Aug 2026· Journal of Pure and Applied Microbiology· 0 citations
TL;DR
The convergence of fungal systems biology with the principles of circular bioeconomy is illustrated and the technological, economic, and regulatory bottlenecks which need to be overcome are pointed out to fully realise the potential of fungi as the biofactories of the future for the sustainable production of energy and materials.
Abstract
Fungal cell factories serve as a robust platform for sustainable biomanufacturing, owing to their unparalleled metabolic diversity, enzymatic properties, and resilience to diverse environmental conditions. Recent advances in fungal biotechnology have vastly enhanced the potential for fungi to be used in the production of renewable bioenergy and functional biomaterials. Concurrent advances in systems biology, metabolic engineering, and synthetic biology have enabled the fine-tuning of metabolic fluxes to facilitate the enhanced biosynthesis of biofuels, including bioethanol, biodiesel, biogas, and biohydrogen, as well as mycelium-derived biopolymers. The lignocellulolytic fungi like Trichoderma reesei, Aspergillus niger, and Phanerochaete chrysosporium have been the main organisms of focus with respect to engineering, which enhances hydrolytic enzyme excretion, growth on substrates, and redox balance in these fungi. This engineering work parallels a new ability in omics technologies and CRISPR–Cas genome editing, permitting the facilitation and identification of regulation of biosynthetic gene clusters responsible for lipid accumulation, secondary metabolite production, and nanomaterial synthesis in fungi. Furthermore, new fungal-derived biomaterials have been reported, such as chitosan, β-glucans, and mycelium composites, which have been advanced as biodegradable alternatives to plastics and building materials derived from petroleum. This review critically reviews some of the more recent developments in respect of the reprogramming of fungal metabolism, process intensification strategies and integrated biorefinery applications. This will illustrate the convergence of fungal systems biology with the principles of circular bioeconomy and point out the technological, economic, and regulatory bottlenecks which need to be overcome to fully realise the potential of fungi as the biofactories of the future for the sustainable production of energy and materials.
Artificial intelligence (AI) and machine learning (ML) have emerged as powerful tools for metabolic engineering by enabling pathway prediction, metabolic flux optimization, enzyme engineering, and identification of bottlenecks throughout terpenoid biosynthesis.
Aakash Kamalesan, K. Kumar, Bharathi Nathan et al.· Antonie van Leeuwenhoek· 0 citations
This review provides the current state of PHAs production from wild yeast strains and the various approaches that have been used to improve yield, and discusses the performance, challenges, and limitations of various synthetic biology and metabolic engineering strategies in yeast strains for PHAs production.
K. Mohanrasu, R. Selvakumar, I. Grainge et al.· International Journal of Bio...· 0 citations
Candida yeasts represent a versatile yet underexploited platform for industrial biotechnology. These yeasts utilize a remarkably broad range of carbon sources, particularly for hydrophobic carbon sources, coupled with robust growth and diverse biosynthetic capacities, making them promising hosts for sustainable production of chemicals, fuels, and proteins. Despite these advantages, industrial deployment of Candida species has been hindered by concerns regarding opportunistic pathogenicity and the historical lack of efficient genetic manipulation tools, leading to a substantial gap between metabolic potential and practical utilization. Recent advances in functional genomics, genome editing, and systems metabolic engineering are rapidly overcoming these barriers, enabling more precise and efficient strain development. In this review, we systematically summarize recent progress in the metabolic engineering of Candida species as microbial cell factories, with particular emphasis on expanding genetic toolkits, utilizting renewable and non-conventional carbon sources, and biosynthesizing high-value compounds. In addition, we propose a biosafety-oriented classification framework to support their safe industrial deployment. Finally, we discuss current challenges and emerging opportunities, emphasizing that the synergy of synthetic biology and artificial intelligence-driven design holds the key to unlocking the biotechnological potential of Candida yeasts.
Bioprocess engineering sits at the interface of biology and chemical engineering and has become a central pillar of the transition towards a low-carbon, circular economy. Over the past decade, advances in strain design, bioreactor engineering, biocatalysis, feedstock diversification, downstream processing and digitalisation have collectively reshaped how biological systems are engineered for industrial production. This review synthesises recent literature on these interconnected domains, with particular emphasis on sustainability outcomes such as reduced water and energy intensity, greenhouse gas mitigation, waste valorisation and circularity of biobased materials. Upstream innovations, including CRISPR-based genome editing, dynamic metabolic control and membrane engineering, have improved the robustness and productivity of microbial cell factories. In parallel, bioreactor engineering has progressed through single-use technologies, continuous and intensified processing and improved oxygen transfer strategies, although trade-offs between operational flexibility and environmental burden remain contested. Biocatalysis has matured through advances in enzyme immobilisation, enabling greener, more selective and reusable industrial catalysts. Feedstock diversification towards lignocellulosic residues, gaseous one-carbon substrates and microalgal biomass has expanded the substrate base available to fermentation industries, while precision fermentation and polyhydroxyalkanoate biosynthesis illustrate the growing convergence between food, materials and waste-valorisation sectors. Digital tools, including process analytical technology, machine learning and digital twins, are increasingly embedded within what is termed Bioprocessing 4.0, offering real-time control and predictive optimisation. This review draws on close to thirty peer-reviewed sources published within the last decade to critically appraise these developments, identify persistent technical and economic bottlenecks and outline priorities for future research. The evidence indicates that sustainable bioprocess engineering is no longer a peripheral consideration but a defining criterion against which new bioprocesses must be evaluated.
Vasudevan Ranganathan, M. Sreeja, A. Gunasri et al.· Journal of Applied Life Scie...· 0 citations
The sustainable bioeconomy fundamentally relies on the effective valorization of lignocellulosic biomass into renewable fuels and high-value biochemicals. Although extensive research has been conducted over several decades, commercialization remains hindered by enzyme instability, low catalytic efficiency, high production costs, and the intrinsic recalcitrance of biomass. While previous reviews have separately discussed lignocellulolytic enzymes, biomass conversion, or circular bioeconomy strategies, comprehensive integration of recent molecular, microbial, and process-engineering advancements remains limited. Therefore, this review provides a multidisciplinary perspective integrating enzyme engineering, microbial co-culturing, heterologous gene expression, advanced biomass pretreatment, and bioprocess optimization within a unified biorefinery framework. The review critically links molecular-level improvements, including protein engineering, codon optimization, and thermostability enhancement, with industrial process strategies such as consolidated bioprocessing, consolidated bio-saccharification, and techno-economic optimization. Emerging approaches including CRISPR/Cas9-mediated strain improvement, artificial cellulosomes, nanobiotechnology, and AI-assisted modeling are discussed as supportive tools for improving biomass conversion efficiency and industrial applicability. In addition, major bottlenecks such as enzyme instability, biomass recalcitrance, and process incompatibilities are critically evaluated along with recent strategies to overcome these limitations. By integrating molecular biology, microbial engineering, and process-level innovations, this review provides a comprehensive framework for the development of sustainable and scalable lignocellulosic biorefineries supporting the circular bioeconomy.
Diterpenoids are natural compounds composed of four isoprene units. They possess diverse biological activities and widespread applications in the cosmetics, food additives and pharmaceutical. With the rapid advancement of synthetic biology, the biomanufacturing of diterpenoids via microbial metabolism has witnessed substantial advancements. Microbial chassis such as Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica and Rhodosporidium toruloides, have been successfully engineered to enable efficient biosynthesis of these compounds, thereby demonstrating substantial potential for industrial-scale applications. In this review, the construction of diterpenoid biosynthetic pathways in microbial cell factories is summarized. The research progress and engineering strategies for efficient microbial synthesis of diterpenoids are discussed, and the key challenges and future directions facilitating the design of high-yield diterpenoid production platforms and their translation into industrial practice are explored.
Yuting Han, Yuanhe Luo, Kaifeng Wang et al.· Bioresources and Bioprocessi...· 0 citations