Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance.

Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic-prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically.

Electrochemical Simulation of the Oxidative Capsaicin Metabolism.

Capsaicin, primarily known as the pungent ingredient in hot peppers, is rapidly metabolized in the human body by enzymatic processes altering the pharmacological as well as toxicological properties. Herein, the oxidative transformation of capsaicin was investigated in vitro with electrochemistry as well as human liver microsomal incubations. The reaction mixtures were analyzed with liquid chromatography-mass spectrometry. Structure elucidation involved accurate mass measurements and multistage tandem mass spectrometry experiments. In total, 126 transformation products were detected. Electrochemistry provided evidence for 101 transformation products and the microsomal incubations for 46 species. 21 compounds were observed with both approaches. Identified oxidative pathways likely occurring during the phase I metabolism included dehydrogenation, O-demethylation, and hydroxylation reactions as well as combinations thereof. Furthermore, trapping of reactive intermediates either with glutathione or with electrochemically activated ribonucleosides provided evidence for the possible production of phase II metabolites and covalent adducts with a genetic material. Evidence for the occurrence of some capsaicin metabolites in humans was obtained by urine screening.

Ultra-fast proteomics with Scanning SWATH.

Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.

Monitoring drug consumption in Innsbruck during coronavirus disease 2019 (COVID-19) lockdown by wastewater analysis.

The coronavirus disease 2019 (COVID-19) has developed into a serious pandemic with millions of cases diagnosed worldwide. To fight COVID-19 pandemic, over 100 countries instituted either a full or partial lockdown, affecting billions of people. In Tyrol, first lockdown measures were taken on 10 March 2020. On 16 March 2020, a curfew went into force which ended on 1 May 2020. On 19 March 2020, Tyrol as a whole was placed in quarantine which ended on 7 April 2020. The governmental actions helped reducing the spread of COVID-19 at the cost of significant effects on social life and behaviour. Accordingly, to provide a comprehensive picture of the population health status not only input from medical and biological sciences is required, but also from other sciences able to provide lifestyle information such as drug use. Herein, wastewater-based epidemiology was used for studying temporal trends of licit and illicit drug consumption during lockdown and quarantine in the area of the Tyrolean capital Innsbruck (174,000 inhabitants). On 35 days between 12 March 2020 and 15 April 2020, loads of 23 markers were monitored in wastewater. Loads determined on 292 days between March 2016 and January 2020 served as reference. During lockdown, changes in the consumption patterns of recreational drugs (i.e. cocaine, amphetamine, 3,4-methylenedioxymethamphetamine, methamphetamine, and alcohol) and pharmaceuticals for short-term application (i.e. acetaminophen, codeine, and trimethoprim) were detected. For illicit drugs and alcohol, it is very likely that observed changes were linked to the shutdown of the hospitality industry and event cancelation which led to a reduced demand of these compounds particularly on weekends. For the pharmaceuticals, further work will be necessary to clarify if the observed declines are indicators of improved population health or of some kind of restraining effect that reduced the number of consultations of medical doctors and pharmacies.

Novel ionic liquid based dispersive liquid-liquid microextraction for the extraction of bergapten and bergamottin in hydroalcoholic cosmetic formulations.

This study reports the synthesis of the room temperature ionic liquid 1-propyloxy-3-ethoxyimidazolium bis(trifluoromethane)sulfonamide for the extraction of bergapten and bergamottin from hydroalcoholic cosmetic samples by means of dispersive liquid-liquid microextraction. Molecular structures of the final ionic liquid as well as intermediate products were confirmed by nuclear magnetic resonance spectroscopy. Analyses were performed with high performance liquid chromatography with subsequent diode array and fluorescence detection. The extraction procedure was optimized with the design of the experiment using a three level Box-Behnken approach. Applying the synthesized room temperature ionic liquid as extraction medium, the optimized workflow demonstrated high recoveries illustrating powerful isolation properties for furanocoumarins, which are comparable or even better than using typical extraction solvents. Moreover, the workflow was validated regarding instrumental limits, linearity, accuracy, repeatability and stability of analytes according to international guidelines. To test its applicability on a more complex matrix, hydroalcoholic cosmetic samples were analyzed. Despite highly complex matrices, accurate and precise quantification in the range of 0.04-1.25 µg mL-1 was achieved in spiked and unspiked samples, with bias <10% and RSD < 12%.

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection.

The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.

Determination of phototoxic furanocoumarins in natural cosmetics using SPE with LC-MS.

Furanocoumarins are a class of naturally occurring phototoxic substances widely spread throughout the Umbelliferae and Rutacea families of plants. Plant extract of these families (e.g. citrus extracts) are commonly used as ingredients in fragrances and cosmetic products. Due to their phototoxicity these substances are regulated within the European Union according to the European Regulation (EC) No. 1223/2009 on cosmetic products. The proposed analytical workflow aims to swiftly screen out and determine the amount of phototoxic furanocoumarins in natural cosmetics employing solid-phase extraction (SPE). Cosmetic samples were first extracted in methanol and subsequently diluted in 35% (v/v) methanol before being applied to solid-phase extraction. The extraction procedure allows extraction of the eight target compounds including the six marker-substances proposed by the International Fragrance Association (IFRA) from complex cosmetic samples with satisfactory recovery levels ranging from 84 to 116% with the exception of bergamottin (68-89%). HPLC-UV and ESI-MS were used for the analysis of the target compounds. Furanocoumarin quantification was performed by standard addition. The workflow was successfully validated according to the ISO 12787 international standard ("Cosmetics - Analytical methods- Validation criteria for analytical results using chromatographic techniques"). Results of the validation on standard solutions highlight a LOQ of 0.01 mg kg-1, acceptable linearity up to 1 mg/kg as well as good accuracy (Bias <15%) and precision (RSD <15%). Total furanocoumarin levels of the examined natural cosmetic products were in general in agreement with the European Regulation. However, it was shown that total levels of furanocoumarins might be significantly higher than assumed using the six proposed marker substances only.

Annotating Nontargeted LC-HRMS/MS Data with Two Complementary Tandem Mass Spectral Libraries.

Tandem mass spectral databases are indispensable for fast and reliable compound identification in nontargeted analysis with liquid chromatography⁻high resolution tandem mass spectrometry (LC-HRMS/MS), which is applied to a wide range of scientific fields. While many articles now review and compare spectral libraries, in this manuscript we investigate two high-quality and specialized collections from our respective institutes, recorded on different instruments (quadrupole time-of-flight or QqTOF vs. Orbitrap). The optimal range of collision energies for spectral comparison was evaluated using 233 overlapping compounds between the two libraries, revealing that spectra in the range of CE 20⁻50 eV on the QqTOF and 30⁻60 nominal collision energy units on the Orbitrap provided optimal matching results for these libraries. Applications to complex samples from the respective institutes revealed that the libraries, combined with a simple data mining approach to retrieve all spectra with precursor and fragment information, could confirm many validated target identifications and yield several new Level 2a (spectral match) identifications. While the results presented are not surprising in many ways, this article adds new results to the debate on the comparability of Orbitrap and QqTOF data and the application of spectral libraries to yield rapid and high-confidence tentative identifications in complex human and environmental samples.