Search Results (219)

Light-flavor Baijiu (LFB) is renowned for its distinct flavor and long history, with the microbial community structure of low-temperature Daqu (LTD) serving as a crucial saccharification fermenter that significantly influences the quality and flavor of Baijiu. With the rapid advancement of biotechnology, research on LTD has become more in-depth, focusing on the identification of core microorganisms and the construction of Synthetic Microbial Communities (SynComs), which have emerged as research hotspots. Core microorganisms play a vital role in fermentation and flavor development, while SynComs are artificially constructed microbial combinations designed to optimize fermentation and improve liquor quality. This paper provides a systematic overview of the core microorganisms associated with LTD and their identification methods, as well as the concepts, advantages, applications, and construction methodologies of SynComs. It compiles relevant research findings to offer a theoretical foundation for a deeper understanding of the brewing mechanism and further optimization of the LFB brewing process, along with insights into future research directions. Full article

The saline–alkali soil environment profoundly influences the diversity and composition of soil microbial communities, reshaping their ecological network structures. As a vital staple crop, rice (Oryza sativa L.) plays a crucial role in global food security, highlighting the urgent need to improve its cultivation efficiency in saline–alkali soils. However, the mechanisms by which rice roots recruit beneficial microorganisms from native soils under prolonged saline–alkali stress remain largely unclear, and limited research has been conducted on the effectiveness of microbial inoculants in enhancing rice salt tolerance. This study investigated microbial communities in a saline field subjected to over a decade of continuous rice cultivation. Plant growth-promoting microorganisms were isolated and screened from the rhizosphere. The findings revealed long-term salt stress significantly altered microbial diversity and community composition, although the overall microbial network structure remained resilient. A total of 21 plant growth-promoting strains were identified, indicating that rice roots under sustained salt stress selectively recruit beneficial microbes that contribute to plant growth and stress adaptation. Further experimental validation demonstrated that synthetic microbial communities outperformed individual strains in promoting rice seedling growth under high-salinity conditions, likely due to synergistic microbe and microbe–plant interactions. In conclusion, while saline–alkali conditions disrupt native microbial communities, rice exhibits adaptive capacity by selectively enriching growth-promoting microorganisms. The application of synthetic microbial consortia presents a promising strategy to enhance rice resilience and productivity in saline–alkali environments. Full article

Accurate genome binning is essential for resolving microbial community structure and functional potential from metagenomic data. However, existing approaches—primarily reliant on tetranucleotide frequency (TNF) and abundance profiles—often perform sub-optimally in the face of complex community compositions, low-abundance taxa, and long-read sequencing datasets. To address these limitations, we present MBGCCA, a novel metagenomic binning framework that synergistically integrates graph neural networks (GNNs), contrastive learning, and information-theoretic regularization to enhance binning accuracy, robustness, and biological coherence. MBGCCA operates in two stages: (1) multimodal information integration, where TNF and abundance profiles are fused via a deep neural network trained using a multi-view contrastive loss, and (2) self-supervised graph representation learning, which leverages assembly graph topology to refine contig embeddings. The contrastive learning objective follows the InfoMax principle by maximizing mutual information across augmented views and modalities, encouraging the model to extract globally consistent and high-information representations. By aligning perturbed graph views while preserving topological structure, MBGCCA effectively captures both global genomic characteristics and local contig relationships. Comprehensive evaluations using both synthetic and real-world datasets—including wastewater and soil microbiomes—demonstrate that MBGCCA consistently outperforms state-of-the-art binning methods, particularly in challenging scenarios marked by sparse data and high community complexity. These results highlight the value of entropy-aware, topology-preserving learning for advancing metagenomic genome reconstruction. Full article

Drought and excess ambient temperature intensify abiotic and biotic stresses on agriculture, threatening food security and economic stability. The development of climate-resilient crops is crucial for sustainable, efficient farming. This review highlights the role of multi-omics encompassing genomics, transcriptomics, proteomics, metabolomics, and epigenomics in identifying genetic pathways for stress resilience. Advanced phenomics, using drones and hyperspectral imaging, can accelerate breeding programs by enabling high-throughput trait monitoring. Artificial intelligence (AI) and machine learning (ML) enhance these efforts by analyzing large-scale omics and phenotypic data, predicting stress tolerance traits, and optimizing breeding strategies. Additionally, plant-associated microbiomes contribute to stress tolerance and soil health through bioinoculants and synthetic microbial communities. Beyond agriculture, these advancements have broad societal, economic, and educational impacts. Climate-resilient crops can enhance food security, reduce hunger, and support vulnerable regions. AI-driven tools and precision agriculture empower farmers, improving livelihoods and equitable technology access. Educating teachers, students, and future generations fosters awareness and equips them to address climate challenges. Economically, these innovations reduce financial risks, stabilize markets, and promote long-term agricultural sustainability. These cutting-edge approaches can transform agriculture by integrating AI, multi-omics, and advanced phenotyping, ensuring a resilient and sustainable global food system amid climate change. Full article

Cardiovascular disease (CVD) remains the leading cause of global mortality, despite advances in adult-focused prevention and therapy. Mounting evidence supports the Developmental Origins of Health and Disease (DOHaD) paradigm, which identifies early-life exposures as critical determinants of long-term cardiovascular health. Among the key mechanistic pathways, oxidative stress and gut microbiota dysbiosis have emerged as central, interrelated contributors to cardiovascular programming. Prenatal and postnatal insults can induce sustained redox imbalance and disrupt microbial homeostasis. This disruption creates a feed-forward loop that predisposes offspring to CVD later in life. Antioxidants offer a promising reprogramming strategy by targeting both oxidative stress and gut microbiota composition. Preclinical studies demonstrate that maternal antioxidant interventions—such as vitamins, amino acids, melatonin, polyphenols, N-acetylcysteine, and synthetic agents—can restore redox homeostasis, modulate gut microbial communities, and attenuate cardiovascular risk in offspring. This review synthesizes current evidence on how oxidative stress and gut microbiota act together to shape cardiovascular trajectories. It also examines how antioxidant-based therapies may disrupt this pathological axis during critical developmental windows. Although human data remain limited due to ethical and practical constraints, advancing microbiota-targeted antioxidant interventions may offer a transformative approach to prevent CVD at its origins. Full article

The biotechnological conversion of CO₂ to biomethane represents an energy-efficient, environmentally friendly, and sustainable approach within the waste-to-energy cycle. This process, in which CO₂ and H₂ are converted to biomethane in anaerobic bioreactors, is referred to as hydrogenotrophic biomethane production. While several studies have investigated hydrogenotrophic biomethane production, there is a lack of research comparing flocculent and granular sludge inoculum in continuously operated systems fed with a gas substrate. Both granular and flocculent sludge possess distinct advantages: granular sludge offers higher density, stronger microbial cohesion, and superior settling performance, whereas flocculent sludge provides faster substrate accessibility and more rapid initial microbial activity. In this study, two UASB (Upflow Anaerobic Sludge Blanket) reactors operated under mesophilic conditions were continuously fed with synthetic off-gas composed of pure H₂ and CO₂ in a 4:1 ratio and were compared in terms of microbial community shifts and their effects on hydrogenotrophic biomethane production. Biomethane production reached 75 ± 2% in the granular sludge reactor, significantly higher than the 64 ± 1.3% obtained with flocculent sludge. Although hydrogen consumption did not differ significantly, the granular sludge reactor exhibited higher CO₂ removal efficiency. Microbial analyses further revealed that granular sludge was more effective in supporting methanogenic archaea under conditions of gas substrate feeding. These findings offer advantageous suggestions for improving biogas production, enhancing waste gas management, and advancing sustainable energy generation. Full article

This study evaluated the effects of different doses of the herbicide fluroxypyr on soil microbial communities under controlled laboratory conditions. Specific enzymatic activities ((dehydrogenase (DA), urease (UA), catalase (CA), phosphatase (PA)) and quantitative variations in bacterial and fungal populations were measured regarding key physico-chemical soil parameters (temperature, pH, electrical conductivity, moisture, organic matter, ammonium, nitrate nitrogen, and available phosphate content). The effects of the herbicide on the targeted parameters were dose- and time-dependent. Fluroxypyr induced a clear decrease in DA, CA, and PA during the first 14 days after administration, while UA showed a decrease in the first 7 days, followed by a slight increase starting on day 14, closely related to the applied dose. Microbial populations decreased in direct relation to the fluroxypyr dose. Organic matter content exhibited a positive correlation with DA, UA, CA, as well as with microbial populations. In addition, three natural compounds structurally similar to fluroxypyr were identified via 3D virtual screening, demonstrating potential herbicidal activity. Fluroxypyr can alter soil metabolic activity and disrupt microbial communities, thereby affecting soil fertility. Used as a reference in 3D screening, fluroxypyr helped identify three natural compounds with potential herbicidal activity as safer alternatives to synthetic herbicides. Full article

The global increase in municipal and industrial wastewater generation has intensified the need for ecologically resilient and technologically advanced treatment systems. Although traditional biological treatment technologies are effective for organic load reduction, they often fail to remove recalcitrant xenobiotics such as pharmaceuticals, synthetic dyes, endocrine disruptors (EDCs), and microplastics (MPs). Engineered microbial consortia offer a promising and sustainable alternative owing to their metabolic flexibility, ecological resilience, and capacity for syntrophic degradation of complex pollutants. This review critically examines emerging strategies for enhancing microbial bioremediation in wastewater treatment systems (WWTS), focusing on co-digestion, biofilm engineering, targeted bioaugmentation, and incorporation of conductive materials to stimulate direct interspecies electron transfer (DIET). This review highlights how multi-omics platforms, including metagenomics, transcriptomics, and metabolomics, enable high-resolution community profiling and pathway reconstructions. The integration of artificial intelligence (AI) and machine learning (ML) algorithms into bioprocess diagnostics facilitates real-time system optimization, predictive modeling of antibiotic resistance gene (ARG) dynamics, and intelligent bioreactor control. Persistent challenges, such as microbial instability, ARG dissemination, reactor fouling, and the absence of region-specific microbial reference databases, are critically analyzed. This review concludes with a translational pathway for the development of next-generation WWTS that integrate synthetic microbial consortia, AI-mediated biosensors, and modular bioreactors within the One Health and Circular Economy framework. Full article

Previous studies have suggested correlations between the microbiota of the black soldier fly and larval growth and bioconversion ability, primarily through functional inference. However, the concrete impact of the microbiota remains to be demonstrated. To address this, we assembled two synthetic microbial communities (SynComs) derived from endogenous bacteria and evaluated their effects on larval growth. SynComs were administered to axenic larvae reared on sterilised diet (gnotobiotic) or as a probiotic in non-sterile treatments. Larvae were reared on vegetable-based (pre-consumer vegetable residues) or on animal-based (chicken hatchery residues) substrates. The SynComs were administered at two concentrations (5 × 10⁷ and 10⁸ CFU per isolate) in the substrate prior to neonate introduction. SynComs improved the growth of axenic larvae compared to untreated controls, although not to the levels observed in conventionally reared larvae. In non-sterile conditions, the combined SynComs increased growth on vegetable-based substrate, but no effect was observed on the animal-based substrate, suggesting a substrate-dependent effect. These results highlight microbiota’s critical role in larval development and the potential of microbiome engineering in insect rearing systems. This preliminary study opens the way for optimisation of SynCom assemblies, which could be enhanced through pre-testing of individual isolates and selecting microbial combinations tailored to specific substrates. Full article

Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity. Full article

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