“In silico organisms” are computational genome-scale metabolic models used in systems and synthetic biology developed by constraint-based metabolic simulations using multi-omics and phenotypic data. The quality of these models is hidden because of the limited availability of genomic information and genome-scale metabolic reconstruction methods. In this review, 237 manually curated genome-scale models for various organisms with industrial and clinical significance were comprehensively reviewed, and their modelling information was tabulated based on literature. This review provides a comprehensive summary of potential applications of systems biology in biotechnology and biomedical research. Their broad applicability has been explored in the process of model improvement and design of experiments in metabolic design and drug development. This review summarizes their recent advances, challenges, and practical applications in Gram-negative bacteria, Gram-positive bacteria, archaea, fungi, algae, plants, and animals. Genome-scale models of microbes have been reviewed to address their various applications in metabolic systems engineering, strain optimization, bioremediation, biomanufacturing, and personalized systems medicine. Several models have been explored to understand the molecular mechanisms underlying pathogenesis, virulence, host-microbe interactions, and metabolic crosstalk. This review provides an overview of the current knowledge on human metabolic reconstructions and their important roles in human, microbiota-related, and complex metabolic disorders. Genome-scale models of human and animal metals offer ethical alternatives to the traditional animal testing methods. Current progress in systems biology research will lead to the development of indispensable databases, computational tools, and analytical platforms. This will strengthen data-driven discovery and facilitate integration of biological information into living systems.

Amidst the ever-evolving landscape of cosmetics, algae and their derived products have captured substantial worldwide interest, heralding a new era of innovation and sustainability in beauty products. Cosmetic formulations are witnessing an escalating incorporation of extracts from algal biomass owing to the diverse metabolites making them ideal for studying physiologically active components with unique biochemical properties. The concept of algal biorefinery plays a pivotal role in this context, as it integrates processes to convert algal biomass into a spectrum of valuable products, maximizing resource efficiency and sustainability. Research has proven that the rich and diverse pool of bioactive compounds in algae holds promise for novel nutraceutical, pharmaceutical, and cosmeceutical products. In marine brown algae, compounds like fucoxanthin, polysaccharides, MAAs, and phlorotannins have a variety of functions to combat ultraviolet radiation and protect human skin. Phlorotannins, for instance, contribute to sunscreen and antioxidant properties. The sea environment, teeming with physiologically essential substances, provides an array of cosmeceutical ingredients. Algae also house nutraceutical compounds like polyphenols, carotenoids, fucoidan, alginate, peptides, terpenoids, and polyunsaturated fatty acids, engaging in various biological activities. Algal compounds are emerging as viable alternatives, showcasing beneficial effects even with prolonged use and diverse algae species find widespread application in addressing skin disorders, serving as moisturizers, texture enhancers, sunscreens, and anti-wrinkling agents. This review delves into the bioactive components sourced from algae, especially seaweed and diatoms, unveiling their potential in anti-aging, photo-protection, and skin whitening. The discourse encompasses current applications, challenges, and prospects, highlighting the role of algal biorefinery in providing a sustainable and innovative future for skincare solutions.

The present study was conducted to explore the growth dynamics and nutraceutical potential of the diatom Nitzschia sp. isolated from a freshwater sample collected from Uttarakhand, India, which is a high-altitude environment. This aspect is particularly noteworthy because high-altitude diatoms are subject to unique environmental conditions that can influence their biochemical and metabolic activities and this aspects were rarely studied in diatoms. The highest biomass productivity attained was 0.5 mg mL⁻¹ when the culture was grown for 15 days. The biochemical protein content was measured as 15.7 mg g⁻¹, carbohydrate content as 76.6 mg g⁻¹, and total chlorophyll content was 87.3 mg g⁻¹. Secondary metabolite screening shows the total flavonoid content as 0.63 mg g⁻¹ and tocopherol content as 0.60 mg g⁻¹. The fatty acid profile shows the monounsaturated fatty acids (MUFA) to be the highest at 56.37%. This study demonstrates the adaptability of diatoms and could offer a helpful vision for future species-specific selection for the mass production of metabolites with potential health benefits, such as fucoxanthin (Fx), docosahexaenoic acid (DHA), and eicosapentaenoic acid (EPA).

Cotton waste fabrics are currently preferred over lignocellulose feedstocks for the production of bioethanol due to presence of higher percentage of cellulose and lower percentage of hemicellulose and lignin. Aspergillus sp. with ability of secreting cellulase enzyme has converted pre-treated lignocellulosic biomass into bioethanol via solid state fermentation process. In this study, A. terreus MZ769058 as new fungal strain had showed significant production of bioethanol by anaerobic fermentation of pre-treated cotton fabrics waste. This fungal strain was immobilized using sodium alginate entrapment methodology. The production of ethanol was estimated as 58.06 g/l via solid state fermentation process of media supplemented with 1.5 g cotton fabrics after inoculation with immobilized beads of A. terreus MZ769058. The production of ethanol was enhanced by 1.03 times after optimization of fermentative condition with immobilized cell beads. Response surface methodology was applied for optimization of parameters such as media pH (1.5–9.5), temperature (20–60 °C), fermentation time (24–72 h), and number of immobilization beads (5–25). Regression analysis with 99.43% value of coefficient of determination (R²) had confirmed the quadratic model for these variables. The interactive effects of variables were studied by contour plots and response surface plots. The predicted yield of bioethanol was further validated by performing experiment of solid-state fermentation process under the optimized predicted variables at pH (5.5), temperature (30 °C), fermentation time period (48 h) and immobilized beads (20). The production of bioethanol was enhanced up to 60.02 g/l under these optimum variables. The product of ethanol was further characterised using Fourier transform infrared (FTIR) spectroscopy. FTIR analysis had confirmed aromatic skeleton vibration in C-O stretching with the functional group at 1007.28, 1069.92, 1122.85 1636.60 and 855.29 cm^{− 1}. The acetyl group in hemicellulose’s molecules with C-H and C-O stretching had been also confirmed with peak at 1381.56 cm^{− 1} and 1122.85 cm^{− 1}. The immobilized beads of this new fungal strain could be used efficiently for production of ethanol in media supplemented with cotton waste fabrics at large scale in industrial sector in future.

The search for environment-friendly and sustainable techniques like microbial enzymatic treatment for processing of natural fibers outcompete traditional techniques of using harsh chemicals and environmental pollution. This investigation explores the application of microbial enzymes in enhancing the quality of banana pseudo-stem fibers. Solid-state fermentation was systematically optimized for the synthesis of pectinase, xylanase, and laccase, utilizing the previously isolated strains Aspergillus niger SKN1 and Pycnoporus sanguineus SKS1. The sequential enzymatic treatment demonstrated substantial degumming efficiency, evident in a reduction of weight (22.6%), moisture sorption (16.83%), and fiber diameter in comparison to the control. Additionally, a noteworthy decline in pectin (73.75%), xylan (61.9%), and lignin (52.3%) content was observed in the enzyme-treated fibers relative to the control. Moreover, scanning electron microscopy confirmed the efficiency of the synergistic enzymatic treatment. The sequential enzymatic treatment exhibited promising potential to transform crude banana fibers into textile-grade fibers, offering an alternative resource for the textile industry.

The aim of this research work was to evaluate the potential of Bacillus velezensis for proteases production by employing eggshells and egg membrane powder as substrate followed by statistical optimization via RSM. While, optimizing the physical parameters maximum protease production was observed at incubation period of 72-h, inoculum size of 2% and substrate concentration of 1.5%. Optimization of nutritional parameters was done through PBD by running 12 experiments, among 7 screened factors (Glucose, peptone, KH₂PO₄, MgSO₄, NaCl, CaCl₂ and yeast extract), 2 factors (Glucose and CaCl₂) was found significant. Significant factors were further optimized through CCD and statistical analysis of results were also performed by running 2-Factor ANOVA. Maximum protease activity of 301.0010 U/mlU/ml was observed. Then, enzyme characterization revealed maximum protease activity at 45 ˚C, pH-8, with highest thermal stability at 60 ˚C. Furthermore, effects of metal ions (Ca^{+ 2}, Cu^{+ 2}, Mn^{+ 2}, Mg^{+ 2}, K⁺, Na⁺) on protease activity was also evaluated and results have shown Cu^{+ 2} ions increase protease activity up-to 100-folds while Na⁺, Mg^{+ 2} and Mn^{+ 2} ions enhanced protease activity by 103.40, 115.42 and 106.01% respectively. The produced protease could be investigated further for potential application as excellent stain remover.

Neomycin, a crucial aminoglycoside antibiotic, is primarily biosynthesized by Streptomyces fradiae through fermentation. Its widespread applications encompass disease management in crops, treatment of bacterial infections in respiratory and gastrointestinal tracts, among other domains, leading to substantial market demand. Increasing evidence underscores the pivotal role of transcription factors in microbial metabolic regulation, orchestrating the coordinated expression of multiple genes in specific pathways. This orchestration holds the potential to enhance engineered microbial strains, thereby facilitating the precise and efficient synthesis of neomycin. Leveraging transcriptomic analyses of the wild-type strain SF-1 and the mutation-derived high-yield strain SF-2, this study identified significant variations in the expression levels of seven transcription factors. By constructing recombinant strains overexpressing these seven transcription factors, the optimal factor NecR, influencing neomycin production, was pinpointed. Further, promoter optimization was employed to augment neomycin synthesis. Under shaken flask cultivation conditions, the titer of neomycin B reached 11,546 U/mL, marking a 23% enhancement over the mutation-derived high-yield strain SF-2. The in vivo fluorescence reporter gene characterization using EMSA binding revealed that NecR can bind to the promoter region of neoS, thereby enhancing the transcriptional levels of neoS, subsequently promoting neomycin synthesis. This investigation not only furnishes pivotal insights for the construction of high-yield neomycin-producing strains but also elucidates the central role of transcription factors in microbial metabolic regulation. This revelation is poised to offer novel avenues and strategies in the realm of microbial metabolic engineering, holding promise for significant breakthroughs in antibiotic production and other bioproduct synthesis domains.