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Microbial sensors on a respiratory basis for wastewater monitoring.

In respect of their rapidity, their online capabilities, and their moderate costs, biosensing systems generally offer an attractive alternative to the existing methods of water analysis. Additionally, one particular advantage of microbial biosensors is the ability to measure direct effects on living cells, e.g., their respiratory activity and its alteration caused by environmental pollutants. It is true that microbial sensors, often do not provide the optimum solution for the determination of individual analytes when compared to established physico-chemical analysis methods. However, these biosensing devices are predestined for the summary determination of environmentally relevant compounds and their complex effects, respectively. For this reason, microbial sensors allow an integral evaluation of the degree of environmental pollution including the interaction of various compounds. Moreover, in some cases specific metabolic pathways in microorganisms are used, resulting in the development of microbial sensors for the more selective analysis for those compounds or pollutants, which cannot be measured by simple enzyme reactions, e.g., the determination of aromatic compounds and heavy metals. This chapter gives an overview of microbiological biosensors on respiratory basis for the measurement of the following environmentally relevant compounds: inorganic N-compounds, heavy metals, organic xenobiotics and the estimation of sum parameters or so-called complex parameters such as BOD, ADOC, N-BOD, and the inhibition of nitrification.

Bacteria↗

Effects of Sodium-Glucose Cotransporter-2 Inhibitors on Modulating Protein-Bound Uremic Toxins and Gut Microbiota in Predialysis CKD Patients: Matched Case-Control Study.

KEY POINTS: A reduction of indoxyl sulfate, p-cresyl sulfate, and several short-chain fatty acids was seen in sodium-glucose cotransporter-2 inhibitor-treated CKD patients. Variations in gut microbiota composition are correlated with levels of gut-derived uremic toxins in sodium-glucose cotransporter-2 inhibitor-treated CKD patients. BACKGROUND: The intricate interplay between CKD and intestinal microbiota has gained increasing attention, with gut dysbiosis being implicated in uremic toxin accumulation and CKD progression. Sodium-glucose cotransporter-2 inhibitors (SGLT2i) are now transforming CKD management but pose uncertain effects on shaping gut microbiota. This study aimed to elucidate the effect of SGLT2i on perturbations of gut microbial composition and metabolic responses in patients with CKD. METHODS: Analysis of fecal microbiota and targeted profiling of serum short-chain fatty acids and gut-derived uremic toxins were conducted in a matched case-control study, including 60 patients with CKD (treated: n=30; untreated: n=30) and 30 non-CKD controls. RESULTS: Gut microbial composition differed significantly among the three study groups. Patients with CKD receiving SGLT2i exhibited distinctive taxonomic profiles, such as enrichment of Bacteroides stercoris and Bacteroides coprocola. Surveys of metabolomic profiles revealed a reduction of two uremic solutes, indoxyl sulfate and p-cresyl sulfate (pCS), and several short-chain fatty acids (formic, acetic, propionic, valeric, and 2-methylbutanoic acid) in SGLT2i-treated CKD patients. Co-occurrence analysis demonstrated a set of intestinal microbes that is positively or negatively correlated with the levels of pCS, and the abundance of these pCS-associated intestinal microorganisms was correlated with the levels of indoxyl sulfate and isovaleric acids in the same and opposite direction, respectively. Further functional prediction indicated attenuated pathways related to protein and carbohydrate metabolism. CONCLUSIONS: Treatment with SGLT2i in patients with CKD is associated with distinct gut microbial composition and metabolite profiles, suggesting potential modulation of gut dysbiosis and metabolic pathways. Further studies are warranted to elucidate the clinical implications of these findings in CKD management.

CKD↗

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing.

The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.

Xylose↗

Physical simulation for low-energy astrobiology environmental scenarios.

Speculations about the extent of life of independent origin and the potential for sustaining Earth-based life in subsurface environments on both Europa and Mars are of current and relevant interest. Theoretical modeling based on chemical energetics has demonstrated potential options for viable biochemical metabolism (metabolic pathways) in these types of environments. Also, similar environments on Earth show microbial activity. However, actual physical simulation testing of specific environments is required to confidently determine the interplay of various physical and chemical parameters on the viability of relevant metabolic pathways. This testing is required to determine the potential to sustain life in these environments on a specific scenario by scenario basis. This study examines the justification, design, and fabrication of, as well as the culture selection and screening for, a psychrophilic/halophilic/anaerobic digester. This digester is specifically designed to conform to physical testing needs of research relating to potential extent physical environments on Europa and other planetary bodies in the Solar System. The study is a long-term effort and is currently in an early phase, with only screening-level data at this time. Full study results will likely take an additional 2 years. However, researchers in electromagnetic biosignature and in situ instrument development should be aware of the study at this time, as they are invited to participate in planning for future applications of the digester facility.

Acetates↗

Plasmacytoid dendritic cell-mediated L-glutamate catabolism links gut microbiota to male infertility.

Emerging evidence suggests that gut microbiota composition influences male reproductive health; however, the immunometabolic mechanisms underlying this association remain insufficiently characterized. We investigated whether specific immune cell-mediated metabolic pathways, particularly plasmacytoid dendritic cell (pDC)-driven L-glutamate catabolism via the hydroxyglutarate pathway, contribute to the causal link between gut microbiota and male infertility. We conducted a 2-sample, 2-step Mendelian randomization (MR) analysis using inverse-variance weighting as the primary estimator and Bayesian weighted MR for robustness. Exposure data comprised 412 gut microbial taxa/metabolic pathways and 731 immune cell phenotypes from large European-ancestry genome-wide association studies. Male infertility genome-wide association studies data (1429 cases; 128,710 controls) were obtained from FinnGen R10. Only exposure-mediator-outcome pairs meeting stringent pleiotropy, heterogeneity, and reverse-causality criteria were retained for mediation analysis. Nine microbial taxa/metabolic pathways and 18 immune traits exhibited putative causal associations with male infertility. The L-glutamate degradation V pathway via hydroxyglutarate was linked to reduced infertility risk (inverse-variance weighting odds ratio [OR] = 0.68; 95% confidence interval, 0.52-0.89; P = .005). Two-step MR suggested that forward scatter area on pDCs may mediate this association, although the mediation effect was imprecise (effect = 0.0277; 95% confidence interval, -0.0348 to 0.0903). This study provides suggestive genetic evidence that pDC-mediated glutamate catabolism may connect gut microbial metabolic activity to male infertility. These findings highlight immunometabolic pathways as testable targets for mechanistic validation and microbiota-directed interventions.

Male↗

TNT biotransformation and detoxification by a Pseudomonas aeruginosa strain.

Successful microbial-mediated remediation requires transformation pathways that maximize metabolism and minimize the accumulation of toxic products. Pseudomonas aeruginosa strain MX, isolated from munitions-contaminated soil, degraded 100 mg TNT L(-1) in culture medium within 10 h under aerobic conditions. The major TNT products were 2-amino-4,6-dinitrotoluene (2ADNT, primarily in the supernatant) and 2,2'-azoxytoluene (2,2'AZT, primarily in the cell fraction), which accumulated as major products via the intermediate 2-hydroxylamino-4,6-dinitrotoluene (2HADNT). The 2HADNT and 2,2'AZT were relatively less toxic to the strain than TNT and 2ADNT. Aminodinitrotoluene (ADNT) production increased when yeast extract was added to the medium. While TNT transformation rate was not affected by pH, more HADNTs accumulated at pH 5.0 than at pH 8.0 and AZTs did not accumulate at the lower pH. The appearance of 2,6-diamino-4-nitrotoluene (2,6DANT) and 2,4-diamino-6-nitrotoluene (2,4DANT); dinitrotoluene (DNT) and nitrotoluene (NT); and 3,5-dinitroaniline (3,5DNA) indicated various routes of TNT metabolism and detoxification by P. aeruginosa strain MX.

Biodegradation, Environmental↗

Microbial biotransformation products of cyclosporin A.

In order to mimic the human metabolic pathway of cyclosporin A (CyA) a total of 28 bacterial and 72 fungal strains was screened for their ability to transform CyA. Among 3 bacteria and 11 fungi, which produced the main human metabolite OL-17 [eta HyMeBmt1]CyA, Actinoplanes sp. (ATCC 53771) achieved the best transformation rate (5.4%). Furthermore, the two N-demethylated minor products [Leu4]CyA (3.2%) and [Leu9]CyA (4.7%) were isolated, both known as minor natural metabolites and the first one also as a human biotransformation product. Microbial conversion of CyA using the actinomycete Sebekia benihana (NRRL 11111) yielded [gamma HyMeLeu4]CyA (35%), [gamma HyLeu4]CyA (4.5%) and [gamma HyMeLeu4, gamma HyMeLeu6]CyA (8.6%). The structures of these derivatives correspond with those of the human metabolic pathway. The related compounds [Nva2]CyA (CyG) and [D-MeSer3]CyA were similarly converted to the corresponding 4-gamma-hydroxylated analogues. None of the biotransformation products showed a better immunosuppressive effect than CyA, although in various cases the cyclophilin binding affinity was comparable to that of CyA.

Bacteria↗

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

The MetaCyc database (see URL http://MetaCyc.org) is a collection of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants. The goal of MetaCyc is to contain a representative sample of each experimentally elucidated pathway, and thereby to catalog the universe of metabolism. MetaCyc also describes reactions, chemical compounds and genes. Many of the pathways and enzymes in MetaCyc contain extensive information, including comments and literature citations. SRI's Pathway Tools software supports querying, visualization and curation of MetaCyc. With its wide breadth and depth of metabolic information, MetaCyc is a valuable resource for a variety of applications. MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to create Pathway/Genome Databases that can be augmented with curation from the scientific literature and published on the world wide web. MetaCyc also serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper.

Biochemical Phenomena↗

Using pyrosequencing to shed light on deep mine microbial ecology.

BACKGROUND: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology. RESULTS: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date. CONCLUSION: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Bacteria↗

Microbial enzymes for creatinine assay: a review.

A novel metabolic pathway for the degradation of creatinine with N-methylhydantoin, N-carbamoylsarcosine and sarcosine as successive intermediates was found to operate in Pseudomonas putida 77 and many other microorganisms. Enzymes involved in this pathway were purified from cells of P. putida 77 and characterized. The first step, deimination of creatinine, is catalyzed by cytosine deaminase/creatinine deiminase. The following two steps, ring-opening of N-methylhydantoin and decarbamoylation of N-carbamoylsarcosine, are catalyzed by new enzymes, N-methylhydantoin amidohydrolase and N-carbamoylsarcosine amidohydrolase, respectively. The former requires ATP, Mg2+, and K+ for the hydrolysis and the reaction proceeds as follows: N-methylhydantoin + ATP + 2 H2O----N-carbamoylsarcosine + ADP + Pi. The latter catalyzes the following reaction; N-carbamoylsarcosine + H2O----sarcosine + NH3 + CO2. Sarcosine dehydrogenase was found to be the responsible enzyme for the oxidation of sarcosine to glycine in P. putida 77, but sarcosine oxidase was also found to be involved in this oxidation in several microorganisms. These enzymes were found to be useful tools for determination of creatinine.

Amidohydrolases↗

Microbial desulfurization of dibenzothiophene: a sulfur-specific pathway.

Rhodococcus rhodochrous strain IGTS8 metabolizes dibenzothiophene, a model compound for organic sulfur in fossil fuels, in a sulfur-specific manner. Two routes of desulfurization have been identified. Under growth conditions, the intermediates are dibenzothiophene sulfoxide, dibenzothiophene sulfone, 2'-hydroxybiphenyl-2-sulfonate, and 2,2'-dihydroxybiphenyl. Stationary phase cells produce 2-hydroxybiphenyl as the desulfurized product and use the 2'-hydroxybiphenyl-2-sulfinate, rather than the sulfonate, as the key intermediate.

Oxidation-Reduction↗

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

MetaCyc is a database of metabolic pathways and enzymes located at http://MetaCyc.org/. Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the BioCyc.org website. These PGDBs also include predicted operons and pathway hole fillers.

Animals↗

Fate studies of the non-ionic surfactant alkyl glucamide by liquid chromatography/electrospray mass spectrometry

Alkyl glucamides (AGs) were analyzed by reversed-phase liquid chromatography (LC) coupled to mass spectrometry with electrospray ionization (ESMS). Analytes were separated according to the chain length of two homologs, C12- and C14-glucamide. Mass spectrometric detection in the positive ion mode exhibited higher overall sensitivity where, apart from fragments, different molecular and quasi-molecular ions were obtained. However, application of the negative ion mode offered advantages in terms of reproducibility and extent of information when analyzing environmental samples. Therefore, a simple and sensitive analytical methodology was developed for the determination of AGs in municipal sewage treatment plant influent and effluent based on solid-phase enrichment, LC separation and negative ion ESMS quantification. After preconcentration of 100 ml of aqueous sample, the recoveries using polymeric LiChrolut EN cartridges exceeded 89%. A quantification limit of 0.1 microg l(-1) was achieved. Studies on the biodegradability and metabolic pathway of C10-glucamide were carried out on a laboratory-scale microbial test unit under aerobic conditions. A postulated metabolism including omega-oxidation of the alkyl chain followed by subsequent beta-oxidations was checked by LC/ESMS. Identification and formation of 'C4-glucamide acid' as a degradation intermediate was confirmed by mass spectrometric studies. Higher homolog acids such as C10-, C8- and C6-glucamide acids, which should be predicted precursors of C4-glucamide acid, and any other metabolites, were not detectable, presumably owing to rapid breakdown.

Journal Article↗

Production of vitamins, coenzymes and related biochemicals by biotechnological processes.

Vitamins and related biofactors belong to those few chemicals with a direct positive appeal to people. There is indeed a large need for extra vitamins, other than those derived from plant and animal food sources, due to unbalanced food habits or processing, food shortage or disease. Added vitamins are now either prepared chemically or biotechnologically via fermentation or bioconversion processes. Several vitamins and related biofactors are now only or mainly produced chemically (vitamin A, cholecalciferol (D3), tocopherol (E), vitamin K2, thiamine (B1), niacin (PP or B3), pantothenic acid (B5), pyridoxine (B6), biotin (H or B8), folic acid (B9) or via extraction processes (beta-carotene or provitamin A, provitamin D3, tocopherol, vitamin F-group). However, for several of these compounds microbiological or algal methods also exist or are rapidly emerging. Others are produced practically exclusively via fermentation (ergosterol or provitamin D2, riboflavin (B2), cyanocobalamin (B12), orotic acid (B13), vitamin F-group, ATP, nucleosides, coenzymes, etc. or via microalgal culture (beta-carotene, E, F). Both chemical and microbial processes are run industrially for vitamin B2 while vitamin C (ascorbic acid) is produced via a combination of chemical reactions and fermentation processes. A survey is given here of the current state of vitamin production, with emphasis on developments and strategies for improved biotechnological production and its significance, as compared to existing chemical processes. The screening or construction of vitamin hyperproducing microbial strains is a difficult task; pathway elucidation and metabolic (de)regulation need further study; r-DNA technology has only recently been introduced; improved fermentation processes and immobilised biocatalysts bioconversions for the synthesis of chiral vitamin compounds or intermediates or derivatives are gaining importance; the recovery and purification of these vitamin compounds from their fermentation broths remains equally complex.

Biotechnology↗

Anti-lymphoma effect of gammadelta T cells.

During the last few years, our knowledge about the activation and control of non-major histocompatibility complex (MHC)-restricted innate effector lymphocytes (such as natural killer (NK) cells, NK T cells and gammadelta T cells) has advanced enormously and immunotherapeutic strategies based on these cell types receive more and more attention. Apart from NK cells, several lines of evidence indicate that T cells, which express an alternative T cell receptor (TCR) composed of a CD3-associated gammadelta heterodimer, also contribute to the innate immune defense against tumors. Human gammadelta T cells represent a small subset of T cells (1-10% of peripheral blood T cells) and differ from conventional MHC-restricted ass T cells in recognition of a unique set of antigens ("phosphoantigens") and the lack of requirement of classical antigen-presenting molecules. Besides their role in the innate immune response against pathogens based on the recognition of distinctive microbial metabolic products (metabolites of the non-mevalonate pathway of isoprenoid synthesis), Vgamma9Vdelta2 T cells that constitute the dominant fraction of gammadelta T cells in humans exert potent cytotoxic activity, especially against lymphoid malignancies, mediated by as yet only partially determined pathway(s) of tumor recognition. This article will review available evidence from pre-clinical and early clinical studies regarding the contribution of gammadelta T cells in the defense against lymphoid malignancies and highlights some important issues that need to be addressed in the future.

Animals↗

Hydrogen peroxide release by rat alveolar macrophages: comparison with blood neutrophils.

Hydrogen peroxide release was examined using biochemical and cytochemical techniques in rat alveolar macrophages, at rest and during phagocytosis, and compared with rat blood neutrophils. Using biochemical techniques, alveolar macrophages released small amounts of hydrogen peroxide at rest, and no increase was observed after challenge with opsonized and nonopsonized zymosan particles at several particle-cell ratios (1:1 to 1:1,000). Neutrophils released similar quantities of hydrogen peroxide at rest but showed a 12-fold increase in hydrogen peroxide release following exposure to opsonized zymosan particles. Using cytochemical techniques to localize sites of hydrogen peroxide release, resting neutrophils showed little deposition of reaction product at the cell surface and occasional deposits in endocytotic vesicles. After exposure to latex particles, a dense reaction product was observed between the particle and the cell membrane, indicating significant increases in hydrogen peroxide release at the sites of particle contact with the neutrophil. The resting macrophage displayed a light, uniform precipitation of cerium over the cell surface and lining intracellular channels and endocytotic vesicles and vacuoles. Following particle exposure, there was no significant difference in the density or distribution of reaction product. These findings, together with previous studies of oxidative metabolism, suggest that alveolar macrophages do not release increased quantities of hydrogen peroxide during phagocytosis. In contrast to neutrophils, oxidative-dependent metabolic pathways may not be of primary importance for microbial killing by alveolar macrophages.

Animals↗

[Thiodiglycol metabolism in Alcaligenes xylosoxydans subsp. denitrificans].

The investigation of the degradation of thiodiglycol (the major product of mustard gas hydrolysis) by Alcaligenes xylosoxydans subsp. denitrificans strain TD2 showed that thiodiglycol is metabolized through the oxidation of its primary alcohol groups and the subsequent cleavage of C-S bonds in the intermediate products, thiodiglycolic and thioglycolic acids. The end products of these reactions are SO4(2-) ions and acetate, the latter being involved in the central metabolism of strain TD2. The oxidation of the sulfur atom gives rise to diglycolsulfoxide, which is recalcitrant to further microbial degradation. Based on the data obtained, a metabolic pathway of thiodiglycol transformation by A. xylosoxydans subsp. denitrificans strain TD2 is proposed.

Alcaligenes↗

Genomic and mechanistic insights into the biodegradation of organic pollutants.

Several new methodologies have enabled recent studies on the microbial biodegradation mechanisms of organic pollutants. Culture-independent techniques for analysis of the genetic and metabolic potential of natural and model microbial communities that degrade organic pollutants have identified new metabolic pathways and enzymes for aerobic and anaerobic degradation. Furthermore, structural studies of the enzymes involved have revealed the specificities and activities of key catabolic enzymes, such as dioxygenases. Genome sequencing of several biodegradation-relevant microorganisms have provided the first whole-genome insights into the genetic background of the metabolic capability and biodegradation versatility of these organisms. Systems biology approaches are still in their infancy, but are becoming increasingly helpful to unravel, predict and quantify metabolic abilities within particular organisms or microbial consortia.

Bacteria↗