Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology

Harnessing the power of microbial consortia for the biodegradation of per- and polyfluoroalkyl substances: Challenges and opportunities

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental pollutants that pose significant risks to human health and ecosystems owing to their widespread use and resistance to degradation. This study examines the potential of microbial consortia as a sustainable and effective strategy for biodegrading PFAS. It highlights how these complex communities interact with various PFAS, including perfluorocarboxylic acids, perfluorosulfonic acids, fluorotelomer alcohols, and fluorotelomer-based precursors. Despite the potential of microbial consortia, several challenges impede their application in PFAS remediation, including effective microbial species identification, inherent toxicity of PFAS compounds, co-contaminants, complications from biofilm formation, diversity of environmental matrices, and competition with native microbial populations. Future research should focus on refining characterization techniques to enhance our understanding of microbial interactions and functions within consortia. Integrating bioinformatics and system biology will enable a comprehensive understanding of microbial dynamics and facilitate the design of tailored consortia for specific PFAS compounds. Furthermore, field applications and pilot studies are essential for assessing the real-world effectiveness of microbial remediation strategies. Ultimately, advancing our understanding and methodologies will lead to efficient biodegradation processes and positioning microbial consortia as viable solutions for PFAS-contaminated environments.

A novel four-species microbial consortium for nutritional value improvement of rapeseed meal

This study explores the potential of artificial microbial consortia to enhance rapeseed meal nutritional value. A novel four-species microbial consortium consisting of Bacillus subtilis, Lactobacillus plantarum and two screened glucosinolates-degradation strains Erwinia tasmaniensis and Enterococcus gallinarum was constructed for nutritional value improvement in rapeseed meal. Results demonstrated significant reductions in the concentrations of glucosinolates (86.08 %), phytic acid (59.41 %), 5-vinyl-1,3-oxazolidine-2-thione (94.40 %), tannins (73.88 %), and fiber (58.69 %). The crude protein and total amino acids concentrations were elevated by 0.46-fold and 1.22-fold higher compared to unfermented rapeseed meal. Comparative analysis revealed that fermented rapeseed meal exhibited superior crude protein digestibility, total amino acids content, and essential amino acids profile compared to six commercial products. Moreover, the fermentation of rapeseed meal significantly increased the abundance and concentration of volatile substances, thereby enhancing its sensory attributes. This research provides a promising strategy for the rapeseed meal valorization in feed industry.

Designing synthetic microbial communities with the capacity to upcycle fermentation byproducts to increase production yields

Microbial cell factories, which convert feedstocks into a product of value, have the potential to help transition toward a bio-based economy with more sustainable ways to produce food, fuels, chemicals, and materials. One common challenge found in most bioconversions is the co-production, together with the product of interest, of undesirable byproducts or overflow metabolites. Here, we designed a strategy based on synthetic microbial communities to address this issue and increase overall production yields. To achieve our goal, we created a Yarrowia lipolytica co-culture comprising a wild-type (WT) strain that consumes glucose to make biomass and citric acid (CA), and an 'upcycler' strain, which consumes the CA produced by the WT strain. The co-culture produced up to two times more β-carotene compared with the WT monoculture using either minimal medium or hydrolysate. The proposed strategy has the potential to be applied to other bioprocesses and organisms.

Rational metabolic engineering of Escherichia coli for the industrial-scale production of l-phenylalanine

Rational metabolic engineering has numerous applications in the optimization of microorganisms for the production of valuable compounds at the laboratory-scale. However, the existing strategies and tools are far from sufficient for engineering of industrial strains due to their specificity. The aim of this project was to implement novel strategies to enhance industrial l-phenylalanine (l-PHE) production and yield, including the regulation of key gene expressions, modifications of global transcription factors, creation of NADPH-independent pentose phosphate pathway and pyruvate-oxaloacetate-phosphoenolpyruvate cycle. The project also involved the identification and engineering of novel byproduct pathways and the development of a tyrosine-nonauxotrophic strain. Through comprehensive rational engineering, an industrial l-PHE producer, designated PHE17, achieved the highest production (103.15 g/L) and yield (0.229 g/g) of l-PHE reported thus far. This study also represents the first report on the iterative engineering of industrial l-PHE producers, thereby offering great significance for the engineering of other aromatic animo acids-producing strains.

Hyper-porous encapsulation of microbes for whole cell biocatalysis and biomanufacturing

Biocatalysis using whole cell biotransformation presents an alternative approach to producing complex molecules when compared to traditional synthetic chemical processes. This method offers several advantages, including scalability, self-contained co-factor recycling systems, the use of cost-effective raw materials, and reduced purification costs. Notably, biotransformation using microbial consortia provides benefits over monocultures by enhancing biosynthesis efficiency and productivity through division of labor and a reduction in metabolic burden. However, reliably controlling microbial cell populations within a consortium remains a significant challenge. In this work, we address this challenge through mechanical constraints. We describe the encapsulation and immobilization of cells in a hyper-porous hydrogel block, using methods and materials that are designed to be amenable to industrial scale-up. The porosity of the block provides ample nutrient access to ensure good cell viability, while the mechanical properties of the hydrogel matrix were optimized for Escherichia coli encapsulation, effectively limiting their proliferation while sustaining recombinant protein production. We also demonstrated the potential of this method for achieving stable co-cultivation of microbes by maintaining two different microbial strains spatially in a single porous hydrogel block. Finally, we successfully applied encapsulation to enable biotransformation in a mixed culture. Unlike its non-encapsulated counterpart, encapsulated E. coli expressing RadH halogenase achieved halogenation of the genistein substrate in a co-culture with genistein-producing Streptomyces. Overall, our strategy of controlling microbial cell populations through physical constraints offers a promising approach for engineering synthetic microbial consortia for biotransformation at an industrial scale.

Single-Cell Analysis of Microbial Degradation Mechanisms and Remediation Potential for Emerging Pollutants: A Case Study on Methylnaphthalene

Polycyclic aromatic hydrocarbon (PAH) derivatives, including alkyl-PAHs, are significant emerging environmental contaminants. Traditional culture techniques often fail to isolate functional microorganisms responsible for their in situ degradation, leaving their metabolic interactions and pathways largely uncharacterized. This study employs 2-methylnaphthalene (MP) as a model compound and utilizes Raman-activated cell sorting with stable isotope probing (RACS-SIP) and single-cell genome sequencing to investigate alkyl-PAH degradation in petroleum-contaminated wastewater. RACS-SIP identified two key in situ MP-degrading microbes, Sphingomonas sp. and Pseudomonas sp., showing Raman shifts from 1001 to 968 cm-1 and 782 to 768 cm-1. Genome analysis linked these microorganisms to their specific genes and metabolic pathways, revealing distinct degradation mechanisms: Sphingomonas sp. hydroxylates nonmethyl-substituted aromatic rings, while Pseudomonas sp. utilizes both hydroxylation and methyl end oxidation. These findings were substantiated by functional gene quantification, emphasizing the potential of microbial consortia with diverse metabolic pathways to enhance degradation efficiency through cooperative interactions and reduced metabolic load. Moreover, the successful cultivation of RACS-sorted bacteria demonstrated superior pollutant removal compared to traditional methods. This study advances our understanding of microbial biotransformation of emerging contaminants and demonstrates the necessity of precisely identifying and cultivating in situ functional microorganisms to develop robust consortia for sustainable pollutant degradation.

Harnessing microbial co-culture to increase the production of known secondary metabolites

Covering: 2019 to 2024Secondary metabolites (SMs) are naturally occurring defense or signaling molecules that are also utilized as human and animal drugs, crop protection agents, and fine chemicals. Currently, SMs are primarily produced in monoculture settings, devoid of the intricate microbial interactions found in natural environments. Monoculture may lead to the silencing of gene clusters, requiring various genetic or bioprocess strategies to activate the biosynthesis of the corresponding metabolites. Less considered is the effect of monoculture on the efficiency of the production of important, known SMs during microbial fermentations. Co-culturing aims to mimic the complexity of natural microbial habitats, thus may increase the titer, the rate and/or the yield of fermentations. This review summarizes the progress in utilizing co-culture to promote the synthesis of known SMs by describing the types of various microbial co-cultures, listing the mechanisms for enhancing the biosynthesis of SMs, and navigating the challenges and strategies for applying such an approach in the biotechnology industries.

A new flavor of synthetic yeast communities sees the light

No organism is an island: organisms of varying taxonomic complexity, including genetic variants of a single species, can coexist in particular niches, cooperating for survival while simultaneously competing for environmental resources. In recent years, synthetic biology strategies have witnessed a surge of efforts focused on creating artificial microbial communities to tackle pressing questions about the complexity of natural systems and the interactions that underpin them. These engineered ecosystems depend on the number and nature of their members, allowing complex cell communication designs to recreate and create diverse interactions of interest. Due to its experimental simplicity, the budding yeast Saccharomyces cerevisiae has been harnessed to establish a mixture of varied cell populations with the potential to explore synthetic ecology, metabolic bioprocessing, biosensing, and pattern formation. Indeed, engineered yeast communities enable advanced molecule detection dynamics and logic operations. Here, we present a concise overview of the state-of-the-art, highlighting examples that exploit optogenetics to manipulate, through light stimulation, key yeast phenotypes at the community level, with unprecedented spatial and temporal regulation. Hence, we envision a bright future where the application of optogenetic approaches in synthetic communities (optoecology) illuminates the intricate dynamics of complex ecosystems and drives innovations in metabolic engineering strategies.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

Challenging the impact of consortium diversity on bioaugmentation efficiency and native bacterial community structure in an acutely PAH-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are priority pollutants. We studied the effect of bioaugmentation using three allochthonous bacterial consortia with increasing diversity: SC AMBk, SC1, and SC4, on the structure and functionality of an artificially and acutely PAH-contaminated soil microbiome. The PAH supplementation increased substrate availability, allowing the inocula to efficiently degrade the supplemented PAHs after 15 days of incubation, become temporarily established, and modify the number of total interactions with soil residents. Sphingobium and Burkholderia, both members of the inoculants, were the major contributors to functional KOs (KEGG orthologs) linked to degradation and were differentially abundant genera in inoculated microcosms, indicating their competitiveness in the soil. Hence, bioaugmentation efficiency relied on them, while further degradation could be carried out by native microorganisms. This is one of the first studies to apply three inocula, designed from naturally occurring bacteria, and to study their effect on the soil's native community through ANCOM-BC. We revealed that when a resource that can be used by the inoculant is added to the soil, a high-diversity inoculant is not necessary to interact with the native community and establish itself. This finding is crucial for the design of microbiome engineering in bioremediation processes.

Towards microbial consortia in fermented foods for metabolic engineering and synthetic biology

The fermented foods microbiota, whose community structures evolve through a succession of different microbial groups, play a central role in fermented food production. The texture and flavor, functions, shelf-life and safety, are largely determined by the interactions among bacteria and yeast within these communities. Although much indispensable work has described the microbial composition and succession in various fermentation foods, yet the specific microbial interactions involved are not well understood. Here, we review the current mechanisms of microbial interactions (amensalism, competition, commensalism, and mutualism) existed in the fermented foods. We also examine the function of these interactions. In addition, we provide our perspectives on the future development of functional and novel fermented foods by combining the new starter cultures with the native microbial consortia and applications of these stable and robust microbial consortia for metabolic engineering and synthetic biology.

Design and regulation of engineered bacteria for environmental release

Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks.

Modular metabolic flux control for kick-starting cascade catalysis through engineering customizable compartment

Microbial compartment provides a promising approach for achieving high-valued chemical biosynthesis from renewable feedstock. However, volatile precursor could be utilized by pathway enzyme, which may hinder and adverse the cascade catalysis within microbial cell factory. Here, a customizable compartment was developed for pathway sequestration using spatially assembled cascade catalysis reaction. Firstly, a phase separation protein was designed to form the intracellular protein condensates, facilitating the construction of a customizable compartment in Escherichia coli. Subsequently, modular assembly and recruitment of customizable compartment were achieved through using a short peptide interaction pair to cluster enzymes or fuse them directly. Finally, the 2'-fucosyllactose (2'-FL) salvage pathway was heterogeneously expressed in microorganisms as a stable targeted chemical and proof-of-concept model, the results showed that anchoring various enzymes required for the 2'-FL cascade catalysis pathway within the customizable compartment created a multiple enzyme condensate system, resulting an improvement of 2'-FL titer compared to both wild type and optimized free enzymes reaction. These findings illustrating an effectively cascade catalysis model that increasing titer and kick-starting metabolic flux control through co-localizing multiple enzymes condensate within microbial cell factories.

Automated adjustment of metabolic niches enables the control of natural and engineered microbial co-cultures

Much attention has focused on understanding microbial interactions leading to stable co-cultures. In this work, substrate pulsing was performed to promote better control of the metabolic niches (MNs) corresponding to each species, leading to the continuous co-cultivation of diverse microbial organisms. We used a cell-machine interface, which allows adjustment of the temporal profile of two MNs according to a rhythm, ensuring the successive growth of two species, in our case, a yeast and a bacterium. The resulting approach, called 'automated adjustment of metabolic niches' (AAMN), was effective for stabilizing both cooperative and competitive co-cultures. AAMN can be considered an enabling technology for the deployment of co-cultures in bioprocesses, demonstrated here based on the continuous bioproduction of p-coumaric acid. The data accumulated suggest that AAMN could be used not only for a wider range of biological systems, but also to gain fundamental insights into microbial interaction mechanisms.

Microbial Synthesis of Nucleosides: Advances and Prospects

Nucleosides and its derivatives are essential chemicals with extensive applications in the food, agricultural, and pharmaceutical industries. Chemical synthesis of these compounds often faces problems such as harsh reaction conditions and environmental pollution, whereas microbial synthesis provides a promising and sustainable alternative. This review discusses recent advances in the biosynthesis of nucleosides and their derivatives. It begins by discussing the biosynthetic pathways and metabolic regulatory systems found in bacteria such as Escherichia coli and Bacillus subtilis. Further, the progress on microbial production of various nucleosides is summarized, focusing on the strategies applied to optimize their synthesis such as feedback inhibition relief, enzyme engineering, and dynamic control. The review finishes with a discussion of the challenges and opportunities for efficient synthesis of nucleosides and their derivatives.

Microbial engineering for monocyclic aromatic compounds production

Aromatic compounds serve pivotal roles in plant physiology and exhibit antioxidative and antimicrobial properties, leading to their widespread application, such as in food preservation and pharmaceuticals. However, direct plant extraction and petrochemical synthesis often struggle to meet current needs due to low yield or facing economic and environmental hurdles. In the past decades, systems metabolic engineering enabled eco-friendly production of various aromatic compounds, with some reaching industrial levels. In this review, we highlight monocyclic aromatic chemicals, which have relatively simple structures and are currently the primary focus of microbial synthesis research. We then discuss systems metabolic engineering at the enzyme, pathway, cellular, and bioprocess levels to improve the production of these chemicals. Finally, we overview the current limitations and potential resolution strategies, aiming to provide reference for future studies on the biosynthesis of aromatic products.

Microbial adaptation and genetic modifications for enhanced remediation in low-permeability soils

Low-permeability soils, characterized by fine texture and high clay content, pose significant challenges to traditional soil remediation techniques due to limited hydraulic conductivity, restricted nutrient flow, and reduced oxygen availability. These unique properties enable low-permeability soils to function as natural barriers in environmental protection; however, they also trap contaminants, making traditional remediation efforts challenging. This review synthesizes current knowledge on microbial adaptation and genetic engineering approaches that enhance the effectiveness of bioremediation in such environments. Key microbial adaptations, including anaerobic metabolism, extracellular enzyme production, and stress response mechanisms, allow individual microbes to adapt in low-permeability soils. Additionally, community-level strategies like microhabitat creation, biofilm formation, and functional redundancy further support microbial resilience. Advancements in genetic engineering now enable the modification of microbial traits-such as soil adhesion, nutrient utilization, and stress tolerance-to enhance bioremediation efficacy. Synthetic biology techniques further allow for the design of tailored microbial consortia that work cooperatively to degrade contaminants in complex soil matrices. This review highlights the integration of microbial and genetic engineering strategies, offering a comprehensive overview that informs current practices and guides future research in low-permeability soil remediation.

Harnessing Microbial Signal Transduction Systems in Natural and Synthetic Consortia for Biotechnological Applications

Signal transduction is crucial for communication and cellular response in microbial communities. Consortia rely on it for effective communication, responding to changing environmental conditions, establishing community structures, and performing collective behaviors. Microbial signal transduction can be through quorum sensing (QS), two-component signal transduction systems, biofilm formation, nutrient sensing, chemotaxis, horizontal gene transfer stress response, and so forth. The consortium uses small signaling molecules in QS to regulate gene expression and coordinate intercellular communication and behaviors. Biofilm formation allows cells to adhere and aggregate, promoting species interactions and environmental stress resistance. Chemotaxis enables directional movement toward or away from chemical gradients, promoting efficient resource utilization and community organization within the consortium. In recent years, synthetic microbial consortia have gained attention for their potential applications in biotechnology and bioremediation. Understanding signal transduction in natural and synthetic microbial consortia is important for gaining insights into community dynamics, evolution, and ecological function. It can provide strategies for biotechnological innovation for enhancing biosensors, biodegradation, bioenergy efficiency, and waste reduction. This review provides compelling insight that will advance our understanding of microbial signal transduction dynamics and its role in orchestrating microbial interactions, which facilitate coordination, cooperation, gene expression, resource allocation, and trigger specific responses that determine community success.

Synthetic Ecosystems: From the Test Tube to the Biosphere

The study of ecosystems, both natural and artificial, has historically been mediated by population dynamics theories. In this framework, quantifying population numbers and related variables (associated with metabolism or biological-environmental interactions) plays a central role in measuring and predicting system-level properties. As we move toward advanced technological engineering of cells and organisms, the possibility of bioengineering ecosystems (from the gut microbiome to wildlands) opens several questions that will require quantitative models to find answers. Here, we present a comprehensive survey of quantitative modeling approaches for managing three kinds of synthetic ecosystems, sharing the presence of engineered strains. These include test tube examples of ecosystems hosting a relatively low number of interacting species, mesoscale closed ecosystems (or ecospheres), and macro-scale, engineered ecosystems. The potential outcomes of synthetic ecosystem designs and their limits will be relevant to different disciplines, including biomedical engineering, astrobiology, space exploration and fighting climate change impacts on endangered ecosystems. We propose a space of possible ecosystems that captures this broad range of scenarios and a tentative roadmap for open problems and further exploration.

Strategies and tools to construct stable and efficient artificial coculture systems as biosynthetic platforms for biomass conversion

Inspired by the natural symbiotic relationships between diverse microbial members, researchers recently focused on modifying microbial chassis to create artificial coculture systems using synthetic biology tools. An increasing number of scientists are now exploring these systems as innovative biosynthetic platforms for biomass conversion. While significant advancements have been achieved, challenges remain in maintaining the stability and productivity of these systems. Sustaining an optimal population ratio over a long time period and balancing anabolism and catabolism during cultivation have proven difficult. Key issues, such as competitive or antagonistic relationships between microbial members, as well as metabolic imbalances and maladaptation, are critical factors affecting the stability and productivity of artificial coculture systems. In this article, we critically review current strategies and methods for improving the stability and productivity of these systems, with a focus on recent progress in biomass conversion. We also provide insights into future research directions, laying the groundwork for further development of artificial coculture biosynthetic platforms.

Rapid screening of indigenous degrading microorganisms for enhancing in-situ bioremediation of organic pollutants-contaminated soil

Organic pollutants (OPs) have caused severe environmental contaminations in the world and aroused wide public concern. Autochthonous bioaugmentation (ABA) is considered a reliable bioremediation approach for OPs contamination. However, the rapid screening of indigenous degrading strains from in-situ environments remains a primary challenge for the practical application of ABA. In this study, 3,5,6-Trichloro-2-pyridinol (TCP, an important intermediate in the synthesis of various pesticides) was selected as the target OPs, and DNA stable isotope probing (DNA-SIP) combined with high-throughput sequencing was employed to explore the rapid screening of indigenous degrading microorganisms. The results of DNA-SIP revealed a significant enrichment of OTU557 (Cupriavidus sp.) in the 13C-TCP-labeled heavy DNA fractions, indicating that it is the key strain involved in TCP metabolism. Subsequently, an indigenous TCP degrader, Cupriavidus sp. JL-1, was rapidly isolated from native soil based on the analysis of the metabolic substrate spectrum of Cupriavidus sp. Furthermore, ABA of strain JL-1 demonstrated higher remediation efficacy and stable survival compared to the exogenous TCP-degrading strain Cupriavidus sp. P2 in in-situ TCP-contaminated soil. This study presents a successful case for the rapid acquisition of indigenous TCP-degrading microorganisms to support ABA as a promising strategy for the in-situ bioremediation of TCP-contaminated soil.

Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine

Over recent years, studies on microbiota research and synthetic biology have explored novel approaches microbial manipulation for therapeutic purposes. However, fragmented information is available on this aspect with key insights scattered across various disciplines such as molecular biology, genetics, bioengineering, and medicine. This review aims to the transformative potential of synthetic biology in advancing microbiome research and therapies, with significant implications for healthcare, agriculture, and environmental sustainability. By merging computer science, engineering, and biology, synthetic biology allows for precise design and modification of biological systems via cutting edge technologies like CRISPR/Cas9 gene editing, metabolic engineering, and synthetic oligonucleotide synthesis, thus paving the way for targeted treatments such as personalized probiotics and engineered microorganisms. The review will also highlight the vital role of gut microbiota in disorders caused by its dysbiosis and suggesting microbiota-based therapies and innovations such as biosensors for real-time gut health monitoring, non-invasive diagnostic tools, and automated bio foundries for better outcomes. Moreover, challenges including genetic stability, environmental safety, and robust regulatory frameworks will be discussed to understand the importance of ongoing research to ensure safe and effective microbiome interventions.

Characterizing A21: Natural Cyanobacteria-Based Consortium with Potential for Steroid Bioremediation in Wastewater Treatment

Microalga-bacteria consortia are increasingly recognized for their effectiveness in wastewater treatment, leveraging the metabolic synergy between microalgae and bacteria to enhance nutrient removal and overall treatment efficiency. These systems offer a sustainable approach to addressing pollutants such as nitrogen and phosphorus. However, their potential in removing specific contaminants like steroid hormones is less explored. In this study, a natural microbial consortium, A21, has been characterized and isolated from primary sewage treatment in Madrid and its potential for bioremediation of steroid hormone effluents has been evaluated. The A21 consortium includes Alphaproteobacteria genera Sphingopyxis and Pseudorhizobium and the Cyanobacterium Cyanobium. Sphingopyxis (31.78%) is known for biodegradation, while Pseudorhizobium (15.68%) exhibits detoxification abilities. Cyanobium (14.2%) may contribute to nutrient uptake and oxygen production. The effects of pH, nitrogen sources, and Sodium chloride concentrations on growth were evaluated. The optimal growth conditions were determined to be a pH range of 7 to 9, a salt concentration below 0.1 M, and the presence of a nitrogen source. The consortium also demonstrated effective growth across various types of wastewaters (primary, secondary, and tertiary treatment effluents). Additionally, A21 exhibited the ability to grow in the presence of steroids and transform them into other compounds, such as converting androstenedione (AD) into androsta-1,4-diene-3,17-dione (ADD) and β-estradiol into estrone.

Key amino acid residues govern the substrate selectivity of the transporter Xltr1p from Trichoderma reesei for glucose, mannose, and galactose

This research identified four amino acid residues (Leu174, Asn297, Tyr301, and Gln291) that contribute to substrate recognition by the high-affinity glucose transporter Xltr1p from Trichoderma reesei. Potential hotspots affecting substrate specificity were selected through homology modeling, evolutionary conservation analyses, and substrate-docking modeling of Xltr1p. Variants carrying mutations at these hotspots were subsequently obtained via in silico screening. Replacement of Leu174 or Asn297 in Xltr1p with alanine resulted in loss of hexose transport activity, indicating that Leu174 and Asn297 play essential roles in hexose transport. The Y301W variant exhibited accelerated mannose transport, but lost galactose transport capacity, and mutation of Gln291 to alanine greatly accelerated mannose transport. These results suggest that amino acids located in transmembrane α-helix 7 (Asn297, Tyr301, and Gln291) play critical roles in substrate recognition by the hexose transporter Xltr1p. Our results will help expand the potential applications of this transporter and provide insights into the mechanisms underlying its function and specificity.

A systematic discussion and comparison of the construction methods of synthetic microbial community

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.

Prospects of formamide as nitrogen source in biotechnological production processes

This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.

A simple model and rules for the evolution of microbial mutualistic symbiosis with positive fitness feedbacks

The evolution of microbe-microbe mutualistic symbiosis is considered to be promoted by repeated exchanges of fitness benefits, which can generate positive fitness feedbacks ('partner fidelity feedback') between species. However, previous evolutionary models for mutualism have not captured feedback dynamics or coupling of fitness between species. Here, a simple population model is developed to understand the evolution of mutualistic symbiosis in which two microbial species (host and symbiont) continuously grow and exchange fitness benefits to generate feedback dynamics but do not strictly control each other. The assumption that individual microbes provide constant amounts of resources, which are equally divided among interacting partner individual, enables us to reveal a simple rule for the evolution of costly mutualism with positive fitness feedbacks: the product of the benefit-to-cost ratios for each species exceeds one. When this condition holds, high cooperative investment levels are favored in both species regardless of the amount invested by each partner. The model is then extended to examine how symbiont mutation, immigration, or switching affects the spread of selfish or cooperative symbionts, which decrease and increase their investment levels, respectively. In particular, when a host associates with numerous symbionts without enforcement, neither mutation nor immigration but rather random switching would allow the spread of cooperative symbionts. Examples using symbiont switching for evolution would include large ciliates hosting numerous intracellular endosymbionts. The simple model and rules would provide a basis for understanding the evolution of microbe-microbe mutualistic symbiosis with positive fitness feedbacks and without enforcement mechanisms.

Laccase is a multitasking protein for synthetic gene circuits in the yeast Saccharomycescerevisiae

Laccase is a multicopper oxidase enzyme that oxidizes a variety of substrates, including polyphenols and polycyclic aromatic hydrocarbons (PAHs). It catalyzes the four-electron reduction of molecular oxygen that results in the production of water as a by-product. Thus, laccase can play an important role in environmental care. Previously, we have successfully expressed Trametes trogii laccase (TtLcc1) in the yeast Saccharomyces cerevisiae. In this work, we have expressed in yeast another laccase, LacA from Trametes sp. AH28-2, and tested its function on PAHs. Yeast cells engineered to produce the two laccases performed efficient PAH degradation. Both TtLcc1 and LacA led to the construction of spatiotemporal fluorescence-pulse generators when combined with a benzoate/salicylate yeast biosensor in a two-population system. Moreover, laccases returned a visual output signal in yeast synthetic circuits-upon reacting with ABTS (2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid)). Thus, in S. cerevisiae, laccases are a powerful alternative to fluorescent reporter proteins.

Bioremediation technologies for remediation of dyes from wastewater

The colored dyes are extensively applied in diverse industrial setups such as textiles, paper, leather, and cosmetics. The unutilized dyes are released in the waste and pose a serious menace to the environment, ecological balance, and human health. Because of their chemical nature, they are extremely resistant to common methods of treatment and often persist in the aquatic environment. A sustainable and eco-friendly approach for treating dye-contaminated wastewater is "bioremediation." This manuscript aims to discuss the exclusive role of diversified microorganisms and plants, immobilized microbial cells/enzymes, microbial consortia, nanomaterials, and combination approaches in the bioremediation of dyes. It also provides a comprehensive understanding of different bio-remedial technologies used to remove dyes from wastewater. In addition, the underlying mechanisms affecting the efficacy of bio-remedial technologies, the latest breakthroughs, challenges, and potential solutions in scaling up, and prospects in this area are also explored. We also detail the noteworthiness of genetic engineering in different bioremediation technologies to solve the issues associated with dye contamination in wastewater and its removal from the environment.

Un-avoided polycyclic aromatic hydrocarbons exposure on human and animals: current detoxication strategies and future prospects

Polycyclic aromatic hydrocarbons (PAHs) are a class of ubiquitous organic compounds mainly produced during the incomplete combustion or pyrolysis of organic materials. Multiple studies have acknowledged PAHs as human carcinogen, which necessitates its detoxication from human and animals. Great and continuous efforts have been made to alleviate the adverse effects of PAHs to human and animals. This study summarizes plenty of techniques, including herbal extraction, phytochemicals, commercial agent and microbes, coupled with some optimized strategies, have utilized for the detoxication of PAHs, which also have limitations. Augmenting the delivery systems of phytochemicals for the improvement of sustained release property and enhancement of the bioavailability, introducing newly screened microbes for PAHs detoxication via biodegrading, as well as engineering microbes for the production of phytochemicals and degradation enzymes are the three future aspects needed to be considered in-depth.

A synthetic bacterial community engineered from Miscanthus floridulus roots enhances ammonia nitrogen removal in ionic rare earth mine tailings

Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen pollution in rare earth elements (REEs) mining areas. Phytoremediation is a promising remediation method, relying on the synergistic relationships between plants and their root-associated microbiome. Nevertheless, harnessing the microbiome to accelerate nitrogen transformation and absorption by plants is challenging. Here, we investigated the composition, activities and culturable fraction of the root bacterial microbiome of the pioneer plant Miscanthus floridulus grown in a REEs tailing soil containing a high ammonia nitrogen (AN) concentration at 344.35 mg kg-1. Based on this, we constructed a simplified synthetic microbial community (SynCom) derived from the roots of M. floridulus, possessing nitrification and denitrification capabilities, to help REEs mine plants efficiently convert pollutant AN into nutrients, thereby enhancing plant growth and AN removal. This SynCom, consisting of 10 bacterial strains, included species of the genera Burkholderia (5) Paraburkholderia (1), Curtobacterium (1), Leifsonia (1) and Sinomonas (2). As a result, this SynCom alone achieved a significant reduction of 24.8% in AN content in tailing soil. When the SynCom inoculated with plants, the reduction in AN was even more significant (32.6%), surpassing the reduction achieved solely by plants (25.5%). Moreover, live SynCom inoculation significantly increased shoot and root biomass by 39.8% and 49.7%, respectively, compared to dead SynCom inoculation. These results indicate that the reduction in AN can be attributed to the SynCom's nitrification and denitrification capabilities, as well as its ability to enhance plant nitrogen absorption by stimulating their growth. Notably, seven nitrifying and denitrifying strains of the SynCom are particularly enriched, suggesting that plant roots selectively recruit nitrogen cycle-related bacteria to accelerate nitrogen transformation and absorption. These results provide a practical solution for harnessing the synergistic relationships between plants and their root microbiome in environmental remediation efforts.

A cross-systems primer for synthetic microbial communities

The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.

Metabolic engineering of Corynebacterium crenatum for enhanced L-tyrosine production from mannitol and glucose

BACKGROUND

L-Tyrosine (L-Tyr) is a significant aromatic amino acid that is experiencing an increasing demand in the market due to its distinctive characteristics. Traditional production methods exhibit various limitations, prompting researchers to place greater emphasis on microbial synthesis as an alternative approach.

RESULTS

Here, we developed a metabolic engineering-based method for efficient production of L-Tyr from Corynebacterium crenatum, including the elimination of competing pathways, the overexpression of aroB, aroD, and aroE, and the introduction of the mutated E. coli tyrAfbr gene for elevating L-Tyr generation. Moreover, the mtlR gene was knocked out, and the mtlD and pfkB genes were overexpressed, allowing C. crenatum to produce L-Tyr from mannitol. The L-Tyr production achieved 6.42 g/L at a glucose-to-mannitol ratio of 3:1 in a shake flask, which was 16.9% higher than that of glucose alone. Notably, the L-Tyr production of the fed-batch fermentation was elevated to 34.6 g/L, exhibiting the highest titers among those of C. glutamicum previously reported.

CONCLUSION

The importance of this research is underscored by its pioneering application of mannitol as a carbon source for the biosynthesis of L-Tyr, as well as its examination of the influence of mannitol-associated genes in microbial metabolism. A promising platform is provided for the production of target compounds that does not compete with human food source.

Engineered cross-feeding creates inter- and intra-species synthetic yeast communities with enhanced bioproduction

Microorganisms can be engineered to sustainably produce a variety of products including fuels, pharmaceuticals, materials, and food. However, highly engineered strains often result in low production yield, due to undesired effects such as metabolic burden and the toxicity of intermediates. Drawing inspiration from natural ecosystems, the construction of a synthetic community with division of labor can offer advantages for bioproduction. This approach involves dividing specific tasks among community members, thereby enhancing the functionality of each member. In this study, we identify six pairs out of fifteen composed of six auxotrophs of Yarrowia lipolytica that spontaneously form robust syntrophic and synergistic communities. We characterize the stability and growth dynamics of these communities. Furthermore, we validate the existence of syntrophic interactions between two yeast species, Y. lipolytica and Saccharomyces cerevisiae, and find a strain combination, Δtrp2 and Δtrp4, forming a stable syntrophic community between two species. Subsequently, we introduce a 3-hydroxypropionic acid (3-HP) biosynthesis pathway into the syntrophic community by dividing the pathway among different strains. Our results demonstrate improved production of 3-HP in both intra- and interspecies communities compared to monocultures. Our results show the stable formation of synthetic syntrophic communities, and their potential in improving bioproduction processes.

Santiago ALCM, Saxena RK, Schoutteten N, Wimalasena MK, Aleoshin VV, Al-Hatmi AMS, Ariyawansa KGSU, Assunção AR, Bamunuarachchige TC, Baral HO, Bhat DJ, Błaszkowski J, Boekhout T, Boonyuen N, Brysch-Herzberg M, Cao B, Cazabonne J, Chen XM, Coleine C, Dai DQ, Daniel HM, da Silva SBG, de Souza FA, Dolatabadi S, Dubey MK, Dutta AK, Ediriweera A, Egidi E, Elshahed MS, Fan X, Felix JRB, Galappaththi MCA, Groenewald M, Han LS, Huang B, Hurdeal VG, Ignatieva AN, Jerônimo GH, de Jesus AL, Kondratyuk S, Kumla J, Kukwa M, Li Q, Lima JLR, Liu XY, Lu W, Lumbsch HT, Madrid H, Magurno F, Marson G, McKenzie EHC, Menkis A, Mešić A, Nascimento ECR, Nassonova ES, Nie Y, Oliveira NVL, Ossowska EA, Pawłowska J, Peintner U, Pozdnyakov IR, Premarathne BM, Priyashantha AKH, Quandt CA, Queiroz MB, Rajeshkumar KC, Raza M, Roy N, Samarakoon MC, Santos AA, Santos LA, Schumm F, Selbmann L, Selçuk F, Simmons DR, Simakova AV, Smith MT, Sruthi OP, Suwannarach N, Tanaka K, Tibpromma S, Tomás EO, Ulukapı M, Van Vooren N, Wanasinghe DN, Weber E, Wu Q, Yang EF, Yoshioka R, Youssef NH, Zandijk A, Zhang GQ, Zhang JY, Zhao H, Zhao R, Zverkov OA, Thines M, Karpov SA. Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Stability of a Mutualistic Escherichia coli Co-Culture During Violacein Production Depends on the Kind of Carbon Source

The L-tryptophan-derived purple pigment violacein (VIO) is produced in recombinant bacteria and studied for its versatile applications. Microbial synthetic co-cultures are gaining more importance as efficient factories for synthesizing high-value compounds. In this work, a mutualistic and cross-feeding Escherichia coli co-culture is metabolically engineered to produce VIO. The strains are genetically modified by auxotrophies in the tryptophan (TRP) pathway to enable a metabolic division of labor. Therein, one strain produces anthranilate (ANT) and the other transforms it into TRP and further to VIO. Population dynamics and stability depend on the choice of carbon source, impacting the presence and thus exchange of metabolites as well as overall VIO productivity. Four carbon sources (D-glucose, glycerol, D-galactose, and D-xylose) were compared. D-Xylose led to co-cultures which showed stable growth and VIO production, ANT-TRP exchange, and enhanced VIO production. Best titers were ∼126 mg L-1 in shake flasks. The study demonstrates the importance and advantages of a mutualistic approach in VIO synthesis and highlights the carbon source's role in co-culture stability and productivity. Transferring this knowledge into an up-scaled bioreactor system has great potential in improving the overall VIO production.

Pattern Formation and Bistability in a Synthetic Intercellular Genetic Toggle

Differentiation within multicellular organisms is a complex process that helps to establish spatial patterning and tissue formation within the body. Often, the differentiation of cells is governed by morphogens and intercellular signaling molecules that guide the fate of each cell, frequently using toggle-like regulatory components. Synthetic biologists have long sought to recapitulate patterned differentiation with engineered cellular communities, and various methods for differentiating bacteria have been invented. Here, we couple a synthetic corepressive toggle switch with intercellular signaling pathways to create a "quorum-sensing toggle". We show that this circuit not only exhibits population-wide bistability in a well-mixed liquid environment but also generates patterns of differentiation in colonies grown on agar containing an externally supplied morphogen. If coupled to other metabolic processes, circuits such as the one described here would allow for the engineering of spatially patterned, differentiated bacteria for use in biomaterials and bioelectronics.

Tunable cell differentiation via reprogrammed mating-type switching

This study introduces a synthetic biology approach that reprograms the yeast mating-type switching mechanism for tunable cell differentiation, facilitating synthetic microbial consortia formation and cooperativity. The underlying mechanism was engineered into a genetic logic gate capable of inducing asymmetric sexual differentiation within a haploid yeast population, resulting in a consortium characterized by mating-type heterogeneity and tunable population composition. The utility of this approach in microbial consortia cooperativity was demonstrated through the sequential conversion of xylan into xylose, employing haploids of opposite mating types each expressing a different enzyme of the xylanolytic pathway. This strategy provides a versatile framework for producing and fine-tuning functionally heterogeneous yet isogenic yeast consortia, furthering the advancement of microbial consortia cooperativity and offering additional avenues for biotechnological applications.

Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes

This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems.

Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms

Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.

The optimization of microbial functions through rational environmental manipulations

Microorganisms play a central role in biotechnology and it is key that we develop strategies to engineer and optimize their functionality. To this end, most efforts have focused on introducing genetic manipulations in microorganisms which are then grown either in monoculture or in mixed-species consortia. An alternative strategy to optimize microbial processes is to rationally engineer the environment in which microbes grow. The microbial environment is multidimensional, including factors such as temperature, pH, salinity, nutrient composition, etc. These environmental factors all influence the growth and phenotypes of microorganisms and they generally "interact" with one another, combining their effects in complex, non-additive ways. In this piece, we overview the origins and consequences of these "interactions" between environmental factors and discuss how they have been built into statistical, bottom-up predictive models of microbial function to identify optimal environmental conditions for monocultures and microbial consortia. We also overview alternative "top-down" approaches, such as genetic algorithms, to finding optimal combinations of environmental factors. By providing a brief summary of the state of this field, we hope to stimulate further work on the rational manipulation and optimization of the microbial environment.

Industrial biotechnology goes thermophilic: Thermoanaerobes as promising hosts in the circular carbon economy

Transitioning away from fossil feedstocks is imperative to mitigate climate change, and necessitates the utilization of renewable, alternative carbon and energy sources to foster a circular carbon economy. In this context, lignocellulosic biomass and one-carbon compounds emerge as promising feedstocks that could be renewably upgraded by thermophilic anaerobes (thermoanaerobes) via gas fermentation or consolidated bioprocessing to value-added products. In this review, the potential of thermoanaerobes for cost-efficient, effective and sustainable bioproduction is discussed. Metabolic and bioprocess engineering approaches are reviewed to draw a comprehensive picture of current developments and future perspectives for the conversion of renewable feedstocks to chemicals and fuels of interest. Selected bioprocessing scenarios are outlined, offering practical insights into the applicability of thermoanaerobes at a large scale. Collectively, the potential advantages of thermoanaerobes regarding process economics could facilitate an easier transition towards sustainable bioprocesses with renewable feedstocks.

Genetic Engineering Bacillus thuringiensis Enable Melanin Biosynthesis for Anti-Tumor and Anti-Inflammation

Collaboration between cancer treatment and inflammation management has emerged as an integral facet of comprehensive cancer care. Nevertheless, the development of interventions concurrently targeting both inflammation and cancer has encountered significant challenges stemming from various external factors. Herein, a bioactive agent synthesized by genetically engineering melanin-producing Bacillus thuringiensis (B. thuringiensis) bacteria, simultaneously achieves eco-friendly photothermal agent and efficient reactive oxygen/nitrogen species (RONS) scavenger benefits, perfectly tackling present toughies from inflammation to cancer therapies. The biologically derived melanin exhibits exceptional photothermal-conversion performance, facilitating potent photonic hyperthermia that effectively eradicates tumor cells and tissues, thereby impeding tumor growth. Additionally, the RONS-scavenging properties of melanin produced by B. thuringiensis bacteria contribute to inflammation reduction, augmenting the efficacy of photothermal tumor repression. This study presents a representative paradigm of genetic engineering in B. thuringiensis bacteria to produce functional agents tailored for diverse biomedical applications, encompassing inflammation and cancer therapy.

Microbial conversion of ethanol to high-value products: progress and challenges

Industrial biotechnology heavily relies on the microbial conversion of carbohydrate substrates derived from sugar- or starch-rich crops. This dependency poses significant challenges in the face of a rising population and food scarcity. Consequently, exploring renewable, non-competing carbon sources for sustainable bioprocessing becomes increasingly important. Ethanol, a key C2 feedstock, presents a promising alternative, especially for producing acetyl-CoA derivatives. In this review, we offer an in-depth analysis of ethanol's potential as an alternative carbon source, summarizing its distinctive characteristics when utilized by microbes, microbial ethanol metabolism pathway, and microbial responses and tolerance mechanisms to ethanol stress. We provide an update on recent progress in ethanol-based biomanufacturing and ethanol biosynthesis, discuss current challenges, and outline potential research directions to guide future advancements in this field. The insights presented here could serve as valuable theoretical support for researchers and industry professionals seeking to harness ethanol's potential for the production of high-value products.

Veillonella parvula promotes root caries development through interactions with Streptococcus mutans and Candida albicans

Root caries is a subtype of dental caries that predominantly impacts older adults. The occurrence and progression of root caries are associated with the homeostasis of dental plaque biofilm, and microbial synergistic and antagonistic interactions in the biofilm play a significant role in maintaining the oral microecological balance. The objective of the current study was to investigate the role of Veillonella parvula in the microbial interactions and the pathogenesis of root caries. The analysis of clinical samples from patients with/without root caries revealed that Veillonella and V. parvula were abundant in the saliva of patients with root caries. More importantly, a significantly increased colonization of V. parvula was observed in root carious lesions. Further in vitro biofilm and animal study showed that V. parvula colonization increased the abundance and virulence of Streptococcus mutans and Candida albicans, leading to the formation of a polymicrobial biofilm with enhanced anti-stress capacity and cariogenicity, consequently exacerbating the severity of carious lesions. Our results indicate the critical role of V. parvula infection in the occurrence of root caries, providing a new insight for the etiological investigation and prevention of root caries.

Reprogramming cellular metabolism to increase the efficiency of microbial cell factories

Recent studies are increasingly focusing on advanced biotechnological tools, self-adjusting smart microorganisms, and artificial intelligent networks, to engineer microorganisms with various functions. Microbial cell factories are a vital platform for improving the bioproduction of medicines, biofuels, and biomaterials from renewable carbon sources. However, these processes are significantly affected by cellular metabolism, and boosting the efficiency of microbial cell factories remains a challenge. In this review, we present a strategy for reprogramming cellular metabolism to enhance the efficiency of microbial cell factories for chemical biosynthesis, which improves our understanding of microbial physiology and metabolic control. Current methods are mainly focused on synthetic pathways, metabolic resources, and cell performance. This review highlights the potential biotechnological strategy to reprogram cellular metabolism and provide novel guidance for designing more intelligent industrial microbes with broader applications in this growing field.

Development of a Pseudomonas-based biocontrol consortium with effective root colonization and extended beneficial side effects for plants under high-temperature stress

The root microbiota plays a crucial role in plant performance. The use of microbial consortia is considered a very useful tool for studying microbial interactions in the rhizosphere of different agricultural crop plants. Thus, a consortium of 3 compatible beneficial rhizospheric Pseudomonas strains previously isolated from the avocado rhizosphere, was constructed. The consortium is composed of two compatible biocontrol P. chlororaphis strains (PCL1601 and PCL1606), and the biocontrol rhizobacterium Pseudomonas alcaligenes AVO110, which are all efficient root colonizers of avocado and tomato plants. These three strains were compatible with each other and reached stable levels both in liquid media and on plant roots. Bacterial strains were fluorescent tagged, and colonization-related traits were analyzed in vitro, revealing formation of mixed biofilm networks without exclusion of any of the strains. Additionally, bacterial colonization patterns compatible with the different strains were observed, with high survival traits on avocado and tomato roots. The bacteria composing the consortium shared the same root habitat and exhibited biocontrol activity against soil-borne fungal pathogens at similar levels to those displayed by the individual strains. As expected, because these strains were isolated from avocado roots, this Pseudomonas-based consortium had more stable bacterial counts on avocado roots than on tomato roots; however, inoculation of tomato roots with this consortium was shown to protect tomato plants under high-temperature stress. The results revealed that this consortium has side beneficial effect for tomato plants under high-temperature stress, thus improving the potential performance of the individual strains. We concluded that this rhizobacterial consortium do not improve the plant protection against soil-borne phytopathogenic fungi displayed by the single strains; however, its inoculation can show an specific improvement of plant performance on a horticultural non-host plant (such as tomato) when the plant was challenged by high temperature stress, thus extending the beneficial role of this bacterial consortium.

Materials-driven strategies in bacterial engineering

This perspective article focuses on the innovative field of materials-based bacterial engineering, highlighting interdisciplinary research that employs material science to study, augment, and exploit the attributes of living bacteria. By utilizing exogenous abiotic material interfaces, researchers can engineer bacteria to perform new functions, such as enhanced bioelectric capabilities and improved photosynthetic efficiency. Additionally, materials can modulate bacterial communities and transform bacteria into biohybrid microrobots, offering promising solutions for sustainable energy production, environmental remediation, and medical applications. Finally, the perspective discusses a general paradigm for engineering bacteria through the materials-driven modulation of their transmembrane potential. This parameter regulates their ion channel activity and ultimately their bioenergetics, suggesting that controlling it could allow scientists to hack the bioelectric language bacteria use for communication, task execution, and environmental response.

Graphical abstract

Engineering an energy-dissipating hybrid tissue in vivo for obesity treatment

Obesity is a global health challenge with limited therapeutic solutions. Here, we demonstrate the engineering of an energy-dissipating hybrid tissue (EDHT) in the body for weight control. EDHT is constructed by implanting a synthetic gel matrix comprising immunomodulatory signals and functional cells into the recipient mouse. The immunomodulatory signals induce the host stromal cells to create an immunosuppressive niche that protects the functional cells, which are overexpressing the uncoupling protein 1 (UCP1), from immune rejection. Consequently, these endogenous and exogenous cells co-develop a hybrid tissue that sustainedly produces UCP1 to accelerate the host's energy expenditure. Systematic experiments in high-fat diet (HFD) and transgenic (ob/ob) mice show that EDHT efficiently reduces body weight and relieves obesity-associated pathological conditions. Importantly, an 18-month observation for safety assessment excludes cell leakage from EDHT and reports no adverse physiological responses. Overall, EDHT demonstrates convincing efficacy and safety in controlling body weight.