Secondary electrospray ionization coupled to high-resolution mass spectrometry (SESI-HRMS) is a powerful method for the analysis of exhaled breath in real time. However, feature annotation is challenging due to the flow-injection nature of the technique. To evaluate alternative methods for enhancing feature annotation, a study was conducted where the exhaled breath of sixteen subjects was condensed and analyzed using dynamic headspace vacuum in-trap extraction gas chromatography-mass spectrometry (DHS-V-ITEX-GC-MS) and liquid chromatography coupled to mass spectrometry (LC-MS) using polar and reverse-phase conditions along with a data-independent MS2-acquisition method based on multiple injections. The annotation results obtained from these methods were compared to those from SESI-HRMS. The use of these techniques on breath condensate is unprecedented. The GC-MS method primarily detected compounds of exogenous origin, particularly additives in oral hygiene products like menthol. On the other hand, LC-MS detected a vast number of features, especially with the utilized data-independent acquisition method. Chemical classes to these features were assigned in-silico. In positive ion mode, mostly amino acids and amines were detected, while the largest group in negative ion mode consisted of carboxylic acids. Approximately 25 % and 5 % of SESI features had a corresponding match with LC-MS and GC-MS. While both GC-MS and LC-MS methods partially overlapped with the SESI features, there was limited overlap of both in the mass-to-charge range from 150 to 200. In conclusion, both GC-MS and LC-MS analysis of breath condensate can serve as supplementary tools for annotating features obtained from SESI-MS. However, to increase confidence in the annotation results, combining these methods with additional on-line fragmentation techniques is recommended.

Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.

We explored appropriate technical setups for the detection of volatile organic compounds (VOCs) from exhaled cow breath by comparing six different polymer-based solid-phase extraction (SPE) cartridges currently on the market for gas chromatography/mass spectrometry (GC-MS) screening. Exhaled breath was sampled at a single timepoint from five lactating dairy cows using six different SPE cartridges (Bond Elut ENV (ENV); Chromabond HRX (HRX); Chromabond HRP (HRP); Chromabond HLB (HLB); Chromabond HR-XCW (XCW) and Chromabond HR-XAW (XAW)). The trapped VOCs were analyzed by dynamic headspace vacuum in-tube extraction GC-MS (DHS-V-ITEX-GC-MS). Depending on the SPE cartridge, we detected 1174-1312 VOCs per cartridge. Most VOCs were alkenes, alkanes, esters, ketones, alcohols, aldehydes, amines, nitriles, ethers, amides, carboxylic acids, alkynes, azoles, terpenes, pyridines, or sulfur-containing compounds. The six SPE cartridges differed in their specificity for the chemical compounds, with the XAW cartridge showing the best specificity for ketones. The greatest differences between the tested SPE cartridges appeared in the detection of specific VOCs. In total, 176 different VOCs were detected with a match factor >80%. The greatest number of specific VOCs was captured by XAW (149), followed by ENV (118), HLB (117), HRP (115), HRX (114), and XCW (114). We conclude that the tested SPE cartridges are suitable for VOC sampling from exhaled cow breath, but the SPE cartridge choice enormously affects the detected chemical groups and the number of detected VOCs. Therefore, an appropriate SPE adsorbent cartridge should be selected according to our proposed inclusion criteria. For targeted metabolomics approaches, the SPE cartridge choice depends on the VOCs or chemical compound groups of interest based on our provided VOC list. For untargeted approaches without information on the animals' metabolic condition, we suggest using multi-sorbent SPE cartridges or multiple cartridges per animal.

Nutritional biomarkers of dairy intake can be affected by both food transformation and the metabolic status of the consumer. To assess these effects, this study investigated the serum volatilome of 14 young (YA) and 14 older (OA) adult men undergoing a 3 week restriction of dairy and fermented foods followed by a randomized crossover acute intake of milk and yogurt. 3,5-Dimethyl-octan-2-one was identified as a potential marker of dairy product intake as its response after both milk and yogurt intake was significantly increased during the postprandial phase but significantly decreased in fasting serum samples of the OA group after the restriction phase. The postprandial response of two metabolites was significantly different for the two dairy products while 19 metabolites were modulated by age. Remarkably, the response of all age-dependent metabolites was higher in the OA than in the YA group after milk or yogurt intake, whereas at the end of the restriction phase, their fasting concentrations were lower in the OA than in the YA group. Among these, p-cresol, a specific marker of colonic protein fermentation, had a significant response in the OA but not the YA group, which may suggest impaired intestinal processing of dietary proteins in the OA group.

Genomic screening of bacteria is common practice to select strains with desired properties. However, 40-60% of all bacterial genes are still unknown, making capturing the phenotype an important part of the selection process. While omics-technologies collect high-dimensional phenotypic data, it remains challenging to link this information to genomic data to elucidate the impact of specific genes on phenotype. To this end, we present Scoary2, an ultra-fast software for microbial genome-wide association studies (mGWAS), enabling integrative data exploration. As proof of concept, we explore the metabolome of 44 yogurts with different strains of Propionibacterium freudenreichii , discovering two genes affecting carnitine metabolism.

Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.

A method based on dynamic headspace vacuum transfer in trap extraction, followed by gas chromatography coupled with a mass spectrometer (DHS-VTT-GC-MS), was validated for the fast quantitation of 1,4-dichlorobenzene (p-dichlorobenzene; PDCB) and thymol residues in beeswax. The quantitation limits (LOQ) were 0.05 mg/kg (PDCB) and 0.25 mg/kg (thymol). Recoveries above 80% were obtained for PDCB concentrations between 0.05 and 10 mg/kg and for thymol concentrations between 0.25 and 200 mg/kg. Analysis of beeswax samples showed a good correlation between the results obtained by DHS-VTT-GC-MS analysis and those of a previous method based on SPE extraction followed by gas chromatography and triple- quadrupole mass spectrometry (GC-MS/MS) (R2 = 0.9770 for PDCB and 0.9666 for thymol). However, the sample preparation and chromatography were much shorter using the DHS-VTT-GC-MS method. Forty comb foundations samples produced in Switzerland in 2019 and 2021 were analysed using DHS-VTT-GC-MS. Fourteen samples contained PDCB above the LOQ of 0.05 mg/kg, ranging up to a maximum of 1.53 mg/kg. The mean concentration of the positive samples was 0.22 mg/kg. All samples contained thymol residues ranging between 3.9 and 84.4 mg/kg with mean and median concentrations of 22.7 mg/kg and 17.4 mg/kg. Residue levels of PCDB and thymol in Swiss beeswax were substantially below those measured 20 (PDCB) and 10 (thymol) years ago, respectively.

The identification of molecular biomarkers that can be used to quantitatively link dietary intake to phenotypic traits in humans is a key theme in modern nutritional research. Although dairy products (with and without fermentation) represent a major food group, the identification of markers of their intake lags behind that of other food groups. Here, we report the results from an analysis of the metabolites in postprandial serum and urine samples from a randomized crossover study with 14 healthy men who ingested acidified milk, yogurt, and a non-dairy meal. Our study confirms the potential of lactose and its metabolites as markers of lactose-containing dairy foods and the dependence of their combined profiles on the fermentation status of the consumed products. Furthermore, indole-3-lactic acid and 3-phenyllactic acid are two products of fermentation whose postprandial behaviour strongly discriminates yogurt from milk intake. Our study also provides evidence of the ability of milk fermentation to increase the acute delivery of free amino acids to humans. Notably, 3,5-dimethyloctan-2-one also proves to be a specific marker for milk and yogurt consumption, as well as for cheese consumption (previously published data). These molecules deserve future characterisation in human interventional and observational studies.

This work aimed to determine the formation over time of 3-methylbutanal and 3-methylbutan-1-ol recognized as malty during the manufacture of Raclette-type cheese and the fermention of reconstituted skim milk, and filter-sterilized MRS broth. Using dynamic headspace-vacuum transfer in trap extraction followed by gas chromatography coupled with mass spectrometry-olfactometry (DHS-VTT-GC-MS-O) as a screening method for the malty compounds, five compounds (2-methylpropanal, 2- and 3-methylbutanal, and 2- and 3-methylbutan-1-ol) were identified as potential compounds causing the malty aroma in starter culture development and Raclette-type cheeses. Focus on compounds having a predominant sensorial effect (3-methylbutanal and 3-methylbutan-1-ol), spikings of leucine, 13C-labeled leucine, α-ketoisocaproic acid, and α-ketoglutaric acid provided a better understanding of their formation pathway. This study highlighted the discrepancies in the formation of 3-methylbutanal and 3-methylbutan-1-ol between the growth media; namely, despite the presence of free leucine available in MRS and the addition of an excess, no increase of the target compounds was observed. The concentration of these compounds in MRS increased only when α-ketoglutaric acid or α-ketoisocaproic acid was added, and a preference for the pathway to α-hydroxyisocaproic acid instead of 3-methylbutanal was shown. In addition, a formation of 3-methylbutanal when the bacteria were not yet active was observed when spiking α-ketoisocaproic acid, which potentially indicates that this part of the metabolism could take place extracellularly. These results could potentially unveil other, not-yet-identified reactants, directly influencing the production of compounds responsible for the malty aroma in Raclette cheese.

Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

The characterization of volatile compounds in biological fluids offers a distinct approach to study the metabolic imprint of foods on the human metabolome, particularly to identify novel biomarkers of food intake (BFIs) that are not captured by classic metabolomics. Using a combination of dynamic headspace vacuum transfer In Trap extraction and gas chromatography coupled with mass spectrometry, we measured volatile compounds (the "volatilome") in plasma and urine samples from a randomized controlled crossover intervention study in which 11 healthy subjects ingested milk, cheese, or a soy-based drink. More than 2000 volatile compounds were detected in plasma, while 1260 compounds were detected in urine samples. A postprandial response in plasma was confirmed for 697 features. Univariate and multivariate analyses identified four molecules in plasma and 31 molecules in urine samples differentiating the ingestion of the foods, of which three metabolites in plasma and nine in urine were specific to the dairy products. Among these molecules, heptan-2-one, 3,5-dimethyloctan-2-one, and undecan-2-one in plasma and 3-ethylphenol, heptan-2-one, 1-methoxy-2-propyl acetate, and 9-decenoic acid were highly discriminative for dairy or cheese intake. In urine, 22 volatile compounds were highly discriminative for soy-based drink intake. The majority of these molecules have not been reported in humans. Our findings highlight the potential of plasma and urinary volatilomics for detection of novel dietary biomarkers.

Aim: Wine quality is influenced by the nitrogen nutrition of grapevines in the vineyard. A deficiency of this nutrient will affect grape quality, decrease yeast available nitrogen (YAN) and influence alcoholic fermentation. Chasselas wines from nitrogen-deficient grapes (YAN < 140 mg N/L) are systematically more astringent and bitter and less fruity than those from grapes with higher YAN content (Spring et al., 2014). The aim of this study was to identify chemical markers in wine linked to nitrogen deficiencies in the vineyard.Methods and results: Wine samples produced from grapes growing in nitrogen-deficient vineyards with nitrogen treatment (HN) and without it (LN) were used over four consecutive years (2006–2009). They were all analysed at the same time (2012) with electronic-nose, GC-MS and UHPLC-TOFMS techniques. A metabolomics approach was used for a comprehensive survey of volatile and nonvolatile compounds in order to identify markers related to nitrogen nutrition. Volatile markers with alcohol and ester functions and nitrogen-containing compounds were found and tentatively identified by GC-MS. Additionally, 16 nonvolatile markers were putatively identified by UHPLC-TOFMS, including compounds from diverse chemical classes, namely, amino acids, vitamins, hormones, organic acids, phenolic compounds and polysaccharides.Conclusion: The nitrogen nutrition of grapevines has a clear but complex effect on the chemical composition of wine. Several markers were tentatively identified and their role in wine composition discussed according to the actual knowledge reported in the literature.Significance of the study: This study is an important starting point for selecting the most relevant chemical markers in wine, and for determining whether organoleptic problems are related to nitrogen nutrition deficiency in the vineyard and changes in vineyard management are needed.

There is limited information about the contribution of Pediococcus acidilactici, a nonstarter lactic acid bacteria, to cheese ripening and flavour development. Model Tilsit-type and Gruyere-type cheeses were produced using P. acidilactici FAM18098 as an adjunct. The adjunct did not influence the cheese manufacturing processes. The pediococcal log counts ranged from 7.0 to 8.0 cfu g(-1) after 90 and 120 days of ripening. P. acidilactici produced ornithine, a result of arginine metabolism by the arginine deiminase pathway, and alpha-aminobutyrate and alanine while simultaneously metabolising serine and threonine. The analysis of the volatile compounds in the cheeses showed that higher acetate, 2-butanone, and 2-butanol levels and lower diacetyl levels were present in the cheeses produced with P. acidilactici than in the control cheeses. The study illustrates that P. acidilactici can influence amino acid metabolism in cheese; further, ornithine, alpha-aminobutyrate, and acetate can serve as indicators for the presence of this species. (C) 2019 The Author(s). Published by Elsevier Ltd.

Headspace in-tube extraction (HS-ITEX) and solid phase microextraction (HS-SPME) sampling, followed by gas chromatography-mass spectrometry (GC-MS), are widely used to analyze volatile compounds in various food matrices. While the extraction efficiency of volatile compounds from foodstuffs is crucial for obtaining relevant results, these efficiency of these extraction methods limited by their long extraction times and requirements for large sample quantity. This study reports on the development and application of a new extraction technique based on HS-ITEX hardware, which improves the extraction rate and capacity by operating under reduced pressure, called Dynamic Headspace Vacuum Transfer In-Trap Extraction (DHS-VTT). The results of the study indicate that DHS-VTT improves the extraction of the target compounds. The area of the mass spectrometer signal for each compound can be up to 450 times more intense than the HS-SPME and HS-ITEX techniques performed in the same experimental conditions of extraction temperature and time. DHS-VTT runs in automated mode, making it possible to work with smaller sample quantity and also favors the HS extraction of all volatile compounds. In addition, the necessary modifications to the installation were cheap and the life of an ITEX trap is up to 10 times longer than an SPME fibre.

To establish the odor profiles of three differently fabricated commercial Swiss Tilsit cheeses, analyses were conducted using headspace solid-phase microexiraction gas chromatography mass spectrometry/pulsed flame photometric detection and gas chromatography olfactometry to identify and quantitate volatile compounds. In addition, odor quality and the impact of target sulfur compounds on the overall odor of the cheeses were investigated. The odor profile was found to be mainly influenced by buttery-cheesy and sulfury odor notes in all cheeses. Buttery-cheesy odor notes were attributed to three main molecules: butanoic acid, 3-methylbutanoic acid, and butane-2,3-dione. Over a dozen volatile sulfur compounds were detected at parts per billion levels, but only a few influenced the odor profile of the cheeses: methanethiol, dimethyl disulfide, bis(methylthio)methane, dimethyl trisulfide, 3-(methylthio)propanal, and 2-methyltetrahydrothiophen-3-one (tentative). In conclusion, the conducted analyses allowed differentiation of the cheeses, and gas chromatography olfactometry results confirmed that partially thermized milk cheese has a more intense and more multifaceted overall flavor.

The GC-mS/PFPD experimental setup used at agroscope's flavour analytical laboratory in Bern: a GC (Thermo Finnigan Trace GC) is equipped with a mass spectrometer (Thermo Scientific DSQ ii Single Quadrupole) and a PFPD (O.i.analytical, detector model 5380) to simultaneously measure the mS trace and the sulphur-specific response chromatogram.Pulsed-flame photometric detector sulphur-specific trace comparison between three different cheeses produced in Switzerland: Gruyère, Camembert, and fresh cheese.