Biology subjects

van Mastrigt, O.

Publications and source records attributed to van Mastrigt, O..

7 recordsLinked to original sources

bioRxiv2026

Stressostat cultivation of Lactococcus lactis improves lactate stress resistance through mutations in RNA polymerase

Adaptive laboratory evolution is used to improve the phenotypes of microorganisms and to characterise the mechanisms underlying resistance against complex growth inhibition. Here we focused on lactic acid bacteria (LAB) as starter cultures for food fermentations. Production of LAB starter cultures is challenging due to growth inhibition by organic acids, mainly lactate, produced during fermentation. By utilising stressostat cultivation we generated Lactococcus lactis isolates with enhanced lactate resistance. Using a combination of (meta)genomics, proteomics and pH-controlled batch fermentations, we deciphered the lactate resistance mechanisms of these L. lactis isolates. Proteome responses of L. lactis, combined with similar growth inhibition at high salt, suggest that high lactate mainly causes osmotic stress. We identified RNA polymerase (RNAP) mutations in subunits {beta} (rpoB) and {beta} (rpoC) as key mutations, causing pleiotropic effects in the proteome. These proteome adaptations are linked to enhanced lactate resistance, particularly the resistance to hyperosmotic stress without glycine-betaine supplementation, likely by altering cross-linking of the peptidoglycan in the cell envelope via downregulation of MurE. The proteome changes indicate that lactate might (indirectly) cause oxidative stress. Combined, our study shows that RNAP mutations enhanced lactate resistance through pleotropic effects in the proteome that changed L. lactis responses against multiple stresses. HighlightsO_LILactate resistant variants were isolated from stressostat cultivations C_LIO_LIMetagenomics revealed evolutionary trajectory during stressostat cultivation C_LIO_LIRNAP mutations were identified as key drivers for improved lactate resistance C_LIO_LIRNAP mutations altered the proteome, enhancing the osmotic stress resistance C_LI

microbiology↗

bioRxiv2025

Solid-state fermentation with mushroom mycelium elevates plant protein quality and umami taste

Solid-state fungal fermentation (SSFF) offers a low-tech, low-energy, and minimal processing method to enhance the protein content and quality of foods. This study evaluates the potential of SSFF executed with mycelium of edible basidiomycetes to improve both nutritional and sensory qualities of brown rice, brewers spent grain (BSG), and lupin. The conventional tempeh fungus, Rhizopus microsporus var. oligosporus, was used as control. Different substrate-fungus combinations varied in impact on flavour and protein quality. SSFF improved the protein quality and umami taste of brown rice and mainly improved in umami taste of lupin, while fermentation of BSG with basidiomycetes even decreased protein quality. Basidiomycetous SSFF products exhibited higher umami potential, with equivalent umami concentrations (EUC) reaching 159 g MSG-eq/100 g DW, surpassing the values found for R. microsporus-fermented products. In terms of substrates, the protein content increased most in brown rice fermentations, while the EUC and protein quality increased most in lupin. Protein quality and content increased more in basidiomycetes, indicated by the up to 35.1% increase in the protein digestibility corrected amino acid score of the limiting amino acid lysine and a 36.4% rise in utilizable amino acids. Basidiomycetous SSFF thus offers a promising approach to upgrade low-quality plant proteins into more palatable and nutritious foods. Highlights- Plant foods were fermented with basidiomycetes and conventional tempeh fungus. (81) - Basidiomycetes improve umami compounds more than conventional fermentation fungus. (85) - Basidiomycetes improve protein quality more than conventional food fungus. (84) - Increase in total utilizable amino acids requires proper substrate-fungus pairing. (85) - Basidiomycota harbours untapped phylogenetic diversity for food fermentation. (79)

microbiology↗

bioRxiv2025

The potential of mycelium from mushroom-producing fungi in alternative protein production: a focus on fungal growth, metabolism, and nutrition

The growing need for high-quality protein with minimal environmental impact necessitates the expansion of alternative proteins on the market. One area with great opportunity for expansion lies in the phylogenetic diversity of the fungal kingdom. Diversifying the use of fungal species, by assessing species from the phylum of mushroom-producing fungi (Basidiomycota) in solid-state fermentation, could open new avenues to foods with improved nutritional and sensorial properties. To assess these properties, we first determined the potential of basidiomycetes to ferment and colonize cereals and legumes. A phylogenetically diverse selection of eight species of basidiomycetes was analyzed on their radial growth speed and biomass yield. The best performing species were successfully fermented on brown rice (high starch), brewers spent grain (high fiber, high protein), and lupin (high protein, high fiber and high fat), and compared to Rhizopus microsporus var. oligosporus. Large variation in performance was observed between the different basidiomycetes on the three substrates in terms of biomass formation and metabolic behavior. The presence of an easily accessible carbon source, such as starch was needed to prevent deamination and thereby loss of valuable protein. With the correct formulation, basidiomycetes could fully ferment and colonize the substrate, thereby increasing the overall protein content and degrading the anti-nutritional factor phytic acid up to 80%. These results provide a methodology for screening of fungal species and substrates and demonstrate that basidiomycetous mycelia represent a promising source of phylogenetic diversity for novel food fermentations. Highlights- Brown rice, brewers spent grain, and lupin were fermented with basidiomycetes. - Readily available carbon prevents protein catabolism during fermentation. - Fungal growth was analysed visually, thermally and through metabolic indicators. - Basidiomycetes increased the protein content and reduced phytate more than Rhizopus.

microbiology↗

bioRxiv2025

Mycelium of mushroom-producing fungi as high-quality protein source

To achieve a more sustainable food system, reducing reliance on animal-based proteins is essential. Mycoprotein from mushroom-producing fungi (Basidiomycota) presents a promising yet underexplored alternative. Basidiomycetous mycelium combines the high protein quality of fungi with the sensory qualities of mushrooms. This study compares the mycelium of commercially cultivated and edible basidiomycetes to their fruiting bodies and to mycelium of Rhizopus microsporus var. oligosporus (tempeh fungus). Nutritional quality was assessed via protein content and PDCAAS, while sensory potential was analysed through equivalent umami concentration (EUC) and pyrazine levels. High-performing species surpassed the EUC of R. microsporus and fruiting bodies, reaching 301.0 g MSG-eq/100 g DW. Basidiomycetous mycelia exhibited superior protein quality (PDCAAS up to 1.20) and utilizable protein content (33.2 g/100 g DW), qualifying as an "Excellent protein source." Given the phylogenetic diversity of basidiomycetes, this study highlights the untapped potential of its mycelium as a high-quality protein source.

microbiology↗

bioRxiv2025

Modulation of gut microbiota through in vitro exposure to a traditional fermented food in the context of pathogen invasion

The gut microbiota consisting of bacteria, fungi, archea, and viruses and plays a role as a barrier against pathogen invasion to promote intestinal health and preventing organismal infections. This study examined the potential protective properties of Mabisi, a widely consumed traditional fermented dairy product in Zambia, against pathogen invasion in the gut. Using the in-vitro static INFOGEST model, we challenged the gut microbiota from a pooled stool sample pf six Zambian children) and previously exposed to Mabisi by adding model pathogens. We hypothesized that pathogen invasion is suppressed in in-vitro gut microbiota treated with Mabisi due to its ability to modulate the gut microbiota composition. Our microbiota challenge treatments were Mabisi, fructooligosaccharides (FOS) as a positive control, sterile water as a negative control, and with and without pathogens. Out of the two strains of pathogens added to the gut microbiota, Escherichia coli established in FOS treated gut microbiota, however not in Mabisi and sterile water treatments. Furthermore, we show that Mabisi modulated gut microbiota by increasing Pediococcus, a commensal bacteria and increased production of short chain fatty acids including acetate, propionate, lactate, isobutyrate, formate, and succinate in Mabisi treated gut microbiota compared to both FOS and sterile water treated gut microbiota. This study contributes to evidence of the beneficial role of fermented foods such as Mabisi through the prevention of pathogen invasion of the gut microbiota in children. ImportanceThis study provides evidence supporting the protective role of Mabisi, a traditional fermented dairy product, in preventing pathogen invasion in the gut microbiota of children. By using an in-vitro approach, we demonstrate that Mabisi treatment suppresses the establishment of Escherichia coli, a key pathogen, unlike fructooligosaccharides (FOS), a well-known prebiotic. Additionally, Mabisi modulates gut microbiota composition by increasing beneficial bacteria such as Pediococcus and enhancing short-chain fatty acid (SCFA) production, which is essential for gut health. These findings highlight the potential of traditional fermented foods as affordable, accessible dietary interventions for improving gut health and preventing infections, particularly in low-resource settings like Zambia.

microbiology↗

bioRxiv2022

Quantitative physiology and proteome adaptations of Bifidobacterium breve NRBB57 at near-zero growth rates

In natural environments, nutrients are usually scarce causing microorganisms to grow slow while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate and ethanol at high growth rates while in the retentostat lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but non-culturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a down-regulation of ribosomal proteins at near-zero growth rates and an up-regulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defence systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut. IMPORTANCEIn natural environments, nutrients are usually scarce causing microorganisms to grow slow while staying metabolically active. In this study we used retentostat cultivation to investigate how the probiotic Bifidobacterium breve adapts its physiology and proteome under severe nutrient limitation resulting in near-zero growth rates (<0.001 h-1). We showed that the nutrient limitation induced a multifaceted response including stress defence and stringent response, metabolic shifts and the activation of novel alternative energy producing pathways.

microbiology↗

bioRxiv2021

Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Strain and environmental nutrient concentrations can affect the production of sensory impact compounds during yeast fermentation. Despite reports on the impact of nutrient conditions on kinetics of cellular growth, it is uncertain to what extent nitrogen utilization by commercial Saccharomyces cerevisiae wine strains affects the production of volatile organic (aroma) compounds (VOCs). Here we ask whether i) consumption of amino acids contribute to VOCs (fusel alcohols, acetate esters, and fatty acid esters) in commercial S. cerevisiae yeast strains, ii) there is inter-strain variation in VOC production, and iii) there is a correlation between the production of aroma compounds and nitrogen utilization. We analyzed the consumption of nutrients as well as the production of major VOCs during fermentation of a chemically defined grape juice medium with four commercial S. cerevisiae yeast strains: Elixir, Opale, R2, and Uvaferm. The production of VOCs was variable among the strains where Uvaferm correlated with ethyl acetate and ethyl hexanoate production, R2 negatively correlated with the acetate esters, and Opale positively correlated with fusel alcohols. The four strains total biomass formation was similar, pointing to metabolic differences in the utilization of nutrients to form secondary metabolites such as VOCs. To understand the strain-dependent differences in VOC production, partial least-squares linear regression coupled with genome-scale metabolic modeling was performed with the objective to correlate nitrogen utilization with fermentation biomass and volatile formation. Total aroma production was found to be a strong function of nitrogen utilization (R2 = 0.87). We found that glycine, tyrosine, leucine, and lysine utilization were positively correlated with fusel alcohols and acetate esters concentrations e.g., 2-phenyl acetate during wine fermentation. Parsimonious flux balance analysis and flux enrichment analysis confirmed the usage of these nitrogen utilization pathways based on the strains VOC production phenotype. IMPORTANCESaccharomyces cerevisiae is widely used in grape juice fermentation to produce wines. Along with the genetic background, the nitrogen in the environment in which S. cerevisiae grows impacts its regulation of metabolism. Also, commercial S. cerevisiae strains exhibit immense diversity in their formation of aromas, and a desirable aroma bouquet is an essential characteristic for wines. Since nitrogen affects aroma formation in wines, it is essential to know the extent of this connection and how it leads to strain-dependent aroma profiles in wines. We evaluated the differences in the production of key aroma compounds among four commercial wine strains. Moreover, we analyzed the role of nitrogen utilization on the formation of various aroma compounds. This work illustrates the unique aroma producing differences among industrial yeast strains and suggests more intricate, nitrogen associated routes influencing those aroma producing differences.

microbiology↗