge for the most probable transformation pathways. A model was developed and integrated into an expert software system named CATABOL that is able to predict the probability of biodegradation of organic chemicals directly from their structure. CATABOL simulates the effects of microbial enzyme systems, generates the most plausible transformation pathways, and quantitatively predicts the persistence and toxicity of the biodegradation products. A subset of 300 organic chemicals were selected from Canada's Domestic Substances List and subjected to CATABOL to compare predicted properties of the parent chemicals with their respective first stable metabolite. The results show that most of the stable metabolites have a lower acute toxicity to fish and a lower bioaccumulation potential compared to the parent chemicals. In contrast, the metabolites appear to be generally more estrogenic than the parent chemicals.

Animals↗
PubMed2000

The University of Minnesota Biocatalysis/Biodegradation database: microorganisms, genomics and prediction.

The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reactions, 600 compounds and 400 enzymes, and containing approximately 250 microorganism entries. It includes information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biodegradation pathways for compounds it does not contain.

Biodegradation, Environmental↗
PubMed2006

Hydroxyquinol pathway for microbial degradation of halogenated aromatic compounds.

Several peripheral metabolic pathways can be used by microorganisms to degrade toxic aromatic compounds that are known to pollute the environment. Hydroxyquinol (1,2,4-trihydroxybenzene) is one of the central intermediates in the degradative pathway of a large variety of aromatic compounds. The present review describes the microorganisms involved in the degradative pathway, the key enzymes involved in the formation and splitting of the aromatic ring of (chloro)hydroxyquinol as well as the central intermediates formed. An attempt was also made to provide some estimation for genetic basis of the hydroxyquinol pathway.

Bacteria↗
PubMed2000

Industrial wastewater bioreactors: sources of novel microorganisms for biotechnology.

Microorganisms exist in nature as members of complex, mixed communities. The microbial communities in industrial wastewater bioreactors can be used as model systems to study the evolution of new metabolic pathways in natural ecosystems. The evolution of microbial metabolic capability in these bioreactors is presumably analogous to phenomena that occur in natural ecosystems. The microorganisms in these bioreactors compete for different carbon sources and constantly have to evolve new metabolic capabilities for survival. Thus, industrial bioreactors should be a rich source of novel biocatalysts.

Bacteria↗
PubMed2001

Biological production of 2,3-butanediol.

2,3-Butanediol (2,3-BDL), which is very important for a variety of chemical feedstocks and liquid fuels, can be derived from the bioconversion of natural resources. One of its well known applications is the formation of methyl ethyl ketone, by dehydration, which can be used as a liquid fuel additive. This article briefly reviews the basic properties of 2,3-BDL and the metabolic pathway for the microbial formation of 2,3-BDL. Both the biological production of 2,3-BDL and the variety of strains being used are introduced. Genetically improved strains for BDL production which follow either the original mechanisms or new mechanisms are also described. Studies on fermentation conditions are briefly reviewed. On-line analysis, modeling, and control of BDL fermentation are discussed. In addition, downstream recovery of 2,3-BDL and the integrated process (being important issues of BDL production) are also introduced.

Bacteria↗
PubMed2003

Bioadsorber efficiency, design, and performance forecasting for alachlor removal.

This study discusses a mathematical modeling and design protocol for bioactive granular activated carbon (GAC) adsorbers employed for purification of drinking water contaminated by chlorinated pesticides, exemplified by alachlor. A thin biofilm model is discussed that incorporates the following phenomenological aspects: film transfer from the bulk fluid to the adsorbent particles, diffusion through the biofilm immobilized on adsorbent surface, adsorption of the contaminant into the adsorbent particle. The modeling approach involved independent laboratory-scale experiments to determine the model input parameters. These experiments included adsorption isotherm studies, adsorption rate studies, and biokinetic studies. Bioactive expanded-bed adsorber experiments were conducted to obtain realistic experimental data for determining the ability of the model for predicting adsorber dynamics under different operating conditions. The model equations were solved using a computationally efficient hybrid numerical technique combining orthogonal collocation and finite difference methods. The model provided accurate predictions of adsorber dynamics for bioactive and non-bioactive scenarios. Sensitivity analyses demonstrated the significance of various model parameters, and focussed on enhancement in certain key parameters to improve the overall process efficiency. Scale-up simulation studies for bioactive and non-bioactive adsorbers provided comparisons between their performances, and illustrated the advantages of bioregeneration for enhancing their effective service life spans. Isolation of microbial species revealed that fungal strains were more efficient than bacterial strains in metabolizing alachlor. Microbial degradation pathways for alachlor were proposed and confirmed by the detection of biotransformation metabolites and byproducts using gas chromatography/mass spectrometry.

Acetamides↗
PubMed2000

Selective inhibition of reactions involved in methanogenesis and fatty acid production on rice roots.

Washed excised roots of rice (Oryza sativa) produced H(2), CH(4) and fatty acids (millimolar concentrations of acetate, propionate, butyrate; micromolar concentrations of isovalerate, valerate) when incubated under anoxic conditions. Surface sterilization of the root material resulted in the inactivation of the production of CH(4), a strong reduction of the production of fatty acids and a transient (75 h) but complete inhibition of the production of H(2). Radioactive bicarbonate was incorporated into CH(4), acetate, propionate and butyrate. About 20-40% of the fatty acid carbon originated from CO(2) reduction. In the presence of phosphate, CH(4) was exclusively produced from H(2)/CO(2), since phosphate selectively inhibited acetoclastic methanogenesis. Acetoclastic methanogenesis was also selectively inhibited by methyl fluoride, while chloroform or 2-bromoethane sulfonate inhibited CH(4) production completely. Production of CH(4), acetate, propionate and butyrate from H(2)/CO(2) was always exergonic with Gibbs free energies <-20 kJ mol(-1) product. Chloroform inhibited the production of acetate and the incorporation of radioactive CO(2) into acetate. Simultaneously, H(2) was no longer consumed and accumulated, indicating that acetate was produced from H(2)/CO(2). Chloroform also resulted in increased production of propionate and butyrate whose formation from CO(2) became more exergonic upon addition of chloroform. Nevertheless, the incorporation of radioactive CO(2) into propionate and butyrate was inhibited by chloroform. The accumulation of propionate and butyrate in the presence of chloroform probably occurred by fermentation of organic matter, rather than by reduction of acetate and CO(2). [U-(14)C]Glucose was indeed converted to acetate, propionate, butyrate, CO(2) and CH(4). Radioactive acetate, CO(2) and CH(4) were also products of the degradation of [U-(14)C]cellulose and [U-(14)C]xylose. Addition of chloroform and methyl fluoride did not affect the product spectrum of [U-(14)C]glucose degradation. The application of combinations of selective inhibitors may be useful to elucidate anaerobic metabolic pathways in mixed microbial cultures and natural microbial communities.

Journal Article↗
PubMed2026

Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.

BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment. RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus. CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.

Animals↗
PubMed2026

Metagenomic insights into the mechanisms of heteroatom-doped, iron-loaded biochar in enhancing anaerobic digestion of waste activated sludge.

Anaerobic digestion is a crucial technology for resource recovery from waste activated sludge. Enhancing its methane production efficiency using conductive materials is a key research objective. This study aimed to elucidate the mechanisms by which conductive materials promote this process. Three types of biochar(FeS@BC300, FeP@BC600, and FeP@BC900) were prepared by doping bamboo powder with N, P, S and iron salts under pyrolysis conditions at 300-900&#xa0;&#xb0;C, and their physical and chemical properties were characterized, including surface functional groups, specific surface area, capacitance, electrical resistance, electron-accepting capacity (EAC), and electron-donating capacity (EDC). These analyses assessed the influence of synthesis parameters. These materials were subsequently introduced into the anaerobic digestion of thermally hydrolyzed sludge to evaluate their impacts on methanogenic performance, microbial community structure, and metabolic pathways. The results show that the FeP@BC600 material, which exhibited the highest EDC, substantially increased microbial cytochrome c production (by 29.2&#xa0;% compared to the control). This enhancement improved interspecies electron transfer, stimulated ATP synthesis (increased by 41.5&#xa0;%), and reinforced both hydrogenotrophic and acetoclastic methanogenic pathways, ultimately elevating methane production by 55&#xa0;%. Integrated analysis of metagenomic data, material properties, and performance metrics revealed that the key mechanism by which FeP@BC600 promotes methanogenesis is through the enrichment of cytochrome c-encoding genes, thereby facilitating direct interspecies electron transfer (DIET) and augmenting ATP synthesis. This study provides a foundation for the subsequent application of conductive materials to enhance anaerobic digestion and offers guidance for the optimized design of such materials.

Sewage↗
PubMed2003

Bioplastics from microorganisms.

The term 'biomaterials' includes chemically unrelated products that are synthesised by microorganisms (or part of them) under different environmental conditions. One important family of biomaterials is bioplastics. These are polyesters that are widely distributed in nature and accumulate intracellularly in microorganisms in the form of storage granules, with physico-chemical properties resembling petrochemical plastics. These polymers are usually built from hydroxy-acyl-CoA derivatives via different metabolic pathways. Depending on their microbial origin, bioplastics differ in their monomer composition, macromolecular structure and physical properties. Most of them are biodegradable and biocompatible, which makes them extremely interesting from the biotechnological point of view.

Bacteria↗
PubMed2026

Characterisation of metabolic burden in Pseudomonas putida reveals precursor limitation in heterologous lycopene production.

BACKGROUND: The introduction of heterologous pathways into microbial hosts often imposes a metabolic burden on the cell, arising from three major physiological constraint layers: competition for gene expression resources, limited precursor availability and flux distribution, and insufficient energy and redox supply. Although Pseudomonas putida KT2440 is considered a robust and metabolically versatile production host, it remains unclear which of these constraint layers primarily limits heterologous terpenoid production in this organism. Here, lycopene biosynthesis was used as a model system to systematically dissect these three potential sources of metabolic burden. RESULTS: A capacity-monitoring system revealed no clear reduction in transcriptional or translational capacity across the tested strains and cultivation conditions, indicating that general gene expression capacity was not the primary limiting factor. Instead, lycopene production depended strongly on promoter architecture and plasmid backbone, showing that regulatory design shaped pathway performance. Enhancing precursor supply by introducing a heterologous mevalonate (MVA) pathway substantially increased product titres, identifying precursor availability from the native MEP pathway as the dominant bottleneck. This conclusion was independently supported by exogenous mevalonate supplementation, which further increased lycopene accumulation but also revealed saturation at higher concentrations, suggesting that downstream pathway balance or enzyme capacity became limiting once precursor supply was relieved. Under controlled bioreactor conditions, lycopene titres increased from approximately 1&#xa0;mg/L to nearly 25&#xa0;mg/L, indicating that process conditions further modulate production performance, suggesting an additional contribution of process-dependent energy and redox constraints. CONCLUSION: Metabolic burden during heterologous lycopene production in P. putida is governed primarily by precursor availability rather than by limitations in general gene expression capacity. Regulatory properties of the vector system strongly influence pathway performance, while controlled cultivation conditions can further improve production by alleviating additional process-dependent constraints. Together, these findings provide a systematic framework for distinguishing constraint layers and guiding the optimisation of heterologous terpenoid production systems.

Lycopene↗
PubMed2002

Computational identification of operons in microbial genomes.

By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genomes to identify putative operon structures. The predicted operons from Escherichia coli were compared with a selected metabolism-related operon dataset from the RegulonDB database, yielding a prediction sensitivity (89%) and specificity (87%) relative to this dataset. Several examples of detected operons are given and analyzed. Modular gene cluster transfer and operon fusion are observed. A further use of predicted operon data to assign function to putative genes was suggested and, as an example, a previous putative gene (MJ1604) from Methanococcus jannaschii is now annotated as a phosphofructokinase, which was regarded previously as a missing enzyme in this organism. GC content changes in the operon region and nonoperon region were examined. The results reveal a clear GC content transition at the boundaries of putative operons. We looked further into the conservation of operons across genomes. A trp operon alignment is analyzed in depth to show gene loss and rearrangement in different organisms during operon evolution.

Algorithms↗
PubMedDate not supplied

Effects of oxygen on anoxic biodegradation of benzoate during continuous culture.

In this study, various amounts of oxygen were added to denitrifying chemostats receiving benzoate to mimic the input of oxygen to anoxic zones of biological nutrient removal systems. The effect of oxygen on the biodegradative capability of the mixed-microbial culture for benzoate was investigated. The anoxic benzoate biodegradative capability of the culture was not significantly changed as the mass flowrate of oxygen was increased to 40% of the input benzoate chemical oxygen demand (COD) mass flowrate, but was decreased approximately 70% when the mass flowrate of oxygen was increased to 70% of the input benzoate COD mass flowrate. The decrease in the anoxic benzoate biodegradative capability was due primarily to the loss of the denitrifying enzymes (measured by the anoxic pyruvate-degrading ability) and not to the loss of the key anoxic catabolic enzyme (benzoyl-coenzyme A reductase). The proportional increase in the concentration of nitrate as the residual terminal electron acceptor and the lack of synthesis of aerobic ring-cleavage enzymes as the oxygen input to the chemostat was increased suggest that the mixed microbial culture preferred oxygen to nitrate as the terminal electron acceptor, but degraded benzoate using the anoxic metabolic pathway. The concentration of the mixed microbial culture increased as the oxygen input to the chemostat was increased, suggesting that the oxygen was used by cytochrome cbb3 rather than quinol oxidase because the energetic yield of cytochrome cbb3 is higher than that of quinol oxidase or the nitrogen oxide reductases.

Anti-Infective Agents↗
PubMed2001

TIRAP: an adapter molecule in the Toll signaling pathway.

Mammalian Toll-like receptors (TLRs) recognize conserved products of microbial metabolism and activate NF-kappa B and other signaling pathways through the adapter protein MyD88. Although some cellular responses are completely abolished in MyD88-deficient mice, TLR4, but not TLR9, can activate NF-kappa B and mitogen-activated protein kinases and induce dendritic cell maturation in the absence of MyD88. These differences suggest that another adapter must exist that can mediate MyD88-independent signaling in response to TLR4 ligation. We have identified and characterized a Toll-interleukin 1 receptor (TIR) domain-containing adapter protein (TIRAP) and have shown that it controls activation of MyD88-independent signaling pathways downstream of TLR4. We have also shown that the double-stranded RNA-binding protein kinase PKR is a component of both the TIRAP- and MyD88-dependent signaling pathways.

Adaptor Proteins, Signal Transducing↗
PubMed2026

Gut microbiota dynamics and metabolic pathways associated with bleomycin-induced pulmonary fibrosis progression.

BACKGROUND: Pulmonary fibrosis (PF) is a progressive respiratory disease characterized by epithelial injury, aberrant repair and excessive extracellular matrix deposition. Although the gut-lung axis is increasingly implicated in respiratory disorders, stage-resolved characterization of gut microbiota taxonomic and functional potential during PF development is limited. METHODS: We established a bleomycin-induced murine PF model and performed cross-sectional shotgun metagenomic sequencing of fecal samples from separate cohorts at three defined stages: baseline (control), day 7 (early fibrosis; M7), and day 14 (established fibrosis; M14). Microbial taxonomy, alpha/beta diversity, and predicted functional capacity were inferred using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZymes (CAZy) annotations; associations were assessed using Procrustes and Spearman correlation analyses. RESULTS: Histopathology and immunohistochemistry confirmed progressive fibrogenesis with increased TGF-&#x3b2;1 and &#x3b1;-SMA expression. Compared with baseline, bleomycin-treated groups exhibited stage-specific shifts in gut microbial composition, including depletion of mucin-associated taxa (e.g., Prevotella, Akkermansia muciniphila) and expansion of Muribaculaceae- and Clostridiaceae-affiliated taxa. Alpha and beta diversity metrics differed across groups. KEGG/CAZy-based annotations revealed predicted, stage-dependent changes in microbial metabolic potential, including early reductions in pathways related to amino acid and glycan metabolism (M7) and later increases in predicted starch/sucrose catabolism, phosphotransferase system (PTS) representation, and secondary bile acid biosynthesis (M14). Correlation analyses linked compositional shifts to these predicted functional changes. CONCLUSION: In a stage-resolved, cross-sectional study, bleomycin-associated pulmonary fibrosis was accompanied by compositional and predicted functional alterations in the gut microbiota. These data identify candidate taxa and predicted pathways for follow-up mechanistic testing, but functional (metabolomic) and causality experiments are required to confirm whether and how microbial changes contribute to PF pathogenesis.

Animals↗
PubMed2025

Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.

Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.

Humans↗
PubMed2003

Dispelling the myths--biocatalysis in industrial synthesis.

Biocatalysis has emerged as an important tool in the industrial synthesis of bulk chemicals, pharmaceutical and agrochemical intermediates, active pharmaceuticals, and food ingredients. However, the number and diversity of the applications are modest, perhaps in part because of perceived or real limitations of biocatalysts, such as limited enzyme availability, substrate scope, and operational stability. Recent scientific breakthroughs in genomics, directed enzyme evolution, and the exploitation of biodiversity should help to overcome these limitations. As a result, we expect many new industrial applications of biocatalysis to be realized, from single-step enzymatic conversions to customized multistep microbial synthesis by means of metabolic pathway engineering.

Biotechnology↗