Search Results (37)

The field of bacterial systems biology is rapidly advancing beyond static genomic analyses, and moving toward dynamic, integrative approaches that connect genetic variation with cellular function. This review traces the progression from genome-wide association studies (GWAS) to multi-omics frameworks that incorporate transcriptomics, proteomics, and interactome mapping. We emphasize recent breakthroughs in high-resolution transcriptomics, including single-cell, spatial, and epitranscriptomic technologies, which uncover functional heterogeneity and regulatory complexity in bacterial populations. At the same time, innovations in proteomics, such as data-independent acquisition (DIA) and single-bacterium proteomics, provide quantitative insights into protein-level mechanisms. Experimental and AI-assisted strategies for mapping protein–protein interactions help to clarify the architecture of bacterial molecular networks. The integration of these omics layers through quantitative trait locus (QTL) analysis establishes mechanistic links between single-nucleotide polymorphisms and systems-level phenotypes. Despite persistent challenges such as bacterial clonality and genomic plasticity, emerging tools, including deep mutational scanning, microfluidics, high-throughput genome editing, and machine-learning approaches, are enhancing the resolution and scope of bacterial genetics. By synthesizing these advances, we describe a transformative trajectory toward predictive, systems-level models of bacterial life. This perspective opens new opportunities in antimicrobial discovery, microbial engineering, and ecological research. Full article

CRISPR technology, which is derived from the bacterial adaptive immune system, has transformed traditional genetic engineering techniques, made strain engineering significantly easier, and become a very versatile genome editing system that allows for precise, programmable modifications to a wide range of microbial genomes. The economies of fermentation-based manufacturing are changing because of its quick acceptance in both academic and industry labs. CRISPR processes have been used to modify industrially significant bacteria, including the lactic acid producers, Clostridium spp., Escherichia coli, and Corynebacterium glutamicum, in order to increase the yields of bioethanol, butanol, succinic acid, acetone, and polyhydroxyalkanoate precursors. CRISPR-mediated promoter engineering and single-step multiplex editing have improved inhibitor tolerance, raised ethanol titers, and allowed for the de novo synthesis of terpenoids, flavonoids, and recombinant vaccines in yeasts, especially Saccharomyces cerevisiae and emerging non-conventional species. While enzyme and biopharmaceutical manufacturing use CRISPR for quick strain optimization and glyco-engineering, food and beverage fermentations benefit from starter-culture customization for aroma, texture, and probiotic functionality. Off-target effects, cytotoxicity linked to Cas9, inefficient delivery in specific microorganisms, and regulatory ambiguities in commercial fermentation settings are some of the main challenges. This review provides an industry-specific summary of CRISPR–Cas9 applications in microbial fermentation and highlights technical developments, persisting challenges, and industrial advancements. Full article

Since the early 2000s, the poultry industry in our nation has steadily progressed towards a larger scale and increased intensification. However, the growing demand for animal-based protein, combined with significant increases in feed ingredient costs, presents substantial challenges to the advancement of egg production. The regulation of feed utilization efficiency in laying hens is a complex process, influenced by various factors including the farming environment, feed composition, microbial ecosystems, and hormonal dynamics. The feed conversion rate in laying hens not only serves as a critical indicator of agricultural productivity but also highlights the significant impact of molecular technologies in improving feed efficiency. These technological advancements have enhanced the precision and effectiveness of breeding practices while providing substantial support for optimizing feed management, improving production metrics, and promoting sustainable agricultural practices. This comprehensive synthesis of factors, regulatory pathways, and cutting-edge molecular methodologies establishes a biological framework for future breeding strategies. Notably, this review uniquely emphasizes the pivotal role of modern molecular biology techniques—such as genomic selection, transcriptomic profiling, and gene-editing tools—in decoding feed conversion efficiency (FCE), contributing to broader goals of agricultural sustainability by balancing productivity gains with eco-friendly and cost-effective egg production. 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

Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems. Full article

Sustainable agriculture and food security are challenged by the indiscriminate use of synthetic nitrogen (N₂) fertilizers, inefficient water management, and land degradation. Hydroponic cultivation uses nutrient-rich aqueous media and is a climate-resilient and resource-efficient alternative to traditional farming methods, whose dependence on synthetic N₂ fertilizers reduces their long-term sustainability. Biological nitrogen fixation (BNF), which is mediated by diazotrophs that reduce atmospheric N₂ to plant-available ammonium, has emerged as a sustainable alternative to synthetic N₂ input in hydroponic systems. This review discusses the integration of BNF into hydroponic systems by exploring the functional diversity of diazotrophs, root–microbe interactions, and environmental constraints. It further highlights recent advances in strain improvement, microbial consortia development, nitrogenase protection, and genome editing tools, novel bioformulation strategies to enhance microbial compatibility with hydroponic nutrient regimes, and omics-based tools for the real-time assessment of N₂ fixation and microbial functionality. Key challenges, such as microbial leaching, nitrate-induced inhibition of nitrogenase activity, and the absence of standardized biostimulant protocols, are discussed. Case studies on staple crops have demonstrated enhanced NUE and yield productivity following diazotroph applications. This review concludes with future perspectives on synthetic biology, regulatory policies, and omics-based tools for the real-time assessment of N₂ fixation and microbial functionality. Full article

The rising demand for sustainable, nutritious, and functional food options has fueled growing interest in plant-based fermented foods. These products offer enhanced sensory, functional, and health-promoting properties, largely driven by microbial activity during fermentation. This review examines recent advances in microbial biotechnology—including the use of novel starter cultures, strain engineering, CRISPR-based genome editing, and precision fermentation that are reshaping the nutritional landscape of plant-based fermented foods. Key benefits such as improved protein digestibility, bioactive compound synthesis, antinutrient reduction, and micronutrient bioavailability are explored. Additionally, the review highlights the potential of microbial innovations to enhance sustainability, address global nutrition challenges, and improve consumer acceptance through better sensory quality. It also discusses challenges related to regulatory frameworks, scalability, and consumer perception. This review aims to provide a comprehensive understanding of how microbial processes can optimize the nutritional and functional value of plant-based fermented foods in alignment with future food system goals. Full article

Traditional materials synthesis often involves energy-intensive processes with significant waste generation and limited control over material properties. This review examines synthetic biology as a sustainable alternative for designing advanced materials with enhanced precision and versatility. It explores microbial biomineralization, detailing how microorganisms influence the formation of mineral deposits and participate in key biogeochemical cycles. It highlights recent research advancements in using a wide variety of microorganisms for the synthesis of inorganic materials such as metal and metal oxide nanoparticles, quantum dots, magnetic nanoparticles, and thin films. The review also discusses the production and properties of various biopolymers. Important factors that can influence the size, morphology, and uniformity of these biomaterials are covered in detail. Emphasis is placed on advancements utilizing synthetic biology tools, such as protein engineering and genome editing, and recent research for creating smart and responsive materials. Considering the present limitations of synthetic biology, challenges related to scale-up, yield, and uniformity are discussed, and suggestions for future research are detailed. Full article

The global nutraceutical industry is experiencing a paradigm shift, driven by an increasing demand for functional foods and dietary supplements that address malnutrition and chronic diseases such as obesity, diabetes, cardiovascular conditions, and cancer. Traditional plant- and animal-derived nutraceuticals face limitations in scalability, cost, and environmental impact, paving the way for microbial biotechnology as a sustainable alternative. Microbial cells act as bio-factories, converting nutrients like glucose and amino acids into valuable nutraceutical products such as polyunsaturated fatty acids (PUFAs), peptides, and other bioactive compounds. By harnessing their natural metabolic capabilities, microorganisms efficiently synthesize these bioactive compounds, making microbial production a sustainable and effective approach for nutraceutical development. This review explores the transformative role of microbial platforms in the production of nutraceuticals, emphasizing advanced fermentation techniques, synthetic biology, and metabolic engineering. It addresses the challenges of optimizing microbial strains, ensuring product quality, and scaling production while navigating regulatory frameworks. Furthermore, the review highlights cutting-edge technologies such as CRISPR/Cas9 for genome editing, adaptive evolution for strain enhancement, and bioreactor innovations to enhance yield and efficiency. With a focus on sustainability and precision, microbial production is positioned as a game-changer in the nutraceutical industry, offering eco-friendly and scalable solutions to meet global health needs. The integration of omics technologies and the exploration of novel microbial sources hold the potential to revolutionize this field, aligning with the growing consumer demand for innovative and functional bioactive products. Full article

Mesophilic microbial sources of prokaryotic Argonaute (pAgo) programmable nucleases have garnered considerable attention for their potential applications in genome editing and molecular diagnostics. In this study, we characterized a novel pAgo from the mesophilic bacterium Chroococcidiopsis sp. (ChAgo), which can cleave single-stranded DNA (ssDNA) using both 5′-phosphorylated guide DNA (5′P-gDNA) and 5′-hydroxylated guide DNA (5′OH-gDNA). Efficient cleavage occurs using 14–25 nt 5′P-gDNA and 13–20 nt 5′OH-gDNA in the presence of Mn²⁺ ions at temperatures ranging from 25 to 75 °C, with optimal activity at 55 °C. ChAgo demonstrates low tolerance for single-base mismatches, similar to other pAgo proteins. The cleavage efficiency varies based on the guide/target pair, with mismatches at specific positions significantly reducing activity. For instance, mismatches at positions 4, 5, or 12 in T-gDNA/target pairs and at positions 5 or 8–10 in g38NT-gDNA/target pairs notably decrease efficiency. ChAgo’s sensitivity to mismatches makes it a promising tool for nucleic acid manipulation and detection, requiring initial screening for high cleavage efficiency sites and subsequent identification of mismatch positions. Full article

This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as next-generation sequencing, meta-omics, and microbiome engineering allow for the targeted manipulation of microbial communities to enhance pathogen suppression. Microbiome-based approaches include the design of synthetic microbial consortia and the transplant of entire or customized soil/plant microbiomes, potentially offering more resilient and adaptable biocontrol strategies. Nanotechnology has also advanced significantly, providing methods for the targeted delivery of biological control agents (BCAs) or compounds derived from them through different nanoparticles (NPs), including bacteriogenic, mycogenic, phytogenic, phycogenic, and debris-derived ones acting as carriers. The use of biodegradable polymeric and non-polymeric eco-friendly NPs, which enable the controlled release of antifungal agents while minimizing environmental impact, is also explored. Furthermore, artificial intelligence and machine learning can revolutionize crop protection through early disease detection, the prediction of disease outbreaks, and precision in BCA treatments. Other technologies such as genome editing, RNA interference (RNAi), and functional peptides can enhance BCA efficacy against pathogenic fungi. Altogether, these technologies provide a comprehensive framework for sustainable and precise management of fungal vascular diseases, redefining pathogen biocontrol in modern agriculture. Full article

Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance through mechanisms such as phytohormone production, nutrient solubilization, osmotic adjustment, and antioxidant enzyme activation. Advances in genomics, metagenomics, transcriptomics, and proteomics have significantly expanded our understanding of plant–microbe molecular communication in the rhizosphere, revealing mechanisms underlying these interactions that promote stress resilience. However, challenges such as inconsistent field performance, knowledge gaps in stress-related molecular signaling, and regulatory hurdles continue to limit broader biostimulant adoption. Despite these challenges, microbial biostimulants hold significant potential for advancing agricultural sustainability, particularly amid climate change-induced stresses. Future studies and innovation, including Clustered Regularly Interspaced Short Palindromic Repeats and other molecular editing tools, should optimize biostimulant formulations and their application for diverse agro-ecological systems. This review aims to underscore current advances, challenges, and future directions in the field, advocating for a multidisciplinary approach to fully harness the potential of biostimulants in modern agriculture. Full article

Antimicrobial resistance (AMR) is an escalating global health threat, often driven by the horizontal gene transfer (HGT) of resistance genes. Detecting AMR genes and understanding their genomic context within bacterial populations is crucial for mitigating the spread of resistance. In this study, we evaluate the performance of three sequence alignment tools—Bandage, SPAligner, and GraphAligner—in identifying AMR gene sequences from assembly and de Bruijn graphs, which are commonly used in microbial genome assembly. Efficiently identifying these genes allows for the detection of neighboring genetic elements and possible HGT events, contributing to a deeper understanding of AMR dissemination. We compare the performance of the tools both qualitatively and quantitatively, analyzing the precision, computational efficiency, and accuracy in detecting AMR-related sequences. Our analysis reveals that Bandage offers the most precise and efficient identification of AMR gene sequences, followed by GraphAligner and SPAligner. The comparison includes evaluating the similarity of paths returned by each tool and measuring output accuracy using a modified edit distance metric. These results highlight Bandage’s potential for contributing to the accurate identification and study of AMR genes in bacterial populations, offering important insights into resistance mechanisms and potential targets for mitigating AMR spread. Full article

Climatic changes and global warming affect the growth, development, and productivity of crops. In this review, we highlight the possible benefits of using innovative breeding techniques like clustered regularly interspaced short palindromic repeats (CRISPRs), exogenous phytohormone-like strigolactones (SLs), nanomaterials (NMs), and beneficial microbial endophytes to address the challenges in sustainable cultivation of horticultural crops. These applications are evaluated by examining how they affect different metabolic, morphological, and biochemical parameters in diverse crops. Endophytes are symbiotic microorganisms and can be used as nematicides for improving crop yield. With an emphasis on quality control, we examined the impacts of applying NMs, a novel family of phytohormones called SLs, and microbial endophytes on horticultural commodities. Furthermore, we reviewed the benefits of CRISPR for the editing of plant genomes, as well as how it affects gene expression and transcription factors to increase crop tolerance and yield. These innovations hold the potential to improve crop yield, quality, and resilience by acting as safe, natural components in biofertilizers and plant protection solutions. Gradually adopting these methods could decrease reliance on agrochemicals, thereby reducing their negative effects on biodiversity, soil fertility, and human health. Full article

Lycopene represents one of the central compounds in the carotenoid pathway and it exhibits a potent antioxidant ability with wide potential applications in medicine, food, and cosmetics. The microbial production of lycopene has received increasing concern in recent years. Corynebacterium glutamicum (C. glutamicum) is considered to be a safe and beneficial industrial production platform, naturally endowed with the ability to produce lycopene. However, the scarcity of efficient genetic tools and the challenge of identifying crucial metabolic genes impede further research on C. glutamicum for achieving high-yield lycopene production. To address these challenges, a novel genetic editing toolkit, CRISPR/MAD7 system, was established and developed. By optimizing the promoter, ORI and PAM sequences, the CRISPR/MAD7 system facilitated highly efficient gene deletion and exhibited a broad spectrum of PAM sites. Notably, 25 kb of DNA from the genome was successfully deleted. In addition, the CRISPR/MAD7 system was effectively utilized in the metabolic engineering of C. glutamicum, allowing for the simultaneous knockout of crtEb and crtR genes in one step to enhance the accumulation of lycopene by blocking the branching pathway. Through screening crucial genes such as crtE, crtB, crtI, idsA, idi, and cg0722, an optimal carotenogenic gene combination was obtained. Particularly, cg0722, a membrane protein gene, was found to play a vital role in lycopene production. Therefore, the CBIEbR strain was obtained by overexpressing cg0722, crtB, and crtI while strategically blocking the by-products of the lycopene pathway. As a result, the final engineered strain produced lycopene at 405.02 mg/L (9.52 mg/g dry cell weight, DCW) in fed-batch fermentation, representing the highest reported lycopene yield in C. glutamicum to date. In this study, a powerful and precise genetic tool was used to engineer C. glutamicum for lycopene production. Through the modifications between the host cell and the carotenogenic pathway, the lycopene yield was stepwise improved by 102-fold as compared to the starting strain. This study highlights the usefulness of the CRISPR/MAD7 toolbox, demonstrating its practical applications in the metabolic engineering of industrially robust C. glutamicum. Full article