Search Results (209)

To explore an industrial fermentation approach for traditional mung bean sour pulp, this study isolated core microorganisms including lactic acid bacteria and yeasts from naturally fermented samples and constructed a synthetic microbial community. The optimized community consisted of Lactiplantibacillus pentosus, Lactococcus garvieae, and Cyberlindnera jadinii at a ratio of 7:3:0.1 and was used to ferment cooked mung bean pulp with a material-to-water ratio of 1:8 and 1% sucrose addition. Under these conditions, the final product exhibited significantly higher levels of protein (4.55 mg/mL), flavonoids (0.10 mg/mL), polyphenols (0.11 mg/mL), and vitamin C (7.75 μg/mL) than traditionally fermented mung bean sour pulp, along with enhanced antioxidant activity. The analysis of organic acids, free amino acids, and volatile compounds showed that lactic acid was the main acid component, the bitter amino acid content was reduced, the volatile flavor compounds were more abundant, and the level of harmful compound dimethyl sulfide was significantly decreased. These results indicate that fermentation using a synthetic microbial community effectively improved the nutritional quality, flavor, and safety of mung bean sour pulp. Full article

The growing environmental concerns associated with petroleum-based plastics require the development of sustainable, biodegradable alternatives. Polyhydroxyalkanoates (PHAs), a family of biodegradable bioplastics, offer a promising potential as eco-friendly substitutes due to their renewable origin and favorable degradation properties. This research investigates the use of synthetic condensate, mimicking the liquid fraction from drying and shredding of household food waste, as a viable substrate for PHA production using mixed microbial cultures. Two draw-fill reactors (DFRs) were operated under different feed organic concentrations (2.0 ± 0.5 and 3.8 ± 0.6 g COD/L), maintaining a consistent carbon-to-nitrogen ratio to selectively enrich microorganisms capable of accumulating PHAs through alternating nutrient availability and deficiency. Both reactors achieved efficient organic pollutant removal (>95% soluble COD removal), stable biomass growth, and optimal pH levels. Notably, the reactor with the higher organic load (DFR-2) demonstrated a modest increase in PHA accumulation (19.05 ± 7.18%) compared to the lower-loaded reactor (DFR-1; 15.19 ± 6.00%), alongside significantly enhanced biomass productivity. Polymer characterization revealed the formation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), influenced by the substrate composition. Microbial community analysis showed an adaptive shift towards Proteobacteria dominance, signifying successful enrichment of effective PHA producers. Full article

Organic amendments provide a sustainable strategy to enhance soil quality in degraded environments while also helping to reduce greenhouse gas emissions, for example, by improving soil structure, minimizing the use of synthetic fertilizers, and promoting a green economy. This study assessed the comparative effects of two organic amendments—vermicompost leachate and biochar—on the performance of popcorn maize (Zea mays L. var. everta) cultivated in saline soil conditions. Four treatments were evaluated: T0 (Control), T1 (Vermicompost leachate), T2 (Biochar), and T3 (Vermicompost leachate + Biochar), each with 10 replicates arranged in a Completely Randomized Design (CRD). Although various soil physicochemical, microbiological, and agronomic parameters displayed no significant differences compared to the control, the application of biochar resulted in considerable improvements in soil total organic carbon, the microbial community (mesophilic aerobic bacteria, molds, and yeasts), and increased seed length and diameter. In contrast, vermicompost leachate alone negatively impacted plant growth, leading to decreases in leaf area, stem thickness, and grain yield. Specifically, grain yield declined by 46% with leachate alone and by 31% when combined with biochar, compared to the control. These findings emphasize the superior effectiveness of biochar over vermicompost leachate as a soil amendment under saline conditions and highlight the potential risks of widely applying compost teas in stressed soils. It is recommended to conduct site-specific assessments and screenings for phytotoxins and phytopathogens prior to use. Additionally, the combined application of leachate and biochar may not be advisable given the tested soil characteristics. Full article

Food fermentation is driven by microbial interactions. This article reviews the types of microbial interactions during food fermentation, the research strategies employed, and their impacts on the quality of fermented foods. Microbial interactions primarily include mutualism, commensalism, amensalism, and competition. Based on these interaction patterns, the safety, nutritional composition, and flavor quality of food can be effectively improved. Achieving precise control of fermented foods’ qualities via microbial interaction remains a critical challenge. Emerging technologies such as high-throughput sequencing, cell sorting, and metabolomics enable the systematic analysis of core microbial interaction mechanisms in complex systems. Using synthetic microbial communities and genome-scale metabolic network models, complicated microbial communities can be effectively simplified. In addition, regulatory targets of food quality can be precisely identified. These strategies lay a solid foundation for the precise improvement of fermented food quality and functionality. Full article

Nitrogen-metabolizing microbes are the keystone drivers of reducing nitrogen pollutants in wastewater and natural waters, but the one-way experiment with fixed screening factors fails to discover the optimal scope of nitrogen-metabolizing microbes performing nitrogen reduction. This study novelly combines the one-way experiment and response surface methodology (RSM) modeling to synthesize an effective nitrogen reduction microbial community, with the RSM model showing high goodness-of-fit (R² = 0.83, p = 0.01) for optimizing the strain combination. Eight bacterial strains were isolated from contaminated sediment and activated sludge. Three efficient strains, arranged to Ignatzschieria indica, Staphylococcus epidermidis, and Acinetobacter baumannii by 16S rDNA sequencing, were screened using the above combination method to synthesize a nitrogen reduction microbial community. Within the synthetic microbial community, Ignatzschieria indica and Staphylococcus epidermidis possessed denitrification abilities, and Acinetobacter baumannii contributed to nitrification with 99% of ammonium oxidation. This synthesis microbial community displayed synchronous nitrification and denitrification under interval aeration and possessed wide pH tolerance from 6 to 10, with a steady >80% total inorganic nitrogen reduction. This research managed to synthesize a tolerant nitrogen reduction microbial community and provides novel insight for constructing synthetic microbial consortia. Full article

The increasing release of nanoparticles into aquatic environments, particularly via wastewater, raises concerns about their biological effects on microbial communities. This study investigated the molecular response of Pseudomonas putida to aluminum oxide nanoparticles (Al₂O₃NPs) under controlled conditions and in synthetic wastewater, both before and after biological treatment. Acute toxicity was evaluated using growth inhibition assays, while the expression of katE, ahpC, and ctaD—genes associated with oxidative stress and energy metabolism—was quantified via RT-qPCR. Exposure to pristine Al₂O₃NPs induced a strong, time-dependent upregulation of all tested genes (e.g., katE and ahpC up to 4.5-fold). In untreated wastewater, this effect persisted but at a lower intensity; bulk Al₂O₃ caused only moderate changes. Treated wastewater samples showed markedly reduced gene expression, indicating partial detoxification. Nanoparticles elicited stronger biological responses than their bulk counterparts, confirming the material form-specific effects. Comparative analysis with Daphnia magna revealed similar patterns of oxidative stress gene activation. These findings highlight the influence of nanoparticle form and environmental matrix on microbial responses and support the use of gene expression analysis as a sensitive biomarker for nanoparticle-induced stress in environmental risk assessment. Full article

Background/Objectives: The gut microbiota (GM) is pivotal for immune regulation, metabolism, and neurodevelopment. Infants undergoing surgery for congenital gastrointestinal anomalies are especially prone to microbial imbalances, with a paucity of beneficial bacteria (e.g., Bifidobacteria and Bacteroides) and diminished short-chain fatty acid production. Dysbiosis has been associated with severe complications, including necrotizing enterocolitis, sepsis, and feeding intolerance. This narrative review aims to critically examine strategies for microbiota modulation in this high-risk cohort. Methods: An extensive literature analysis was performed to compare the evolution of GM in healthy neonates versus those requiring gastrointestinal surgery, synthetizing strategies to maintain eubiosis, such as early nutritional interventions—particularly the use of human milk—along with antibiotic management and supplementary treatments including probiotics, prebiotics, postbiotics, and lactoferrin. Emerging techniques in metagenomic and metabolomic analysis were also evaluated for their potential to elucidate microbial dynamics in these patients. Results: Neonates undergoing gastrointestinal surgery exhibit significant alterations in microbial communities, characterized by reduced levels of eubiotic bacteria and an overrepresentation of opportunistic pathogens. Early initiation of enteral feeding with human milk and careful antibiotic stewardship are linked to improved microbial balance. Adjunctive therapies, such as the administration of probiotics and lactoferrin, show potential in enhancing gut barrier function and immune modulation, although confirmation through larger-scale studies remains necessary. Conclusions: Modulating the GM emerges as a promising strategy to ameliorate outcome in neonates with congenital gastrointestinal surgical conditions. Future research should focus on the development of standardized therapeutic protocols and the execution of rigorous multicenter trials to validate the efficacy and safety of these interventions. Full article

Yeast genetic improvement is entering a transformative phase, driven by the integration of artificial intelligence (AI), big data analytics, and synthetic microbial communities with conventional methods such as sexual breeding and random mutagenesis. These advancements have substantially expanded the potential for innovative re-engineering of yeast, ranging from single-strain cultures to complex polymicrobial consortia. This review compares traditional genetic manipulation techniques with cutting-edge approaches, highlighting recent breakthroughs in their application to beer and wine fermentation. Among the innovative strategies, adaptive laboratory evolution (ALE) stands out as a non-GMO method capable of rewiring complex fitness-related phenotypes through iterative selection. In contrast, GMO-based synthetic biology approaches, including the most recent developments in CRISPR/Cas9 technologies, enable efficient and scalable genome editing, including multiplexed modifications. These innovations are expected to accelerate product development, reduce costs, and enhance the environmental sustainability of brewing and winemaking. However, despite their technological potential, GMO-based strategies continue to face significant regulatory and market challenges, which limit their widespread adoption in the fermentation industry. Full article

Microbiome data analysis is essential for understanding the role of microbial communities in human health. However, limited data availability often hinders research progress, and synthetic data generation could offer a promising solution to this problem. This study aims to explore the use of machine learning (ML) to enrich an unbalanced dataset consisting of microbial operational taxonomic unit (OTU) counts of 148 samples, belonging to 61 patients. In detail, 34 samples are from 16 adenomatous polyps (AP) patients, while 114 samples are from 46 colorectal cancer (CRC) patients. Synthesis of AP and CRC samples was conducted using the Synthetic Data Vault Python library, employing a Gaussian Copula synthesiser. Subsequently, the synthesised data quality was evaluated using a logistic regression model in parallel with an optimised support vector machine algorithm (polynomial kernel). The data quality is considered good when neither of the two algorithms can discriminate between real and synthetic data, showing low accuracy, F1 score, and precision values. Furthermore, additional statistical tests were employed to confirm the similarity between real and synthetic data. After data validation, layer-wise relevance propagation (LRP) was performed on a deep learning classifier to extract important OTU features from the generated dataset, to discriminate between CRC patients and those affected by AP. Exploiting the acquired features, which correspond to unique bacterial taxa, ML classifiers were trained and tested to estimate the validity of such microorganisms in recognising AP and CRC samples. The simplified version of the original OTU table opens up opportunities for further investigations, especially in the realm of extensive data synthesis. This involves a deeper exploration and augmentation of the condensed data to uncover new insights and patterns that might not be readily apparent in the original, more complex form. Digging deeper into the simplified data may help us better grasp the biological or ecological processes reflected in the OTU data. Transitioning from this exploration, the synergy of ML and synthetic data enrichment holds promise for advancing microbiome research. This approach enhances classification accuracy and reveals hidden microbial markers that could prove valuable in clinical practice as a diagnostic and prognostic tool. Full article

Microbial interactions within the rhizosphere are fundamental to plant health, influencing nutrient availability, stress tolerance, and pathogen resistance. Beneficial microbes, such as plant growth-promoting microbes (PGPMs), including bacteria and mycorrhizal fungi, enhance plant resilience through mechanisms like nutrient solubilization, phytohormone production, and pathogen suppression via antimicrobial compounds and siderophores. Root exudates, composed of sugars, organic acids, and secondary metabolites, act as chemoattractants that shape the rhizosphere microbiome by recruiting beneficial microbes. Microbial metabolites can, in turn, modulate plant physiology and exudate profiles, thereby reinforcing mutualistic interactions. Stress conditions alter exudate composition, enabling plants to attract specific microbes that aid in stress mitigation. Given the growing interest in microbiome-based agricultural solutions, this review aims to synthesize recent literature on plant–microbe interactions, with a focus on bidirectional signaling between plants and microbes. A structured literature search was conducted using databases such as PubMed, Scopus, and ScienceDirect to identify key studies on root exudation, microbial functions, and synthetic microbial communities (SynComs). We highlight major findings on how engineered microbiomes can enhance plant growth, resilience, and productivity, particularly under stress conditions. This review also explores how advances in SynCom design can promote sustainable agriculture by reducing reliance on chemical inputs. Full article

Tyre wear particles (TWPs), generated from tyre-road abrasion, are a pervasive and under-regulated environmental pollutant, accounting for a significant share of global microplastic contamination. Recent estimates indicate that 1.3 million metric tons of TWPs are released annually in Europe, dispersing via atmospheric transport, stormwater runoff, and sedimentation to contaminate air, water, and soil. TWPs are composed of synthetic rubber polymers, reinforcing fillers, and chemical additives, including heavy metals such as zinc (Zn) and copper (Cu) and organic compounds like polycyclic aromatic hydrocarbons (PAHs) and N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6PPD). These constituents confer persistence and bioaccumulative potential. While TWP toxicity in aquatic systems is well-documented, its ecological impacts on terrestrial environments, particularly in agricultural soils, remain less understood despite global soil loading rates exceeding 6.1 million metric tons annually. This review synthesizes global research on TWP sources, environmental fate, and ecotoxicological effects, with a focus on soil–plant systems. TWPs have been shown to alter key soil properties, including a 25% reduction in porosity and a 20–35% decrease in organic matter decomposition, disrupt microbial communities (with a 40–60% reduction in nitrogen-fixing bacteria), and induce phytotoxicity through both physical blockage of roots and Zn-induced oxidative stress. Human exposure occurs through inhalation (estimated at 3200 particles per day in urban areas), ingestion, and dermal contact, with epidemiological evidence linking TWPs to increased risks of respiratory, cardiovascular, and developmental disorders. Emerging remediation strategies are critically evaluated across three tiers: (1) source reduction using advanced tyre materials (up to 40% wear reduction in laboratory tests); (2) environmental interception through bioengineered filtration systems (60–80% capture efficiency in pilot trials); and (3) contaminant degradation via novel bioremediation techniques (up to 85% removal in recent studies). Key research gaps remain, including the need for long-term field studies, standardized mitigation protocols, and integrated risk assessments. This review emphasizes the importance of interdisciplinary collaboration in addressing TWP pollution and offers guidance on sustainable solutions to protect ecosystems and public health through science-driven policy recommendations. Full article

In insect–microbe symbiosis, understanding the diversity of associated bacteria is crucial. DNA-dependent sequence methods are widely used to assess microbial diversity in insects, but they cannot distinguish between live and dead microbes. In contrast, RNA-dependent sequencing can identify alive bacterial communities, making them more suitable for evaluating alive microbiota diversity. However, its practical reliability in insect–microbe symbiosis remains poorly validated. This study investigated larval gut bacteria diversity of Delia antiqua, a major pest of Liliaceae crops, by employing both DNA- and RNA-dependent 16S rRNA amplicon sequencing. The reliability of both sequencing methods was evaluated by comparing the effects of synthetic communities (SynComs, constructed according to DNA- or RNA-dependent sequencing) and bacterial communities from wild larvae on axenic larvae. Results revealed significant differences in bacterial community between DNA- and RNA-dependent sequence samples. Compared to bacterial communities from wild larvae, the SynCom constructed based on RNA-dependent sequencing exhibited inhibition effects on D. antiqua larvae survival and body weight, while DNA-dependent SynCom did not, suggesting that DNA-dependent methods were superior for assessing symbiotic microbiota in D. antiqua. This work will provide insights into microbial diversity detection in D. antiqua and offer a framework for other insect–microbe studies. Full article

Polyethylene terephthalate (PET) is one of the most frequently used synthetic polymers and it plays a major role in plastic pollution in aquatic environments. As PET undergoes environmental degradation, it sheds microplastics and chemical leachates, which have an effect on microbial communities, including benthic cyanobacteria. This review focuses on the molecular processes by which PET microplastics and their associated leachate affect the growth, physiological performance, and ecological performance of benthic cyanobacteria. We explore how PET-derived compounds serve as carbon and energy sources or signaling molecules, possibly affecting photosynthesis, nitrogen fixation, or stress response pathways through changes in gene expression. Moreover, the function of PET leachates as environmental modulators of microbial community structure, generators of reactive oxygen species (ROS), and disruptors of hormonal and quorum sensing networks are also outlined. Knowledge of these interactions is essential for the evaluation of the wider ecological risks resulting from plastic pollution and the likelihood of cyanobacterial blooms in PET-polluted environments. This review synthesizes evidence on how PET microplastics and leachates act as carbon sources and stressors, modulating gene expression to promote benthic cyanobacterial growth and toxin production, potentially exacerbating ecological risks in polluted aquatic systems. Full article

Climate-change-induced drought threatens forest restoration by limiting seedling establishment. To address this, we developed synthetic bacterial communities (SynComs) tailored to support drought tolerance in two Mediterranean tree species, Quercus pubescens and Sorbus domestica. Bacteria were isolated from forest soil exposed to long-term drought, sampling across soil depths and root-associated compartments. We selected strains with key plant-beneficial traits, including exopolysaccharide (EPS) production, hormone synthesis (auxin, ABA), siderophore release, and osmotic tolerance. SynComs were assembled based on functional complementarity and ecological origin. Biofilm assays showed that even weak individual producers could enhance community-level performance. After initial screening on Arabidopsis thaliana, the most and least effective SynComs were tested on Q. pubescens and S. domestica seedlings. Compared to controls, the best-performing SynComs reduced the proportion of drought-symptomatic seedlings by 47% in Q. pubescens and 71% in S. domestica, outperforming single-strain inoculants. Notably, EPS-rich SynCom B aligned with the conservative root traits of Q. pubescens, while hormone-rich SynCom F matched the acquisitive strategy of S. domestica. Predictive modeling identified bacterial identity and symptom timing as key predictors of drought resilience. Our results highlight the value of matching microbial traits with plant strategies and drought context for climate-smart forest restoration. Full article

Pepper (Capsicum annuum) production faces significant challenges from soil-borne pathogens, particularly Phytophthora capsici, which induces root rot and damping-off diseases. Management of this pathogen remains challenging owing to the scarcity of resistant cultivars and the ineffectiveness of chemical control methods. A single strain has been used to prevent pathogenic disease, and this approach limits the exploration of consortia comprising different genera. In this study, we isolated five bacterial strains (Bacillus sp. T3, Flavobacterium anhuiense T4, Cytobacillus firmus T8, Streptomyces roseicoloratus T14, and Pseudomonas frederiksbergensis A6) from the rhizosphere of healthy pepper plants. We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum to evaluate its efficacy in improving pepper resilience against P. capsici. The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity, siderophore synthesis, and strong antagonism against P. capsici. The SynCom reduced disease severity and enhanced the growth of pepper plants. Furthermore, the beneficial genera such as Bacillus, Fusicolla, and Trichoderma, significantly increased in the rhizosphere of pepper after the application of the SynCom. Microbial functional prediction analysis revealed that these microbial shifts were associated with nitrogen cycling and pathogen suppression. Our SynCom approach demonstrates the effectiveness of microbial consortia in promoting the growth of pathogen-infected plants by reprogramming the microbial community in the rhizosphere. Full article