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Ricinoleic acid (RA) from castor oil was employed in biotransformation of peach-flavoured γ-decalactone (GDL), using a Candida parapsilosis strain (MTCC13027) which was isolated from waste of pineapple crown base. Using four variables—pH, cell density, amount of RA, and temperature—the biotransformation parameters were optimized using RSM and BBD. Under optimized conditions (pH 6, 10 % of microbial cells, 10 g/L RA at 28°C), the conversion was maximum and resulted to 80 % (+)-GDL (4.4 g/L/120 h) yield in shake flask (500 mL). Furthermore, optimization was achieved by adjusting the aeration and agitation parameters in a 3 L bioreactor, which were then replicated in a 10 L bioreactor to accurately determine the amount of (+)-GDL. In bioreactor condition, 4.7 g/L (>85 %) of (+)-GDL is produced with 20 % and 40 % dissolved oxygen (1.0 vvm) at 150 rpm in 72 h and 66 h, respectively. Further, a new Al-Mg-Ca-Si composite column-chromatography method is developed to purify enantiospecific (+)-GDL (99.9 %). This (+)-GDL is 100 % nature-identical as validated through 14C-radio-carbon dating. Thorough chemical investigation of enantiospecific (+)-GDL is authenticated for its use as flavour. This bioflavour has been developed through a cost-effective biotechnological process in response to the demand from the food industry on commercial scale. • Efficient Candida parapsilosis (MTCC 13027) strain produces (+)- γ -Decalactone (GDL). • Biotransformation parameters were optimized through RSM and Box Behnken Design. • (+)- γ -GDL is produced 4.4 g/L/120 h in shake-flask and 4.7 g/L/64 h in 10 L bioreactor. • Novel Al-Mg-Ca-Si composite produced to purify 99 % (+)- γ -GDL through Column. • (+)-GDL is identified 100 % biobased and safe for food-flavour application. [ABSTRACT FROM AUTHOR]

Modern cosmetic products, with rich formulations of components, have become an ideal breeding ground for microorganisms. Implementing effective preservative systems is crucial to prevent microbial growth and contamination. Titanium dioxide nanoparticles, a familiar ingredient in cosmetics, can decompose the outer membrane of microbial cells by producing free radicals. Chitosan has shown antimicrobial activities by impairing cell wall integrity by binding to it aiding in the release of cytosolic contents. In line with this, this work was centered on evaluating the antimicrobial efficiency of chitosan-coated titanium dioxide (CS-TiO2) nanoparticles against three bacterial species viz. Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) and use them as a self-preservative agent in cosmetic formulations. The growth curve analysis exhibited a dose-dependent delay in bacterial growth. The minimum inhibitory concentration (MIC50) results revealed that the nanoparticles were effective at 31.25μg/ml and 62.5μg/ml concentrations in suppressing S. aureus, P. aeruginosa and E. coli, respectively. The redox imbalance, membrane lipid peroxidation, DNA damage and cell viability analyses showed that the CS-TiO2 nanoparticles could disrupt the membrane leading to reactive oxygen species (ROS) formation and altering the genetic material. Therefore, the conclusions drawn from this research highlight the proficient microbial performance of CS-TiO2, proposing its suitability for incorporation into consumer products, especially cosmetics. As far as the authors are aware, this study is believed to be the first to investigate the potential of CS-TiO2 nanoparticles as a self-preservative. [ABSTRACT FROM AUTHOR]

Experimental evolution of microbial cells provides valuable information on evolutionary dynamics, such as mutations that contribute to fitness gain under given selection pressures. Although experimental evolution is a promising tool in evolutionary biology and bioengineering, long‐term culture experiments under multiple environmental conditions often impose an excessive workload on researchers. Therefore, the development of automated systems significantly contributes to the advancement of experimental evolutionary research. This review presents several specialized devices designed for experimental evolution studies, such as an automated system for high‐throughput culture experiments, a culture device that generate a temperature gradient, and an automated ultraviolet (UV) irradiation culture device. The ongoing development of such specialized devices is poised to continually expand new frontiers in experimental evolution research. [ABSTRACT FROM AUTHOR]

Whole cell microbial biosensors (WCMB) are mostly genetically modified microorganisms used to detect target molecules as indicators of biological and chemical contaminants as well as in the identification of compounds of interest in the food industry. The specificity and sensitivity of these biosensors are achieved through the design of genetic circuits that make use of genetic sequences such as promoters, terminators, genes encoding regulatory proteins or reporter proteins, among others. Despite the advances of WCMBs for their application, significant challenges are faced, such as cell stability, regulatory restrictions, and the need to optimize response times so that they can be a competitive detection tool in the market. This review explores the technological progress, potential and limitations of WCMBs in the food industry, starting by reviewing the operating principles of biosensors. The importance of selecting appropriate chassis cells and the integration of recognition elements and transducers to maximize their effectiveness in the detection of contaminants and compounds of interest in the food industry is highlighted. [ABSTRACT FROM AUTHOR]

Practical Application The present study aimed to identify the metabolites associated with the physiological activity of kimchi‐derived lactic acid bacteria (LAB). A clear difference was observed between the 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid (ABTS) radical scavenging rates when the pyruvate content was high (273.5 ng/µL; radical removal speed 6.50% per min) and the rates when the pyruvate content had decreased (131.9 ng/µL; radical removal speed 3.63% per min). Additionally, the characteristics of LAB antioxidant activity (increase in ABTS radical scavenging activity with reaction time, low level of 2,2‐diphenyl‐1‐picrylhydrazyl radical scavenging activity) were similar to those of pyruvate‐derived activity. Hydrogen peroxide content (WiKim0124, 2.08 → 0.26; WiKim0121, 0.99 → 0.47; WiKim39, 1.93 → 0.24) and lactate dehydrogenase activity (WiKim0124, 1.53 → 0.00; WiKim0121, 0.73 → 0.01; WiKim39, 1.72 → 0.02) decreased more in heat‐killed LAB than in non‐heat‐killed LAB. Accordingly, this resulted in increased pyruvate content and the inhibitory activity of lipid peroxide production increased by 2–3 times. Our findings indicate that pyruvate is one of the major metabolites regulating LAB physiological activity.The safety of utilizing live probiotics remains a topic of debate. To mitigate associated risks, there is a growing interest in non‐viable microorganisms or microbial cell extracts for use as probiotics. Various methods can be employed for probiotic inactivation. Heat treatment typically emerges as the preferred choice for inactivating probiotic strains in many instances. The present study shows the distinctions between inactivating lactic acid bacteria (LAB) through heat treatment and non‐heat treatment. It may serve as a valuable reference for selecting an appropriate inactivation method for LAB in industrial processes. [ABSTRACT FROM AUTHOR]

The morphological dynamics of microbial cell proliferation on an antimicrobial surface at an early growth stage was studied with Escherichia coli on the surface of a gel supplied with AgNbO3 antimicrobial particles. We demonstrated an inhibitory surface concentration, analogous to minimum inhibitory concentration, beyond which the growth of colonies and formation of biofilm are inhibited. In contrast, at lower concentrations of particles, after a lag time the cells circumvent the antimicrobial activity of the particles and grow with a rate similar to the case in the absence of particles. The lag time depends on the surface concentration of the particles and amounts to 2 h at a concentration of ½ minimum inhibitory concentration. The applicability of these findings, in terms of estimating inhibitory surface concentration, was tested in the case of antimicrobial polymethyl methacrylate (PMMA) bone cement. [ABSTRACT FROM AUTHOR]

Valencene, a sesquiterpene with the odor of sweet and fresh citrus, is widely used in the food, beverage, flavor and fragrance industry. Valencene is traditionally obtained from citrus fruits, which possess low concentrations of this compound. In the past decades, the great market demand for valencene has attracted considerable attention from researchers to develop novel microbial cell factories for more efficient and sustainable production modes. This review initially discusses the biosynthesis of valencene in plants, and summarizes the current knowledge of the key enzyme valencene synthase in detail. In particular, we highlight the heterologous production of valencene in different hosts including bacteria, fungi, microalgae and plants, and focus on describing the engineering strategies used to improve valencene production. Finally, we propose potential engineering directions aiming to further increase the production of valencene in microorganisms. [ABSTRACT FROM AUTHOR]

In this study, green synthesis of Ag doped ZnO (AZNPR) has been carried out using the sol-gel method at pH 8.0, using two types of microbial cells, namely Aspergillus niger and Bacillus subtilis as capping and reducing agents. This work centred on the phytomediated biosynthesis and characterisation of AZNPR and its biological utility. Based on infrared analysis, phytochemicals present in microbial cells are extracellular enzymes namely proteolytic, amylolytic, lipolytic, cellulolytic, and pectinase, which can be extracted from A. niger and B. subtilis and are responsible for controlling the growth of AZNPR. The formation of AZNPR was characterised using different analyses. The FTIR shows absorption band located at ∼864 cm−1 that shows the interaction between Ag and ZnO. The XRD results showed the presence of crystalline AZNPR in the forms of hexagonal wurtzite ZnO and Ag. Microstructural and size examination showed that AZNPR was in the form of nanorods with homogeneous distribution with a size of rods in A. nige r media 137.0 nm, while in B. subtili s media 197.4 nm. The Ag–ZnO nanorods revealed the ability to inhibit Candida albicans species, a fungus causing infectious disease, with an inhibition zone measuring 2.1–3.2 mm at 24 h. [ABSTRACT FROM AUTHOR]

Monogalactosyldiacylglycerol (MGDG), a predominant photosynthetic membrane lipid derived from plants and microalgae, has important applications in feed additives, medicine, and other fields. The low content and various structural stereoselectivity differences of MGDG in plants limited the biological extraction or chemical synthesis of MGDG, resulting in a supply shortage of monogalactosyldiacylglycerol with a growing demand. Herein, we established Saccharomyces cerevisiae as a cell factory for efficient de novo production of monogalactosyldiacylglycerol for the first time. Heterologous production of monogalactosyldiacylglycerol was achieved by overexpression of codon-optimized monogalactosyldiacylglycerol synthase gene MGD1, the key Kennedy pathway genes (i.e. GAT1, ICT1, and PAH1), and multi-copy integration of the MGD1 expression cassette. The final engineered strain (MG-8) was capable of producing monogalactosyldiacylglycerol with titers as high as 16.58 nmol/mg DCW in a shake flask and 103.2 nmol/mg DCW in a 5 L fed-batch fermenter, respectively. This is the first report of heterologous biosynthesis of monogalactosyldiacylglycerol in microorganisms, which will provide a favorable reference for study on heterologous production of monogalactosyldiacylglycerol in yeasts. [ABSTRACT FROM AUTHOR]

Background: The escalating global burden of diabetes and its associated cognitive impairment underscores the urgency for effective interventions. Bergenin shows promise in regulating glucose metabolism, mitigating inflammation, and improving cognitive function. Zebrafish models offer a unique platform for assessing drug efficacy and exploring pharmacological mechanisms, complemented by subsequent investigations in cell and rat models. Methods: The experimental subjects included zebrafish larvae (CZ98:Tg (mpeg1: EGFP)ihb20Tg/+), adult zebrafish (immersed in 2% glucose), BV2 cell line (50 mM glucose + 10 μm Aβ1-42), and a streptozotocin (STZ) bilateral intracerebroventricular injection rat model. Bergenin's effects on the toxicity, behavior, and cognitive function of zebrafish larvae and adults were evaluated. The Morris water maze assessed cognitive function in rats. Neuronal histopathological changes were evaluated using HE and Nissl staining. qPCR and Western blot detected the expression of glycolysis enzymes, inflammatory factors, and Bergenin's regulation of PPAR/NF-κB pathway in these three models. Results: 1) In zebrafish larvae, Bergenin interventions significantly reduced glucose levels and increased survival rates while decreasing teratogenicity rates. Microglial cell fluorescence in the brain notably decreased, and altered swimming behavior tended to normalize. 2) In adult zebrafish, Bergenin administration reduced BMI and blood glucose levels, altered swimming behavior to slower speeds and more regular trajectories, enhanced recognition ability, decreased brain glucose and lactate levels, weakened glycolytic enzyme activities, improved pathological changes in the telencephalon and gills, reduced expression of pro-inflammatory cytokines, decreased ins expression and increased expression of irs1, irs2a, and irs2b, suggesting a reduction in insulin resistance. It also altered the expression of pparg and rela. 3) In BV2 cell line, Bergenin significantly reduced the protein expression of glycolytic enzymes (GLUT1, HK2, PKFKB3, and PKM2), lowered IL-1β, IL-6, and TNF-α mRNA expression, elevated PPAR-γ protein expression, and decreased P-NF-κB-p65 protein expression. 4) In the rat model, Bergenin improves learning and memory abilities in STZ-induced rats, mitigates neuronal damage in the hippocampal region, and reduces the expression of inflammatory factors IL-1β, IL-6, and TNF-α. Bergenin decreases brain glucose and lactate levels, as well as glycolytic enzyme activity. Furthermore, Bergenin increases PPARγ expression and decreases p-NF-κB p65/NF-κB p65 expression in the hippocampus. Conclusion: Bergenin intervenes through the PPAR-γ/NF-κB pathway, redirecting glucose metabolism, alleviating inflammation, and preventing high glucoseinduced neuronal damage. [ABSTRACT FROM AUTHOR]

Bacterial biofilms are organized heterogeneous assemblages of microbial cells encased within a self-produced matrix of exopolysaccharides, extracellular DNA and proteins. Over the last decade, more and more biofilm-associated proteins have been discovered and investigated. Furthermore, omics techniques such as transcriptomes, proteomes also play important roles in identifying new biofilmassociated genes or proteins. However, those important data have been uploaded separately to various databases, which creates obstacles for biofilm researchers to have a comprehensive access to these data. In this work, we constructed BBSdb, a state-of-the-art open resource of bacterial biofilmassociated protein. It includes 48 different bacteria species, 105 transcriptome datasets, 21 proteome datasets, 1205 experimental samples, 57,823 differentially expressed genes (DEGs), 13,605 differentially expressed proteins (DEPs), 1,930 'Top 5% differentially expressed genes', 444 'Threshold-based DEGs' and a predictor for prediction of biofilm-associated protein. In addition, 1,781 biofilm-associated proteins, including annotation and sequences, were extracted from 942 articles and public databases via text-mining analysis. We used E. coli as an example to represent how to explore potential biofilmassociated proteins in bacteria. We believe that this study will be of broad interest to researchers in field of bacteria, especially biofilms, which are involved in bacterial growth, pathogenicity, and drug resistance. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) presents an escalating global challenge as conventional antibiotic treatments become less effective. In response, photodynamic therapy (PDT) and photothermal therapy (PTT) have emerged as promising alternatives. While rooted in ancient practices, these methods have evolved with modern innovations, particularly through the integration of lasers, refining their efficacy. PDT harnesses photosensitizers to generate reactive oxygen species (ROS), which are detrimental to microbial cells, whereas PTT relies on heat to induce cellular damage. The key to their effectiveness lies in the utilization of photosensitizers, especially when integrated into nano- or micron-scale supports, which amplify ROS production and enhance antimicrobial activity. Over the last decade, carbon dots (CDs) have emerged as a highly promising nanomaterial, attracting increasing attention owing to their distinctive properties and versatile applications, including PDT and PTT. They can not only function as photosensitizers, but also synergistically combine with other photosensitizers to enhance overall efficacy. This review explores the recent advancements in CDs, underscoring their significance and potential in reshaping advanced antimicrobial therapeutics. [ABSTRACT FROM AUTHOR]

BACKGROUND: Flax lignan has attracted much attention because of its potential bioactivities. However, the bioavailability of secoisolariciresinol diglucoside (SDG), the main lignan in flaxseed, depends on the bioconversion by the colon bacteria. Lactic acid bacteria (LAB) with β‐glucosidase activity has found wide application in preparing bioactive aglycone. RESULTS: LAB strains with good β‐glucosidase activity were isolated from fermented tofu. Their bioconversion of flax lignan extract was investigated by resting cell catalysis and microbial fermentation, and the metabolism of SDG by Lactiplantibacillus plantarum C5 following fermentation was characterized by widely targeted metabolomics. Five L. plantarum strains producing β‐glucosidase with broad substrate specificity were isolated and identified, and they all can transform SDG into secoisolariciresinol (SECO). L. plantarum C5 resting cell reached a maximum SDG conversion of 49.19 ± 3.75%, and SECO generation of 21.49 ± 1.32% (0.215 ± 0.013 mm) at an SDG substrate concentration of 1 mM and 0.477 ± 0.003 mm SECO was produced at 4 mm within 24 h. Although sixteen flax lignan metabolites were identified following the fermentation of SDG extract by L. plantarum C5, among them, four were produced following the fermentation: SECO, demethyl‐SECO, demethyl‐dehydroxy‐SECO and isolariciresinol. Moreover, seven lignans increased significantly. CONCLUSION: Fermentation significantly increased the profile and level of flax lignan metabolites, and the resting cell catalysis benefits from higher bioconversion efficiency and more straightforward product separation. Resting cell catalysis and microbial fermentation of flax lignan extract by the isolated β‐glucosidase production L. plantarum could be potentially applied in preparing flax lignan ingredients and fermented flaxseed. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Genetic circuits can endow microbial cell factories with the ability for self-learning and decision-making. Many standardized formats or automated software are developed to design genetic circuits. Many methods are developed to select and construct genetic parts. Recent advances in synthetic biology have provided a toolbox for constructing high-performance genetic circuits. Genetic circuits are widely employed for the dynamic regulation of metabolic networks and high-throughput screening of overproducers. In recent years, genetic circuit-based regulation of metabolic flux in microbial cell factories has received significant attention. In this review, we describe a pipeline for the design and construction of genetic circuits for metabolic flux optimization. In particular, we summarize the recent advances in computationally assisted prediction of critical metabolic nodes and genetic circuit design automation. Further, we introduce strategies for constructing high-performance genetic circuits. We also summarize the latest applications of genetic circuits in the dynamic regulation of metabolism and high-throughput screening. Finally, we discuss the challenges and prospects associated with the design and construction of sophisticated genetic circuits. Through this review, we aim to provide a theoretical basis for designing and constructing high-performance genetic circuits to optimize metabolic flux. [ABSTRACT FROM AUTHOR]

Diminishing fossil resources and the environmental risks associated with the use of fossil fuels have raised concerns about the production of future sustainable fuels. Fatty acid-derived advanced biofuels (alkanes and alkenes) synthesized from microbial species may serve as appealing alternatives to overcome energy-related issues. Alka(e)nes of medium chain length are major constituents of gasoline, diesel and jet fuel and are produced naturally by different microbial genera as a part of their cellular metabolism. The present review aims to extend the existing knowledge toward the different biosynthetic pathways that have been reported among the different microbial species for the production of alka(e)nes of various carbon lengths. This study also provides deep insight into the possibility of enhancing the production of next-generation biofuels through metabolic engineering of different pathways in heterologous hosts. The introduction of multiple gene/enzyme cascades and their compartmentalization in different organelles will further facilitate the maximum production of mimic fuels, which in turn will reduce the dependence on current transportation fuels. • Alka(e)nes from microorganisms have properties similar to fossil fuels. • These bio-fuels are sustainable and may serve as future sustainable fuels. • Gene/s and mechanisms has been identified for production of alka(e)nes. • Co-expression of specific genes may enhance titer rate and yield of hydrocarbons. [ABSTRACT FROM AUTHOR]

β-Alanine is a versatile amino acid with wide-range industrial applications, but its production from glucose has been limited by a low yield. This study addresses this challenge by developing efficient Escherichia coli strains with modified carbon metabolism as microbial cell factories and implementing a two-stage fermentation strategy. The introduction of aspartate decarboxylase (PanDE56S/I88M) facilitates the conversion of aspartate to β-alanine, while the overexpression of key enzymes such as phosphoenolpyruvate carboxylase and aspartate dehydrogenase increases the carbon flow from phosphoenolpyruvate to aspartate. To mitigate oxidative stress, the glutathione cycle was enhanced by overexpressing BtuE and Gor. In a bioreactor, the optimized strain achieved β-alanine production of 71.7 g/L with a yield of 1.0 mol/mol glucose, reaching a peak of 1.29 mol/mol. Notably, the utilization of acetate as a carbon feedstock enabled the production of 50 g/L of β-alanine with a 0.33 mol/mol acetate yield, showcasing the potential for sustainable production. This research offers valuable insights into improving the carbon yield in β-alanine production, which is of great importance for industrial applications. [ABSTRACT FROM AUTHOR]

Sesquiterpenes and tetraterpenes are classes of plant-derived natural products with antineoplastic effects. While plant extraction of the sesquiterpene, germacrene A, and the tetraterpene, lycopene suffers supply chain deficits and poor yields, chemical synthesis has difficulties in separating stereoisomers. This review highlights cutting-edge developments in producing germacrene A and lycopene from microbial cell factories. We then summarize the antineoplastic properties of β-elemene (a thermal product from germacrene A), sesquiterpene lactones (metabolic products from germacrene A), and lycopene. We also elaborate on strategies to optimize microbial-based germacrene A and lycopene production. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The present research aims to investigate the biosorption capacity of microbial biomass supported onto granular pozzolana toward Chlortetracycline hydrochloride (CTC). Biosorption studies were carried out in a discontinuous system and various experimental conditions that may affect the biosorption process were evaluated including particle size of the support, the speed of agitation, the mass of the support, contact time, initial pH of the solution, and the initial concentration of CTC. At 25°C, the optimum conditions for maximum removal of CTC by immobilized microbial cells were as follows: grain size of pozzolana was between 4 and 5 mm, a stirring speed (SS) was 160 rpm, pozzolana masse was 45 g, initial pH was 7.44, the initial CTC concentration was 40 mg/L, and the equilibrium time was 5 h. Under the optimal process parameters, a maximum CTC removal rate of 93.76% was obtained. Langmuir, Freundlich and Temkin models have been applied to describe isothermal equilibrium studies of biosorption. The Freundlich model was well-fitted with the equilibrium data (R2 = 0.99). The isotherm behaviour indicated that the biosorbent surface was heterogeneous, and the biosorption capacity of the microbial biomass calculated from the Langmuir model was 118.98 mg/g. The kinetic behaviour showed that the CTC biosorption followed pseudo-second-order kinetics, which suggested a chemisorption process. [ABSTRACT FROM AUTHOR]

This study aims to improve the performance of microbial desalination cell (MDC) using Vigna mungo (Black gram) wash water, reported for the first time as an anolyte utilizing a graphite plate and carbon brush as the anode. Power generation was facilitated by the exoelectrogen, Shewanella putrefaciens MTCC 8104. Polarization studies revealed that the graphite plate MDC attained a high power density of 2720 ± 50 μW/m2 compared to carbon brush for two electrode pairs. The COD removal and desalination efficiency were better for carbon brush MDC, achieving 58.17 ± 2% and 38.14 ± 2% removal, respectively. Power production can be enhanced by increasing the cathode's ability to accept the electrons, reducing the ageing of biofilm and promoting complete oxidation of the substrates. Upon improving its performance, MDC can act as a sustainable technology, collaborating with industries seeking solutions for wastewater treatment, energy generation and agricultural sectors on a large scale. Highlights: MDC integrates wastewater treatment, power generation and desalination.Vigna mungo wash water was reported for the first time as an anolyte in MDC.Graphite plate showcases a better power density, 2720 ± 50 μW/m2.Carbon brush establishes better COD removal and desalination efficiency. [ABSTRACT FROM AUTHOR]

Background: 2-Phenylethanol (2-PE) is one of the most widely used spices. Recently, 2-PE has also been considered a potential aviation fuel booster. However, the lack of scientific understanding of the 2-PE biosynthetic pathway and the cellular response to 2-PE cytotoxicity are the most important obstacles to the efficient biosynthesis of 2-PE. Results: Here, metabolic engineering and tolerance engineering strategies were used to improve the production of 2-PE in Komagataella phaffii. First, the endogenous genes encoding the amino acid permease GAP1, aminotransferase AAT2, phenylpyruvate decarboxylase KDC2, and aldehyde dehydrogenase ALD4 involved in the Ehrlich pathway and the 2-PE stress response gene NIT1 in K. phaffii were screened and characterized via comparative transcriptome analysis. Subsequently, metabolic engineering was employed to gradually reconstruct the 2-PE biosynthetic pathway, and the engineered strain S43 was obtained, which produced 2.98 g/L 2-PE in shake flask. Furthermore, transcriptional profiling analyses were utilized to screen for novel potential tolerance elements. Our results demonstrated that cells with knockout of the PDR12 and C4R2I5 genes exhibited a significant increase in 2-PE tolerance. To confirm the practical applications of these results, deletion of the PDR12 and C4R2I5 genes in the hyper 2-PE producing strain S43 dramatically increased the production of 2-PE by 18.12%, and the production was 3.54 g/L. Conclusion: This is the highest production of 2-PE produced by K. phaffii via l-phenylalanine conversion. These identified K. phaffii endogenous elements are highly conserved in other yeast species, suggesting that manipulation of these homologues might be a useful strategy for improving aromatic alcohol production. These results also enrich the understanding of aromatic compound biosynthetic pathways and 2-PE tolerance, and provide new elements and strategies for the synthesis of aromatic compounds by microbial cell factories. [ABSTRACT FROM AUTHOR]

Due to its high spatial resolution, Raman microspectroscopy allows for the analysis of single microbial cells. Since Raman spectroscopy analyzes the whole cell content, this method is phenotypic and can therefore be used to evaluate cellular changes. In particular, labeling with stable isotopes (SIPs) enables the versatile use and observation of different metabolic states in microbes. Nevertheless, static measurements can only analyze the present situation and do not allow for further downstream evaluations. Therefore, a combination of Raman analysis and cell sorting is necessary to provide the possibility for further research on selected bacteria in a sample. Here, a new microfluidic approach for Raman-activated continuous-flow sorting of bacteria using an optical setup for image-based particle sorting with synchronous acquisition and analysis of Raman spectra for making the sorting decision is demonstrated, showing that active cells can be successfully sorted by means of this microfluidic chip. [ABSTRACT FROM AUTHOR]

The bacterial anode of microbial electrolysis cells (MECs) is the limiting factor in a high hydrogen evolution reaction (HER). This study focused on improving biofilm attachment to a carbon-cloth anode using an alginate hydrogel. In addition, the modified bioanode was encapsulated by a filter bag that served as a physical barrier, to overcome its low mechanical strength and alginate degradation by certain bacterial species in wastewater. The MEC based on an encapsulated alginate bioanode (alginate bioanode encapsulated by a filter bag) was compared with three controls: an MEC based on a bare bioanode (non-immobilized bioanode), an alginate bioanode, and an encapsulated bioanode (bioanode encapsulated by a filter bag). At the beginning of the operation, the Rct value for the encapsulated alginate bioanode was 240.2 Ω, which decreased over time and dropped to 9.8 Ω after three weeks of operation when the Geobacter medium was used as the carbon source. When the MECs were fed with wastewater, the encapsulated alginate bioanode led to the highest current density of 9.21 ± 0.16 A·m−2 (at 0.4 V), which was 20%, 95%, and 180% higher, compared to the alginate bioanode, bare bioanode, and encapsulated bioanode, respectively. In addition, the encapsulated alginate bioanode led to the highest reduction currents of (4.14 A·m−2) and HER of 0.39 m3·m−3·d−1. The relative bacterial distribution of Geobacter was 79%. The COD removal by all the bioanodes was between 62% and 88%. The findings of this study demonstrate that the MEC based on the encapsulated alginate bioanode exhibited notably higher bio-electroactivity compared to both bare, alginate bioanode, and an encapsulated bioanode. We hypothesize that this improvement in electron transfer rate is attributed to the preservation and the biofilm on the anode material using alginate hydrogel which was inserted into a filter bag. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease (IBD) is one of the most challenging diseases in the 21st century, and more than 10 million people around the world suffer from IBD. Because of the limitations and adverse effects associated with conventional IBD therapies, there has been increased scientific interest in microbial‐derived biomolecules, known as postbiotics. Postbiotics are defined as the preparation of inanimate microorganisms and/or their components that confer a health benefit on the host, comprising inactivated microbial cells, cell fractions, metabolites, etc. Postbiotics have shown potential in enhancing IBD treatment by reducing inflammation, modulating the immune system, stabilizing intestinal flora and maintaining the integrity of intestinal barriers. Consequently, they are considered promising adjunctive therapies for IBD. Recent studies indicate that postbiotics offer distinctive advantages, including spanning clinical (safe origin), technological (easy for storage and transportation) and economic (reduced production costs) dimensions, rendering them suitable for widespread applications in functional food/pharmaceutical. This review offers a comprehensive overview of the definition, classification and applications of postbiotics, with an emphasis on their biological activity in both the prevention and treatment of IBD. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The crisis of obtaining drinking water and electrical energy from clean sources has been the primary focus of researchers seeking ecologically acceptable and cost‐effective alternatives. The microbial desalination cell (MDC) has shown to be one of the most cost‐effective and promising ways for creating electricity, cleaning sewage water, and naturally desalinating water. In this work, the AEM (Anion Exchange Membrane) was used in the anodic chamber, and potassium ferricyanide in the cathodic chamber as catholyte solution. Meanwhile, SEM (Scanning electron microscopy) analyses was used to define the resulting surface morphologies. This study gave an optimization model by Central Composite Design model, where all the variables affecting the microbial desalination cell (the initial concentration of COD (Chemical Oxygen Demand), the initial concentration of TDS (Total dissolved solids) and the operating time of the cell) were entered to obtain an equation for each response (electrical energy productivity, COD removal efficiency and water desalination efficiency) in addition to study the ANOVA (Analysis of variance) for each response and study the interactions of the variables with each other that affect the response. The variables were determined for the initial concentration of (COD) from (300‐1200 mg/L) and the initial concentration of (TDS) from (15–35 g/L) and the duration of the operating time was from (4–24 h) the maximum productivity was obtained. The power was 2.2 mW, and the maximum water desalination gave 42 %, and the optimum COD removal was 35 %. In addition to diagnosing the active sludge employed and defining the kind of bacteria controlling it, this research looked at the breakdown of the yield of ion exchange membranes, which had a negative impact on the desalination process and the productivity of electrical energy. [ABSTRACT FROM AUTHOR]

Enhancing the production of biochemicals from lignocellulosic biomass is one potential way to decrease society's dependence on fossil fuels. Aromatic compounds obtained from plant biomass can be used as substrates for microbial production of dicarboxylic acids such as 2-pyrone-4,6-dicarboxylic acid (PDC) and cis,cis-muconic acid, which are building blocks for the manufacturing of polymer-based fibers and materials. In this study, we used an engineered strain of the bacterium Novosphingobium aromaticivorans to investigate how to increase PDC productivity in flow-through bioreactors receiving aqueous solutions of aromatics. At the best operational conditions tested, we achieved stable PDC production rates of 0.77 gPDC L−1 h−1 with p-hydroxybenzoic acid, 1.93 gPDC L−1 h−1 with syringic acid, and 1.53 gPDC L−1 h−1 with the products from alkaline pretreated poplar biomass. PDC titers in these reactors ranged from 7.7 to 15 g L−1 (42 to 80 mM) and were limited by aromatic solubility in the case of syringic acid, or by accumulation of protocatechuic acid from p-hydroxybenzoic acid when high aromatic loading rates were used. The use of high aromatic loading rates, hollow-fiber membranes to concentrate the microbial cells, and NH4OH for pH control were factors that contributed to this study achieving the highest PDC productivities reported to date. Overall, our findings demonstrate strategies that can be used to increase bioreactor productivity when aromatic substrates are delivered in aqueous form. These findings may also provide useful insight for production of other biochemicals from aromatic streams using N. aromaticivorans or other microbial chassis. [ABSTRACT FROM AUTHOR]

Previous studies have shown that antimicrobial photodynamic inactivation (aPDI) can be strongly potentiated by the addition of the non-toxic inorganic salt, potassium iodide (KI). This approach was shown to apply to many different photosensitizers, including the xanthene dye Rose Bengal (RB) excited by green light (540 nm). Rose Bengal diacetate (RBDA) is a lipophilic RB derivative that is easily taken up by cells and hydrolyzed to produce an active photosensitizer. Because KI is not taken up by microbial cells, it was of interest to see if aPDI mediated by RBDA could also be potentiated by KI. The addition of 100 mM KI strongly potentiated the killing of Gram-positive methicillin-resistant Staphylocccus aureus, Gram-negative Eschericia coli, and fungal yeast Candida albicans when treated with RBDA (up to 15 µM) for 2 hours followed by green light (540 nm, 10 J/cm2). Both RBDA aPDI regimens (400 µM RBDA with or without 400 mM KI followed by 20 J/cm2 green light) accelerated the healing of MRSA-infected excisional wounds in diabetic mice, without damaging the host tissue. [ABSTRACT FROM AUTHOR]

In recent years, the probiotic product market has experienced rapid growth driven by the increasing consumer demand for functional products. Probiotics, defined as 'live microorganisms that have positive effects on host health when taken in sufficient amounts' are widely used in the production of functional foods. Studies have demonstrated that probiotic cells can provide beneficial health effects even when they are not active. The terms paraprobiotic and postbiotic have emerged as alternatives to probiotics, offering potential opportunities in the functional food market. Paraprobiotics are defined as non-living microbial cells that confer health benefits on the host when administered in sufficient quantities. To obtain paraprobiotics, the living cell must be inactivated while preserving its intact structure. Postbiotics are metabolic products secreted by beneficial microorganisms or low molecular weight soluble compounds released into the environment because of microbial cell lysis. Paraprobiotics and postbiotics, which are reported to possess beneficial properties such as antimicrobial, anti-inflammatory, anticarcinogenic, antiproliferative, and immunomodulatory effects, are applied in the food and pharmacology industries. This study evaluates the definitions of paraprobiotics and postbiotics, their uses in the food and pharmaceutical industries, and their effects on health. [ABSTRACT FROM AUTHOR]

Efficient hydrogen production in biocathode-driven microbial electrolysis cells (MECs) can be obtained by electroautotrophic microbes with the ability to regenerate biocatalytic activity. Inoculation and enrichment of a pure defined culture in the cathode are critical for high performance in hydrogen production. Zero-gap MECs with anion exchange membranes (AEMs) enhance hydrogen production due to low internal resistance and better pH balance. Engineered microbes and optimized microbe–electrode interactions can further increase MEC performance and accelerate its commercialization. Electroautotrophic microbes at biocathodes in microbial electrolysis cells (MECs) can catalyze the hydrogen evolution reaction with low energy demand, facilitating long-term stable performance through specific and renewable biocatalysts. However, MECs have not yet reached commercialization due to a lack of understanding of the optimal microbial strains and reactor configurations for achieving high performance. Here, we critically analyze the criteria for the inocula selection, with a focus on the effect of hydrogenase activity and microbe–electrode interactions. We also evaluate the impact of the reactor design and key parameters, such as membrane type, composition, and electrode surface area on internal resistance, mass transport, and pH imbalances within MECs. This analysis paves the way for advancements that could propel biocathode-assisted MECs toward scalable hydrogen gas production. [ABSTRACT FROM AUTHOR]

The mechanism of photodamage of E. coli Gram-negative bacterial cells sensitized with indotricarbocyanine dye PK220 was studied upon exposure to radiation from an LED source with emission spectrum maximum wavelength λmax = 745 nm corresponding to the long-wavelength absorption band of the dye. The intensity of the cells' own (not enhanced by activator additives) light-induced chemiluminescence was used to assess the magnitude of the photobiological effect. The main contribution to their photodestruction immediately after cessation of cell-suspension irradiation came from singlet oxygen and to a lesser extent from H2O2. Hydroxyl radicals did not play a significant role in the mechanism of sensitized photochemical processes. [ABSTRACT FROM AUTHOR]

Halophilic archaea are promising microbial cell factories for bacterioruberin (BR) production. BR is a natural product with multi-bioactivities, allowing potential application in many fields. In the previous work, a haloarchaeon Halorubrum sp. HRM-150 with a high proportion of BR (about 85%) was isolated, but the low yield impeded its large-scale production. This work figured out BR synthesis characteristics and mechanisms, and proposed strategies for yield improvement. First, glucose (10 g/L) and tryptone (15 g/L) were tested to be better sources for BR production. Besides, the combination of glucose and starch achieved the diauxic growth, and the biomass and BR productivity increased by 85% and 54% than using glucose. Additionally, this work first proposed the BR synthesis pattern, which differs from that of other carotenoids. As a structural component of cell membranes, the BR synthesis is highly coupled with growth, which was most active in the logarithm phase. Meanwhile, the osmotic down shock at the logarithm phase could increase the BR productivity without sacrificing the biomass. Moreover, the de-novo pathway for BR synthesis with a key gene of lyeJ, and its competitive pathways (notably tetraether lipids and retinal) were revealed through genome, transcriptome, and osmotic down shock. Therefore, the BR yield is expected to be improved through mutant construction, such as the overexpression of key gene lyeJ and the knockout of competitive genes, which need to be further explored. The findings will contribute to a better understanding of the metabolism mechanism in haloarchaea and the development of haloarchaea as microbial cell factories. [ABSTRACT FROM AUTHOR]

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Lipopeptides are a class of lipid–peptide‐conjugated compounds with differing structural features. This structural diversity is responsible for their diverse range of biological properties, including antimicrobial, antioxidant, and anti‐inflammatory activities. Lipopeptides have been attracting the attention of food scientists due to their potential as food additives and preservatives. This review provides a comprehensive overview of lipopeptides, their production, structural characteristics, and functional properties. First, the classes, chemical features, structure–activity relationships, and sources of lipopeptides are summarized. Then, the gene expression and biosynthesis of lipopeptides in microbial cell factories and strategies to optimize lipopeptide production are discussed. In addition, the main methods of purification and characterization of lipopeptides have been described. Finally, some biological activities of the lipopeptides, especially those relevant to food systems along with their mechanism of action, are critically examined. [ABSTRACT FROM AUTHOR]

One of the main barriers to MEC applicability is the bacterial anode. Usually, the bacterial anode contains non-exoelectrogenic bacteria that act as a physical barrier by settling on the anode surface and displacing the exoelectrogenic microorganisms. Those non-exoelectrogens can also compete with exoelectrogenic microorganisms for nutrients and reduce hydrogen production. In this study, the bacterial anode was encapsulated by a dialysis bag including suspended graphite particles to improve current transfer from the bacteria to the anode material. An anode encapsulated in a dialysis bag without graphite particles, and a bare anode, were used as controls. The MEC with the graphite-dialysis-bag anode was fed with artificial wastewater, leading to a current density, hydrogen production rate, and areal capacitance of 2.73 A·m−2, 134.13 F·m−2, and 7.6 × 10−2 m3·m−3·d−1, respectively. These were highest when compared to the MECs based on the dialysis-bag anode and bare anode (1.73 and 0.33 A·m−2, 82.50 and 13.75 F·m−2, 4.2 × 10−2 and 5.2 × 10−3 m3·m−3·d−1, respectively). The electrochemical impedance spectroscopy of the modified graphite-dialysis-bag anode showed the lowest charge transfer resistance of 35 Ω. The COD removal results on the 25th day were higher when the MEC based on the graphite-dialysis-bag anode was fed with Geobacter medium (53%) than when it was fed with artificial wastewater (40%). The coulombic efficiency of the MEC based on the graphite-dialysis-bag anode was 12% when was fed with Geobacter medium and 15% when was fed with artificial wastewater. [ABSTRACT FROM AUTHOR]

The recent discovery of nanoplastics in most ecosystems is a major, yet poorly known health issue. Here, we review nanoplastics with focus on their presence in the environment, their methods of detection, and their impact on the nitrogen cycle. Nanoplastics are widely distributed in ecosystems; however, their real concentrations are not known due to the limitation of actual detection methods. Detection methods include techniques based on mass spectrometry, optical instruments, and total organic carbon. Total organic carbon-based methods involve first membrane filtration and oxidation as pretreatment, then the measurement of total organic carbon as the total concentration of nanoplastics. Total organic carbon-based methods are easy and cost-effective, compared with other methods. Nanoplastics negatively impact ecosystems and nitrogen removal. Nanoplastics can adsorb on microbial cell membranes then disrupt the membrane integrity. Nanoplastics can also induce oxidative stress. Nitrogen cycling is substantially inhibited by nanoplastics during laboratory tests. [ABSTRACT FROM AUTHOR]

Background: Oritavancin is a new generation of semi-synthetic glycopeptide antibiotics against Gram-positive bacteria, which served as the first and only antibiotic with a single-dose therapeutic regimen to treat ABSSSI. A naturally occurring glycopeptide A82846B is the direct precursor of oritavancin. However, its application has been hampered by low yields and homologous impurities. This study established a multi-step combinatorial strategy to rationally construct a high-quality and high-efficiency biosynthesis system for A82846B and systematically optimize its fermentation process to break through the bottleneck of microbial fermentation production. Results: Firstly, based on the genome sequencing and analysis, we deleted putative competitive pathways and constructed a better A82846B-producing strain with a cleaner metabolic background, increasing A82846B production from 92 to 174 mg/L. Subsequently, the PhiC31 integrase system was introduced based on the CRISPR-Cas12a system. Then, the fermentation level of A82846B was improved to 226 mg/L by over-expressing the pathway-specific regulator StrR via the constructed PhiC31 system. Furthermore, overexpressing glycosyl-synthesis gene evaE enhanced the production to 332 mg/L due to the great conversion of the intermediate to target product. Finally, the scale-up production of A82846B reached 725 mg/L in a 15 L fermenter under fermentation optimization, which is the highest reported yield of A82846B without the generation of homologous impurities. Conclusion: Under approaches including blocking competitive pathways, inserting site-specific recombination system, overexpressing regulator, overexpressing glycosyl-synthesis gene and optimizing fermentation process, a multi-step combinatorial strategy for the high-level production of A82846B was developed, constructing a high-producing strain AO-6. The combinatorial strategies employed here can be widely applied to improve the fermentation level of other microbial secondary metabolites, providing a reference for constructing an efficient microbial cell factory for high-value natural products. [ABSTRACT FROM AUTHOR]

AbstractA new series of 1,3,4-thiadiazole linked to sulfa-azo derivatives via hydrazono-methyl bridge were synthesized via the reaction of methyl ((E)-(sulfa-derivatives)diazenyl) benzylidene)hydrazine-1-carbodithioates 1a-e with ethyl ester and acetyl hydrazonyl halides 2a-d. The chemical structures of the newly 1,3,4-thiadiazoles 3a-t have been clarified considring their elemental and spectral analysis. Antimicrobial activity of the newly 1,3,4-thiadiazoles was determined for Staphylococcus aureus, Escherichia coli, Candida albicans, as well as Aspergillus niger using the cup agar plate diffusion method. Out of the twenty compounds, compounds 3j, 3k, 3l, and 3s with isoxazole sulfonamides were selected for MIC assay. Compound 3j was equipotent with neomycin control drug against all tested strains, while compound 3k was 4-fold higher than neomycin against S. aureus, E. coli, and C. albicans with MIC values of 9.77, 19.53, and 19.53 μg/mL, respectively. Compound 3l was equipotent with neomycin against S. aureus and C. albicans, while it was 2-fold higher than neomycin against E. coli with MIC of 39.06 μg/mL. For 3s, it was less potent than neomycin against all tested microbs with 2-fold and 4-fold less potent. Further scanning electron microscopy (SEM) investigation has been studied to reveal the disruption effect of the selected potent antimicrobial compound (3k) on the intact cells of tested microbs S. aureus, E. coli in addition to C. albicans. Results showed that 3k exhibited a noticeable effect on destroying microbial cell walls. Furthermore, molecular docking study has been done to assess the binding behavior of two most effective compounds 3k and 3l with the target crystal structure of dihydropteroate synthase (PDB: 6CLV for S. aureus) and (PDB: 5U14 for E. coli). Compound 3k was shown to be able to form stable complexes with both target enzymes of dihydropteroate synthase through hydrogen bonding and hydrophobic interactions. [ABSTRACT FROM AUTHOR]

Although CRISPR-dCas13, the RNA-guided RNA-binding protein, was recently exploited as a translation-level gene expression modulator, it has still been difficult to precisely control the level due to the lack of detailed characterization. Here, we develop a synthetic tunable translation-level CRISPR interference (Tl-CRISPRi) system based on the engineered guide RNAs that enable precise and predictable down-regulation of mRNA translation. First, we optimize the Tl-CRISPRi system for specific and multiplexed repression of genes at the translation level. We also show that the Tl-CRISPRi system is more suitable for independently regulating each gene in a polycistronic operon than the transcription-level CRISPRi (Tx-CRISPRi) system. We further engineer the handle structure of guide RNA for tunable and predictable repression of various genes in Escherichia coli and Vibrio natriegens. This tunable Tl-CRISPRi system is applied to increase the production of 3-hydroxypropionic acid (3-HP) by 14.2-fold via redirecting the metabolic flux, indicating the usefulness of this system for the flux optimization in the microbial cell factories based on the RNA-targeting machinery. It's difficult to precisely modulate translation-level gene expression using CRISPR-dCas13 due to the lack of detailed characterization of the system. Here, the authors fill the knowledge gap and develop a synthetic tunable Tl-CRISPRi system to enable precise and predictable control of mRNA translation. [ABSTRACT FROM AUTHOR]

Background: Chelerythrine is an important alkaloid used in agriculture and medicine. However, its structural complexity and low abundance in nature hampers either bulk chemical synthesis or extraction from plants. Here, we reconstructed and optimized the complete biosynthesis pathway for chelerythrine from (S)-reticuline in Saccharomyces cerevisiae using genetic reprogramming. Results: The first-generation strain Z4 capable of producing chelerythrine was obtained via heterologous expression of seven plant-derived enzymes (McoBBE, TfSMT, AmTDC, EcTNMT, PsMSH, EcP6H, and PsCPR) in S. cerevisiae W303-1 A. When this strain was cultured in the synthetic complete (SC) medium supplemented with 100 µM of (S)-reticuline for 10 days, it produced up to 0.34 µg/L chelerythrine. Furthermore, efficient metabolic engineering was performed by integrating multiple-copy rate-limiting genes (TfSMT, AmTDC, EcTNMT, PsMSH, EcP6H, PsCPR, INO2, and AtATR1), tailoring the heme and NADPH engineering, and engineering product trafficking by heterologous expression of MtABCG10 to enhance the metabolic flux of chelerythrine biosynthesis, leading to a nearly 900-fold increase in chelerythrine production. Combined with the cultivation process, chelerythrine was obtained at a titer of 12.61 mg per liter in a 0.5 L bioreactor, which is over 37,000-fold higher than that of the first-generation recombinant strain. Conclusions: This is the first heterologous reconstruction of the plant-derived pathway to produce chelerythrine in a yeast cell factory. Applying a combinatorial engineering strategy has significantly improved the chelerythrine yield in yeast and is a promising approach for synthesizing functional products using a microbial cell factory. This achievement underscores the potential of metabolic engineering and synthetic biology in revolutionizing natural product biosynthesis. [ABSTRACT FROM AUTHOR]

Flavors and fragrances are an important class of specialty chemicals for which interest in biomanufacturing has risen during recent years. These naturally occurring compounds are often amenable to biosynthesis using purified enzyme catalysts or metabolically engineered microbial cells in fermentation processes. In this review, we provide a brief overview of the categories of molecules that have received the greatest interest, both academically and industrially, by examining scholarly publications as well as patent literature. Overall, we seek to highlight innovations in the key reaction steps and microbial hosts used in flavor and fragrance manufacturing. • Biosynthesis of flavors and fragrances provides a green alternative to chemical synthesis and natural product extraction. • Flavors and fragrances are used in a diverse range of products like food and drink, cosmetics and insecticides. • Patent and market analysis illustrates current trends and future interest in biosynthesized flavor and fragrance molecules. • Host optimization, enzyme engineering and bioprospecting can boost yields and improve product retention and selectivity. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Shared and more specific genetic determinants and pathways underlying yeast tolerance to acetic, butyric, and octanoic acids" published in the journal Microbial Cell Factories. The authors identified an error in Table 1 of the original article, where a section titled "Gene/ORF Description of the encoded protein function Susceptibility C2 C4 C8" was mistakenly placed in the middle of the table. The correct version of Table 1 is provided in the correction notice. Additionally, there are some changes to the legends of Table 1 and Table 2 that need to be made. The correction notice also includes a statement from the publisher, Springer Nature, regarding their neutrality in jurisdictional claims and institutional affiliations. [Extracted from the article]

Base editors (BEs) are widely used as revolutionary genome manipulation tools for cell evolution. To screen the targeted individuals, it is often necessary to expand the editing window to ensure highly diverse variant library. However, current BEs suffer from a limited editing window of 5–6 bases, corresponding to only 2–3 amino acids. Here, by engineering the CRISPR‒Cas12b, the study develops dCas12b‐based CRISPRi system, which can efficiently repress gene expression by blocking the initiation and elongation of gene transcription. Further, based on dCas12b, a new‐generation of BEs with an expanded editing window is established, covering the entire protospacer or more. The expanded editing window results from the smaller steric hindrance compared with other Cas proteins. The universality of the new BE is successfully validated in Bacillus subtilis and Escherichia coli. As a proof of concept, a spectinomycin‐resistant E. coli strain (BL21) and a 6.49‐fold increased protein secretion efficiency in E. coli JM109 are successfully obtained by using the new BE. The study, by tremendously expanding the editing window of BEs, increased the capacity of the variant library exponentially, greatly increasing the screening efficiency for microbial cell evolution. [ABSTRACT FROM AUTHOR]

Biosynthesis is the application of enzymes in microbial cell factories and has emerged as a promising alternative to chemical synthesis. However, natural enzymes with limited catalytic performance often need to be engineered to meet specific needs through a time‐consuming trial‐and‐error process. This study presents a quantum mechanics (QM)‐incorporated design–build–test–learn (DBTL) framework to rationally design phosphatase BT4131, an enzyme with an ambiguous substrate spectrum involved in N‐acetylglucosamine (GlcNAc) biosynthesis. First, mutant M1 (L129Q) is designed using force field‐based methods, resulting in a 1.4‐fold increase in substrate preference (kcat/Km) toward GlcNAc‐6‐phosphate (GlcNAc6P). QM calculations indicate that the shift in substrate preference is caused by a 13.59 kcal mol−1 reduction in activation energy. Furthermore, an iterative computer‐aided design is conducted to stabilize the transition state. As a result, mutant M4 (I49Q/L129Q/G172L) with a 9.5‐fold increase in kcat‐GlcNAc6P/Km‐GlcNAc6P and a 59% decrease in kcat‐Glc6P/Km‐Glc6P is highly desirable compared to the wild type in the GlcNAc‐producing chassis. The GlcNAc titer increases to 217.3 g L−1 with a yield of 0.597 g (g glucose)−1 in a 50‐L bioreactor, representing the highest reported level. Collectively, this DBTL framework provides an easy yet fascinating approach to the rational design of enzymes for industrially viable biocatalysts. [ABSTRACT FROM AUTHOR]

The integrated system of anaerobic digestion and microbial electrolysis cells (AD-MEC) was a novel approach to enhance the degradation of food waste anaerobic digestate and recover methane. Through long-term operation, the start-up method, organic loading, and methane production mechanism of the digestate have been investigated. At an organic loading rate of 4000 mg/L, AD-MEC increased methane production by 3–4 times and soluble chemical oxygen demand (SCOD) removal by 20.3% compared with anaerobic digestion (AD). The abundance of bacteria Fastidiosipila and Geobacter, which participated in the acid degradation and direct electron transfer in the AD-MEC, increased dramatically compared to that in the AD. The dominant methanogenic archaea in the AD-MEC and AD were Methanobacterium (44.4–56.3%) and Methanocalculus (70.05%), respectively. Geobacter and Methanobacterium were dominant in the AD-MEC by direct electron transfer of organic matter into synthetic methane intermediates. AD-MEC showed a perfect SCOD removal efficiency of the digestate, while methane as clean energy was obtained. Therefore, AD-MEC was a promising technology for deep energy transformation from digestate. [ABSTRACT FROM AUTHOR]

The electrode is a key component in a microbial electrolysis cell (MEC) that needs significant improvement for practical implementation. Accurate and reproducible analytical methods are substantial for the effective development of electrode technology. Linear sweep voltammetry (LSV) is an essential analytical method for evaluating electrode performance. In this study, inoculated carbon brush (IB), abiotic brush (AB), Pt wire (PtW), stainless steel wire (SSW), and mesh (SSM) were tested to find the most suitable counter electrode under different medium conditions. The coefficient of variation (Cv) of maximum current (Imax) was the most decisive indicator of the reproducibility test. This study shows that (i) the electrode used in operation is an appropriate counter electrode in an acetate-added condition, (ii) the anode LSV test should avoid the use of Pt wire as counter electrodes, and (iii) PtW is an appropriate counter electrode in cathode LSV in all conditions. [ABSTRACT FROM AUTHOR]

This study aims to determine the effect of microbial fertilizers that contain living cells or microbial strains that strengthen plant roots and promote early germination, applied to corn seeds, on corn and Amaranthus palmeri growth under competition. In the pot studies, four microbial fertilizers with different contents (Accudo, BMusa Green, BMusa Vita, Bontera) were applied to corn seeds according to the label instructions, and the effects of applications on height, fresh and dry weights of corn and A. palmeri were investigated under monoculture, one and two A. palmeri competition. Experiments were conducted with 15 treatments, 2 repetitions, and 4 replications. When the experiments were terminated, no effect of microbial fertilizer treatments was observed in terms of height, fresh and dry weight of corn plants grown under the same competitive conditions. The effect of the treatments on A. palmeri was obtained only in the corn + one A. palmeri condition, when Accudo application reduced the height of A. palmeri. However, this effect was not seen in fresh and dry weights and other competitive conditions. It is thought that carrying out the studies in pot conditions where plant growth is limited may have produced these results, and different results may be obtained in field conditions. [ABSTRACT FROM AUTHOR]

Butyl butyrate is a short‐chain fatty acid ester (C8) with a fruity aroma. It has broad prospects in the fields of foods, cosmetics and biofuels. At present, butyl butyrate is produced by chemical synthesis in the industry, but it is highly dependent on petroleum‐based products. The growing concerns regarding the future scarcity of fossil fuels have been strongly promoted the transition from traditional fossil fuels and products to renewable bioenergy and biochemicals. Therefore, it is necessary to develop a green biochemical technology to replace traditional petroleum‐based materials. In recent years, microorganisms such as Escherichia coli and Clostridium have been engineered to serve as cell factories for the sustainable one‐pot production of short‐chain fatty acid esters, including butyl butyrate. This opinion highlights the recent development in the use of lipases and alcohol acyltransferases (AATs) for butyl butyrate production in microbial fermentation, as well as future perspectives. [ABSTRACT FROM AUTHOR]

Shake-flask culture, an aerobic submerged culture, has been used in various applications involving cell cultivation. However, it is not designed for forced aeration. Hence, this study aimed to develop a small-scale submerged shaking culture system enabling forced aeration into the medium. A forced aeration control system for multiple vessels allows shaking, suppresses volatilization, and is attachable externally to existing shaking tables. Using a specially developed plug, medium volatilization was reduced to less than 10%, even after 45 h of continuous aeration (~ 60 mL/min of dry air) in a 50 mL working volume. Escherichia coli IFO3301 cultivation with aeration was completed within a shorter period than that without aeration, with a 35% reduction in the time-to-reach maximum bacterial concentration (26.5 g-dry cell/L) and a 1.25-fold increase in maximum concentration. The maximum bacterial concentration achieved with aeration was identical to that obtained using the Erlenmeyer flask, with a 65% reduction in the time required to reach it. [ABSTRACT FROM AUTHOR]

The microbial ecology of the human gut is made up of many different species of beneficial microorganisms, mostly bacteria. The integrity of the gut and general health are crucially dependent on these beneficial bacterial species. A variety of microbial communities reside in the human gut in symbiotic interactions, the majority of which are advantageous. According to reports, aberrant bacterial species colonization causes gut dysbiosis and serves as a catalyst for a number of human diseases. Understanding the diverse microbial species that live in the human gut and how they are related to human health and a number of disorders has been the subject of extensive research. Less research has been done on the postbiotics, such as chemistry and biochemistry, and their connections to human health. Postbiotics are defined as non-viable microbial cells, metabolic metabolites, and their microbial by-products released after lysis. Understanding the postbiotic landscape is essential to determining its source and method of synthesis, whether natural or artificial. Therefore, it is crucial to profile the ecology of the gut's microbes as well as the habitat since these factors have an impact on the postbiotic metabolites that are created. In order to relate human health and disease based on postbiotic rather than microbial species, it will be more important to address specific metabolites. The present study stresses the importance of gut microbial ecology in human physiology and health. Postbiotics profiles may be helpful in gaining access to gut ecology, and these molecular markers may act as early diagnostic tools for a variety of disorders. The most recent studies show that postbiotics increase immunological function, allergic reactions, neurological diseases, acute and chronic diarrhoea, and immune function. In the future, effort can be made to develop a quantitative-effect relationship evaluation method that is more rational, scientific, and better to give stronger support for the healthy and long-term development of postbiotic preparations. [ABSTRACT FROM AUTHOR]

Peanut hairy root culture serves as a potent tool for producing valuable prenylated stilbenoids. A significant amount of chitosan (CHT), methyl jasmonate (MeJA), and methyl-β-cyclodextrin (CD) was used to elicit hairy roots in a bioreactor, which were later subjected to freeze-drying and extracted with acetone. The group Gr.4, obtained from the first-column chromatography and consisting of partially purified mixed arachidin, exhibited the highest antioxidant activity, measuring 3,067.53 ± 176.98 µmole Trolox/g crude extract. Moreover, when examining the antimicrobial activity, the partially purified Gr.4 showed the lowest minimum inhibition concentration (MIC) values against Staphylococcus aureus, Salmonella Typhimurium, Escherichia coli, and Candida albicans, with values of 31, 63, 125, and 78 µg/ml, respectively. Furthermore, the DNA nicking assay using the Fenton reaction demonstrated the DNA damage effect when plasmid DNA was exposed to concentrations of 25–100 µg/ml of partially purified Gr.4. Additionally, the scanning electron microscopy (SEM) results revealed irregularities and abnormalities in all tested microbial cells after treatment with 2xMIC of partially purified Gr.4. The enhanced activity exhibited by mixed arachidin compounds compared to the crude extract indicates a high potency of mixed arachidin. Moreover, the simplicity of isolation and purification suggests that the mixed arachidin compounds could be a preferable alternative for further applications as effective compounds rather than using them in individually purified forms. [ABSTRACT FROM AUTHOR]