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PubMed2026

Upcycling Vegetable Waste Into Functional Food Ingredients via Synergistic Microbial Engineering and Artificial Intelligence.

The escalating generation of global vegetable waste represents a critical loss of bioactive resources, necessitating a paradigm shift from passive disposal to active nutrient upcycling. However, the industrial conversion of this heterogeneous biomass into standardized functional food ingredients is currently impeded by significant techno-economic barriers, primarily structural recalcitrance, compositional inconsistency, and the presence of toxic fermentation inhibitors. This review provides a comprehensive analysis of the synergistic application of microbial engineering and artificial intelligence (AI) to resolve these bioprocessing bottlenecks within a food-to-food closed-loop framework (as shown in the graphical abstract). We evaluate recent advances in engineering food-grade microbial chassis (e.g., Saccharomyces cerevisiae and Escherichia coli) to enhance lignocellulose degradation and stress tolerance. Concurrently, we examine the integration of AI across the entire value chain, covering deep learning-based rational enzyme design, genome-scale metabolic modeling, and intelligent process control for precision fermentation. Current evidence demonstrates that the hardware-software coupling of engineered strains and AI algorithms significantly enhances conversion efficiency and process robustness. Key findings highlight that AI-driven Design-Build-Test-Learn cycles facilitate the de novo creation of enzymes with superior kinetics and strains with adaptive stress response capabilities against toxins. Moreover, dynamic digital twin models effectively mitigate the impact of substrate variability, ensuring the batch-to-batch consistency required for food applications. We conclude that this data-driven synergistic paradigm is pivotal for establishing a resilient circular bioeconomy, enabling the reliable bioconversion of waste into high-value single-cell proteins, natural flavor additives, and sustainable packaging materials.

Artificial Intelligence↗

PubMed2026

Integrated GC-HRAM-MS and UHPLC-QTOF-MS metabolomics reveal mineral-induced metabolic adaptation of Lactiplantibacillus pentosus 9D3 during milk fermentation.

Milk fermentation by plant-associated probiotic strains is constrained by poor adaptation to dairy matrices. This study evaluated genome-guided micronutrient supplementation to improve the performance and metabolomic profile of Lactiplantibacillus pentosus 9D3 in milk. Individual supplementation with Mn2+ or Mg2+ significantly enhanced bacterial growth and acidification, whereas Fe2+, Zn2+, and B-group vitamins showed limited effects. Optimal supplementation with 50 mg/L Mn2+ and 100 mg/L Mg2+ increased viable counts from 7.54 to 8.89 log CFU/mL. A cell population increase of ∼1.9 log CFU/mL was achieved despite reducing the inoculum level from 10% to 6%. Integrated metabolomic profiling using GC-HRAM-MS and UHPLC-QTOF-MS identified 299 metabolites across supplemented fermented milk, non-supplemented fermented milk, and unfermented milk, with group separation. Pathway analysis revealed significant enrichment of seven metabolic pathways, including purine, pyrimidine, galactose, propanoate, butanoate, amino sugar and nucleotide sugar, and α-linolenic acid metabolism. These findings support cost-efficient precision fermentation of functional dairy products.

Dairy products↗

PubMed2026

Bioactive macromolecules in LAB-fermented cereals: Mechanisms of formation, functional properties, and health benefits.

Cereal and pseudo-cereal based fermented food products represent a substantial segment of global diet, nutrition as well as food security. Fermentation, especially by Lactic Acid Bacteria (LAB) increases the nutritional and functional values of foods by increasing palatability, bioavailability and minimizing antinutritional factors. LAB plays a pivotal role in synthesizing bioactive peptides, vitamins, minerals and reducing anti-nutrients parallelly. This review elucidates the mechanism through which LAB revamping nutritional macromolecules, such as peptides and polysaccharides, during fermentation and their role in the development of traditional as well as modern fermented foods. Additionally, these fermented foods have been associated with several health benefits. Recent advancement in biotechnology such as genome sequencing, functional genomics, and AI-assisted bioinformatics, have significantly enhanced our understanding of the diversity of LAB, the metabolism, and adaptation mechanisms. The combination of in silico and experimental methods has enabled the development of novel food enzymes as well as highly precise fermentation processes. Together with new innovations, growing demands for quality, consistency, safety as well as health benefits point out the significance of continued research. More studies employing both conventional and modern methods are necessary to explore these food groups completely and achieve better food quality, increased nutrition, more health benefits and comprehensive socioeconomic advantages.

Bioactive macromolecules↗

PubMed2025

Uncoupling protein production from growth: different strategies for intracellular and secreted proteins in yeast.

BACKGROUND: Precision fermentation offers a sustainable alternative production route for proteins but still suffers from moderate productivities and low yields. Especially compared to biomass yields, recombinant protein yields on substrate are very low. Uncoupling recombinant protein production from growth would allow higher product yields, but requires that productivity is maintained. So far, two-phase production processes mostly rely on inducers to activate recombinant protein production after an initial growth phase, e.g., a change in carbon source. On large scale, specific growth rates can be controlled by nutrient availability, and we aim to use this as trigger to uncouple recombinant protein production from growth. RESULTS: We investigated the correlation between low specific growth rates (0.02 h- 1 < µ < 0.1 h- 1) and specific recombinant protein production rates, both for intracellularly accumulating and secreted proteins. By comparing two differently regulated promoters, the strong, constitutive PTEF1 and stress-induced PHSP12, we show that recombinant protein production rates and yields in Saccharomyces cerevisiae can be partially uncoupled from growth. The optimal strategy thereby differs for intracellular and secreted production. The PHSP12 resulted in increased product yields of intracellular protein at very low growth rates, including a 10-fold increase in intracellular protein titer, while titers remained virtually constant for the benchmark PTEF1. The PTEF1 on the other hand led to increased protein secretion rates and efficiencies at lower specific growth rates cumulating in higher extracellular protein titers. CONCLUSION: Our results demonstrate that promoter selection plays a critical role in production performance under slow growing conditions. Moreover, it highlights that optimising intracellular and extracellular recombinant protein production requires distinct, strategy-specific approaches.

Saccharomyces cerevisiae↗

PubMed1977

[Use of a polarographic method for determining trichothecin].

The polarographic behaviour of trichothecin was studied. It was shown that the antibiotic could be detected in solutions at concentrations of 7.10(-7) moles with the help of the polarographic method. Conditions for the polarographic determination of trichothecin in fermentation broth were developed. The error was not more than 3 per cent. The reliability of the results was shown by statistical treatment of data performed in accordance with the requirement of the USSR State Pharmacopeia, X ed., prescribing that the precision of the assay is such that the fiducial limits at p = 95 per cent deviate from the average value by not more than 5 per cent. Comparison of the results of trichothecin determination in the fermentation broth with the polarographic and biological methods showed no significant difference. Therefore, the polarographic method may be recommended for trichothecin determination in the fermentation broth.

Culture Media↗

PubMed2025

Bacteriophages as a modern diagnostic tool: innovations, applications and challenges.

Bacteriophages, viruses that specifically infect bacteria, have emerged as a valuable tool in diagnostics due to their unique specificity and adaptability. This review explores the diverse applications of bacteriophages in diagnostic methods, from traditional phage typing to advanced molecular techniques such as phage display and PCR-based diagnostics. It highlights their use in identifying bacterial strains, monitoring fermentation processes, and diagnosing critical conditions like tuberculosis, MRSA infections, and cancer. Innovations such as phage-based biosensors and reporter phages enhance the speed and precision of diagnostics, offering significant advantages over traditional methods. Challenges, including bacterial resistance and immune responses to phages, are also discussed alongside strategies for mitigation, such as phage cocktails and engineering. Integrating phage technology with modern bioscience holds promise for addressing antibiotic resistance and revolutionizing clinical and industrial diagnostics. This comprehensive analysis underscores the potential of bacteriophages to transform the diagnostic landscape while identifying areas requiring further research and development.

Bacteriophages↗

PubMed2026

Gut microbiota and metabolic alterations in participants with flatulence identify Faecalibacterium prausnitzii as a key microbial target for clinical intervention.

Flatulence is closely associated with gut dysbiosis, yet the characteristic microbial signatures, metabolic alterations, and actionable intervention targets remain unclear. This limited mechanistic understanding has hindered the development of precise microbiota-based strategies for managing flatulence. Here, we found that participants with flatulence exhibited marked shifts in gut microbial functions and fecal metabolic profiles compared with healthy controls, characterized by enhanced abnormal fermentation, enrichment of oxidative stress-related functions, elevated low-grade inflammatory signatures, and reduced anti-inflammatory and mucosal-protective metabolic features. Faecalibacterium prausnitzii was significantly negatively associated with the high-gas-producing phenotype. In vitro replenishment experiments further validated the role of F. prausnitzii in reducing gas production, promoting butyrate generation, and remodeling butyrate-associated microbial communities. Based on microbial interaction analysis, we identified Bifidobacterium longum CCFM1319 as a candidate strain for targeting F. prausnitzii. In a double-blind, randomized, placebo-controlled clinical trial, supplementation with B. longum CCFM1319 significantly increased intestinal F. prausnitzii abundance and improved flatulence-related symptoms. Collectively, these findings reveal the microbiota and metabolic dysbiosis underlying flatulence, highlight the key regulatory role of F. prausnitzii, and lays the foundation for targeted microbiota-based intervention strategies for flatulence.

Humans↗

PubMed1977

Application of quantitative high-performance thin-layer chromatography in the antibiotic industry.

For the in-process control of antibiotic fermentations and for routine assays of samples for scaling up and for pure products, quantitative high-performance thin-layer chromatography (HPTLC) can be used with advantage. Rapid chromatography on high-performance layers, combined with an automatic spraying device for exact derivatization on the plate and precise computation of the calibration line within an automatic measurement and evaluation, represents a new, inexpensive analysis system. There are only 2 min of labour time (one fifth of that required in thin-layer chromatography) required for one sample and the total analysis time varies from 3 to 9 min (one third to one quarter of that required in thin-layer chromatography) based on one plate with 12 samples. The 95% confidence limits (N = 10) range between 0.5 and 3.0%.

Anti-Bacterial Agents↗

PubMed2025

Breeding of yeast strains with intracellular amino acid accumulation for value-added alcoholic beverages.

The yeast Saccharomyces cerevisiae converts amino acids into volatile compounds with fruity and floral aromas during fermentation. These amino acid-derived aroma compounds play a critical role in defining the taste and flavor of alcoholic beverages such as sake, beer, and wine. The productivity of amino acid-derived aroma compounds depends on the intracellular availability of their precursor amino acids. Therefore, breeding yeast strains that accumulate amino acids provides a practical approach to developing alcoholic beverages with more unique and attractive sensory characteristics. In this minireview, we describe the isolation of yeast strains that overproduce branched-chain amino acids and phenylalanine, obtained through conventional mutagenesis of industrial brewing yeasts. We also discuss the mechanisms responsible for the increased production of these amino acids in the mutant strains, including altered feedback regulation and transcriptional control of key enzymes involved in their biosynthesis. In addition, we briefly introduce a plasmid-free genome editing system that enables precise modification of metabolic pathways without the integration of foreign DNA, allowing the construction of strains that are not classified as genetically modified organisms. This method represents a promising tool that allows flexible and fine-tuned engineering of yeast metabolic pathways, including the development of strains with tailored aroma profiles.

Saccharomyces cerevisiae↗

PubMed2026

Natural products alleviate exercise-induced fatigue by modulating gut microbiota: a systematic review.

BACKGROUND: Exercise-induced fatigue critically impairs athletic performance and training quality. The gut microbiota, as a key regulator of the "gut-muscle axis," has emerged as a promising anti-fatigue target. Natural products - owing to their diverse sources, structural complexity, and favorable safety profiles - have attracted growing research interest. However, a systematic synthesis comparing their anti-fatigue effects via gut microbiota modulation across different sources is lacking. SCOPE AND APPROACH: We systematically searched PubMed, Web of Science, the Cochrane Library, and CNKI for original studies that administered natural products and concurrently assessed gut microbiota changes and anti-fatigue outcomes. Twenty-six studies (25 animal experiments and 1 human trial) were included and categorized into seven groups by source and chemical characteristics. A descriptive systematic review was conducted to identify common mechanisms and source-specific differentiations. KEY FINDINGS AND CONCLUSIONS: The enrichment of short-chain fatty acid (SCFA)-producing bacteria and the activation of the SCFA-AMPK/PGC-1α axis were shared core events across all product categories. However, source-dependent mechanistic divergences emerged: polysaccharides acted primarily as fermentable substrates with an optimal dose window; polyphenols and saponins exerted dual modulation on both microbiota and host signaling pathways; compound extracts achieved systemic synergy through functional complementation; marine- and animal-derived products exhibited unique targeting profiles and rapid action. Intestinal barrier maintenance and brain-gut axis regulation further extended the anti-fatigue repertoire. Collectively, natural products possess a solid mechanistic basis for alleviating exercise-induced fatigue via gut microbiota remodeling. The differentiated characteristics of these methods in targeting precision and pathway engagement provide a theoretical foundation for designing precision intervention strategies tailored to specific fatigue contexts.

Humans↗

PubMed2026

Engineering Bacillus Subtilis for Efficient Biosynthesis of Riboflavin: Current Knowledge and Future Perspectives.

Riboflavin is an essential water-soluble vitamin that serves as a precursor for the biosynthesis of the flavin cofactors FMN and FAD, which play pivotal roles in numerous redox and energy metabolism reactions. With the growing global demand for sustainable vitamin production, microbial fermentation has become an attractive alternative to chemical synthesis due to its environmental and economic advantages. Among microbial hosts, Bacillus subtilis has emerged as a leading cell factory for riboflavin production owing to its GRAS status, well-characterized genetics, and efficient protein secretion system. This review provides a comprehensive overview of recent advances in metabolic engineering strategies to enhance riboflavin biosynthesis in B. subtilis. Key topics include strengthening biosynthetic and precursor pathways, relieving feedback inhibition, balancing metabolic flux and cell growth, employing adaptive laboratory evolution, and utilizing omics-guided optimization and 13C metabolic flux analysis. Moreover, the integration of synthetic biology tools such as riboswitch engineering, regulatory element design, and high-throughput screening has significantly accelerated strain improvement. Despite remarkable progress, challenges remain in achieving precise regulatory control, optimizing multi-gene expression, and enhancing genome integration efficiency. Future research combining multi-omics data, synthetic regulatory design, and machine learning-driven predictive modeling is expected to further advance the development of intelligent B. subtilis cell factories. However, the practical implementation of these systems remains constrained by the metabolic burden of overproduction and the lack of universal regulatory models that can predict strain performance across varying industrial scales.

Bacillus subtilis↗