Olfactometry Profiles and Quantitation of Volatile Sulfur Compounds of Swiss Tilsit Cheeses

To establish the odor profiles of three differently fabricated commercial Swiss Tilsit cheeses, analyses were conducted using headspace solid-phase microextraction 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.

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

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.

Development and performance evaluation of a novel dynamic headspace vacuum transfer "In Trap" extraction method for volatile compounds and comparison with headspace solid-phase microextraction and headspace in-tube extraction

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.

Bacterial Volatiles Known to Inhibit Phytophthora infestans Are Emitted on Potato Leaves by Pseudomonas Strains

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.

Formation of 3-Methylbutanal and 3-Methylbutan-1-ol Recognized as Malty during Fermentation in Swiss Raclette-Type Cheese, Reconstituted Milk, and de Man, Rogosa, and Sharpe Broth

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.

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

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.

Age-Dependent Serum Volatilomics of Milk and Yogurt Intake: A Randomized Crossover Study in Healthy Young and Older Men

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.

Robinia pseudoacacia (Black Locust) – An Invasive Species with Unsuspected Potential in Grappa Ageing

No abstract.

Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes

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.

Biotechnological formation of dairy flavor inducing δ-lactones from vegetable oil

Agroscope Culture Collection was screened to identify bacterial strains effective in production of dairy flavor inducing lactones using grapeseed oil as a substrate. Lentilactobacillus parafarraginis FAM-1079, Lactococcus lactis subsp. lactis FAM-17918, and L. lactis subsp. lactis biovar diacetylactis FAM-22003 showed the most efficient formation of targeted δ-lactones. The application of sublethal heat stress significantly increased target lactone production. The most profound improvement was for L. lactis subsp. lactis biovar diacetylactis where δ-octadecalactone generation was improved by factor of 9. The pre-fermentation step as well as growth phase in which bacteria are harvested did not have a significant impact on lactones yield. The lactone production process from vegetable oil developed in this study offers a new way of developing a natural flavor ingredient for incorporation into plant-based products.

Usability of volatile organic compounds from exhaled breath compared with those from ruminal fluid, serum, urine, and milk to identify diet-specific metabolite profiles in lactating dairy cows

To investigate dietary influences on the volatilome, the volatile subcategory of the metabolome, we performed a comparative untargeted volatilome analysis of exhaled breath, ruminal fluid, serum, urine, and milk from lactating Holstein cows fed different diets. Thirty-two cows (83.3 ± 31.40 DIM, 30.6 ± 5.03 kg of milk/d) were assigned to 4 diets. The experiment lasted 16 wk. Throughout the experiment, half of the animals were fed a hay-based diet (HD; n = 16), and the other half were fed a silage-based diet (SIL; n = 16). In experimental wk 5 to 12, half of the animals in each group received the control concentrate (CON), and the other half was fed with the CON supplemented with a blend of essential oils (EXP). We hypothesized that the basal diet and the essential oils influence the volatile organic compound (VOC) profiles of the cows through potential changes in ruminal fermentation, digestion, and metabolism (hypothesis 1). Furthermore, we hypothesized that the potential effects of essential oils would have a delayed onset and a carryover effect (hypothesis 2). Every 4 experimental weeks (i.e., in wk 4, wk 8, wk 12, and wk 16), samples of exhaled breath, ruminal fluid, serum, urine, milk, and feed were collected for dynamic headspace extraction and gas chromatographic analysis of VOC in their gaseous phase. Milk yield, milk composition, BW, and feed intake were recorded regularly. Linear mixed models and multivariate and univariate data analyses were performed. The total DMI and basal diet intake was similar between cows fed HD and SIL diets. However, SIL cows consumed less of the concentrate, NDF, and water-soluble carbohydrates and more starch than HD cows. The SIL cows had a higher milk production than the HD cows. No effect was found regarding the concentrate type on feed intake or milk production. Irrespective of diet, 2,957 VOC were detected in the gaseous phase of serum; 2,771 in exhaled breath; 1,016 in urine; 1,001 in milk; and 921 in ruminal fluid. Across the experimental wk 4, 8, 12, and 16, the basal diet altered the VOC profiles of ruminal fluid, urine, and exhaled breath but not those of serum and milk. The concentrate type affected only the VOC profiles of the exhaled breath. Most diet-influenced VOC in the affected biological matrices were identified as dietary components. The experimental week influenced the VOC profiles of all matrices, especially those of exhaled breath. The VOC profile of exhaled breath strongly correlated with that of urine, followed by that of ruminal fluid, milk, and serum. This study provides the first description of diet- and time-specific VOC profiles from the biological matrices of dairy cows. The identified discriminatory VOC seem suitable as markers to discriminate between HD and SIL cows. Exhaled breath may be a promising, sensitive, and less invasive tool to follow diet- and time-related metabolic changes.

Pathway mapping of exhaled volatile organic compounds associated with blood and ruminal fluid metabolites to describe the nutritional and metabolic status of lactating dairy cows

Exhaled breath offers an interesting matrix for low invasive sampling of potentially relevant information about the organism's metabolism in the form of volatile organic compounds (VOC). The VOC can be exhaled by the ructus or pass the blood-lung barrier for expiration through the lungs. In this work, we consider exhaled breath as a mixture of VOC derived from the lungs and from the upper gastrointestinal tract. However, the informative value of exhaled breath in ruminants remains largely unstudied. The aim of this study was to identify exhaled VOC that could be used to assess the nutritional and metabolic status of dairy cows. To do so, we performed untargeted analysis of exhaled VOC from dairy cows, investigated their correlations with commonly analyzed blood and ruminal fluid metabolites and the calculated energy balance (EB), and explored the underlying pathways of correlated exhaled VOC. This was done as part of a feeding experiment in which 32 lactating Holstein dairy cows were assigned to 2 basal diets for 12 wk. Half of the cows were fed a hay-based diet, and the other half were fed a silage-based diet. During experimental wk 1 through 8, half of the cows in each basal diet group were supplemented with a control concentrate, and the other half received an experimental concentrate containing essential oils. During experimental wk 9 through 12, all cows received the control concentrate. Exhaled breath, blood, and ruminal fluid samples were collected every 4 experimental weeks (wk 4, 8, and 12) on 3 consecutive sampling days. Exhaled breath was analyzed for VOC, ruminal fluid for VFA and ammonia, and serum samples for albumin, total protein, urea, glucose, cholesterol, BHB, and nonesterified fatty acid (NEFA) concentrations. Pearson correlations were calculated to assess the associations between exhaled VOC and concentrations of blood and ruminal fluid metabolites and the calculated EB. Fifteen correlations were found between exhaled VOC (tetradecanal and γ-hydroxybutyrate [GHB], 3-penten-2-one, 4-hydroxy-4-methylpentan-2-one, 2-ethylhexanal, 2-ethylhexan-1-ol, p-cymene) and ruminal fluid (acetate, butyrate, valerate, and ammonia) and blood metabolite concentrations (BHB, NEFA, glucose, urea, and cholesterol) across the cow groups. The underlying pathways of 3-penten-2-one, GHB, and tetradecanal were mainly related to fat and protein catabolism and therefore to the actual animal metabolism. The correlations with the other 4 exhaled VOC, 4-hydroxy-4-methylpentan-2-one, p-cymene, 2-ethyl-hexan-1-ol, and 2-ethylhexanal, were diet- or time-related, specifically due to differences in feed ingredients. The results demonstrate the associations of single exhaled VOC with the nutritional and metabolic status of healthy dairy cows. Their potential as new biomarkers should be further investigated in cows in various nutritional and metabolic states.

Optimization of volatile organic compounds sampling from dairy cow exhaled breath using polymer-based solid-phase extraction cartridges for gas chromatographic analysis

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.

Analytical Mapping of Swiss Hard Cheese to Highlight the Distribution of Volatile Compounds, Aroma, and Microbiota

Cheese is one of the most consumed fermented animal-based products globally, rendering its quality assessment and evaluation of substantial economic interest. Understanding the degree of cheese homogeneity is paramount for designing effective sampling strategies, yet this information is largely lacking. This study investigates the homogeneity of a cheese wheel based on the distribution of volatile compounds, microbiota, sodium chloride content, and pH, combined with sensory analyses. The outer zones of the cheese wheel were primarily characterized by the presence of sulfur compounds, esters, pyrazines, ketones, Streptococcus thermophilus, high sodium chloride concentration and high pH. In contrast, the inner zones of the cheese wheel were dominated by lactones, carboxylic acids, aldehydes, Lactobacillus delbrueckii subsp. lactis and Lacticaseibacillus paracasei. The presence of alcohols and Lactobacillus helveticus was observed throughout the cheese wheel. Furthermore, sensory descriptions were found to match predominantly with the aroma of the volatile compounds identified. The cheese wheel was found to be heterogeneous in all investigated characteristics. Our results indicate that the level of cheese homogeneity should be considered when designing sampling strategies, as these significantly impact the accuracy and reproducibility of analytical outcomes.

Comparative analysis of feature annotation methods for SESI-HRMS in exhaled breath analysis

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.