Corrigendum: Emerging microfluidic technologies for microbiome research.

[This corrects the article DOI: 10.3389/fmicb.2022.906979.].

Emerging microfluidic technologies for microbiome research.

The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.

Development of a reliable UHPLC-MS/MS method for simultaneous determination of zearalenone and zearalenone-14-glucoside in various feed products.

A reliable ultra-high-performance liquid chromatography-tandem mass spectrometry method (UHPLC-MS/MS) was developed for the simultaneous determination of two mycotoxins, that is, zearalenone (ZEN) and zearalenone-14-glucoside (ZEN-14G) in formula feed, concentrated feed, and premixed feed products. An improved sample pretreatment was achieved with the hydrophilic-lipophilic balance (HLB) cartridges efficiently removing the impurities and enriching the target analytes in different feeds. The critical parameters affecting the performance of the solid-phase extraction (SPE) procedure were carefully optimized, and 20% acetonitrile in water as the loading solution, 50% methanol in water as the washing solvent, and 5 ml of methanol as the elution solvent yielded the optimal purification efficiencies. The established method was thoroughly validated in terms of linearity (R 2 ≥ 0.999), sensitivity (limit of quantification in the range of 0.50-5.00 µg kg-1), recovery (89.35 ± 2.67% to 110.93 ± 1.56%), and precision (RSD, 3.00-14.20%), and it was then successfully applied to investigate a total of 60 feed samples. Among them, 50 samples were found to be contaminated with ZEN (an incidence of 83.3%) at levels ranging from 0.63 to 615.24 µg kg-1, whereas 22 samples were contaminated with ZEN-14G (an incidence of 36.7%) in the range of 0.89-15.31 µg kg-1. The developed method proved to be a specific and reliable tool for intensive monitoring of ZEN and ZEN-14G in complex feed matrices.

Universal screening of 200 mycotoxins and their variations in stored cereals in Shanghai, China by UHPLC-Q-TOF MS.

Due to the challenge of hundreds of potential mycotoxins that may be present in cereals, a rapid and reliable ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight tandem mass spectrometry (UHPLC-Q-TOF MS) technique was developed for universal screening of 200 mycotoxins (prototype, emerging and related derivatives) in cereals. With satisfactory sensitivity of accurate mass full-spectrum acquisition, it is feasible to preliminarily identify tentative untargeted mycotoxins with a large range of polarity without reference materials. The current screening method was also validated by the determination of 33 typical mycotoxins, and the screening detection limits in the range of 0.5-100 µg kg-1 were established in cereals. In total, 138 stored samples were contaminated by 46 mycotoxins and their metabolites, some of which were firstly reported in cereals, posing emerging potential health risks to humans and animals. Furthermore, the accumulation, transformation and degradation mechanisms of typical mycotoxins in cereals were investigated under real storage conditions.

A 65nm/0.448 mW EEG processor with parallel architecture SVM and lifting wavelet transform for high-performance and low-power epilepsy detection.

In recent years, low-power and wearable biomedical testing devices have emerged as a key answer to the challenges associated with epilepsy disorders, which are prone to crises and require prolonged monitoring. The feature vector of the electroencephalographic (EEG) signal was extracted using the lifting wavelet transform algorithm, and the hardware of the lifting wavelet transform module was optimized using the canonic signed digit (CSD) coding method. A low-power EEG feature extraction circuit with a power consumption of 0.42 mW was constructed. This article employs the support vector machine (SVM) technique after feature extraction to categorize and identify epilepsy. A parallel SVM processing unit was constructed to accelerate classification and identification, and then a high-speed, low-power EEG epilepsy detection processor was implemented. The processor design was completed using TSMC 65 nm technology. The chip size is 0.98 mm2, operating voltage is 1 V, operating frequency is 1 MHz, epilepsy detection latency is 0.91 s, power consumption is 0.448 mW, and energy efficiency of a single classification is 2.23 µJ/class. The CHB-MIT database test results show that this processor has a sensitivity of 91.86% and a false detection rate of 0.17/h. Compared to other processors, this processor is more suitable for portable/wearable devices.

A Multifunctional N-Doped Cu-MOFs (N-Cu-MOF) Nanomaterial-Driven Electrochemical Aptasensor for Sensitive Detection of Deoxynivalenol.

Deoxynivalenol (DON) is one of the most common mycotoxins in grains, causing gastrointestinal inflammation, neurotoxicity, hepatotoxicity and embryotoxicity, even at a low quantity. In this study, a facile electrochemical aptasensor was established for the rapid and sensitive determination of DON based on a multifunctional N-doped Cu-metallic organic framework (N-Cu-MOF) nanomaterial. The N-Cu-MOF, with a large specific surface area and good electrical conductivity, served not only as an optimal electrical signal probe but also as an effective supporting substrate for stabilizing aptamers through the interactions of amino (-NH2) and copper. Under the optimal conditions, the proposed sensor provided a wide linear concentration range of 0.02-20 ng mL-1 (R2 = 0.994), showing high sensitivity, with a lower detection limit of 0.008 ng mL-1, and good selectivity. The sensor's effectiveness was also verified in real spiked wheat samples with satisfactory recoveries of 95.6-105.9%. The current work provides a flexible approach for the rapid and sensitive analysis of highly toxic DON in food samples and may also be easily extended to detect other hazardous substances with alternative target-recognition aptamers.

Recyclable and superior selective CO2 adsorption of C4B32 and Ca@C4B32: a new category of perfect cubic heteroborospherenes.

The capture and separation of CO2 have attracted significant interest as a strategy to control the global emission of greenhouse gases. From the perspective of environmental protection, it is crucial to explore high-performance adsorbents that can efficiently capture CO2. Herein, we report a density functional theory study on the viability of the heteroborospherene C4B32 for the first time. C2v C4B32 was revealed to be a perfect cubic heteroborospherene with the HOMO-LUMO gap of 3.47 eV at the PBE0 level. Then, we evaluated the potential application of C4B32 in the capture and separation of CO2. Our results indicate that the cubic-like C4B32 can efficiently capture CO2 with a -1.34 eV adsorption energy via chemisorption at the most acidic and basic sites of the cage. The strong interaction between CO2 and C4B32 could be supported by an effective charge transfer and orbital overlap. C4B32 also displayed high selectivity for the separation of CO2 from NH3, N2, CH4, CO, and H2 mixtures. Furthermore, it was feasible to tune the CO2-capture ability of C4B32 by metal-doping, which regulated the Lewis acidity/basicity of the C4B32 surface. In particular, Ca-doping could significantly enhance the CO2-capture ability of C4B32. Our results show that as a highly symmetrical and stable heteroborospherene, C4B32 can be used as a building block for the design and synthesis of novel nanomaterials for the capture and separation of CO2.

Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories.

Metabolic engineering and synthetic biology approaches have prospered the field of biotechnology, in which the main focus has been on Escherichia coli and Saccharomyces cerevisiae as microbial workhorses. In more recent years, improving the Gram-positive bacteria Lactococcus lactis and Bacillus subtilis as production hosts has gained increasing attention. This review will demonstrate the different levels at which these bacteria can be engineered and their various application possibilities. For instance, engineered L. lactis strains show great promise for biomedical applications. Moreover, we provide an overview of recent synthetic biology tools that facilitate the use of these two microorganisms even more.

Carbon chain growth by formyl coupling over the Cu/γ-AlOOH(001) surface in syngas conversion.

Catalytic conversion of syngas to valuable chemicals and fuels such as ethanol is an extremely desirable process route. In the present study, the elementary steps leading to the formation of ethanol via syngas conversion over the Cu/γ-AlOOH(001) surface have been explored using density functional theory (DFT) calculations. The reaction pathway CO + H → CHO, CHO + CHO → OHCCHO → CHCHO + O, CHCHO + 4H → CH2CHO + 3H → CH3CHO + 2H → CH3CH2O + H → C2H5OH is the most favorable; during the whole process, CH3CHO formation needs to overcome the highest activation barrier. Different from the γ-AlOOH(001) surface, carbon chain growth is realized via the formyl coupling mechanism on the Cu/γ-AlOOH(001) surface; this step needs to overcome a 1.07 eV activation barrier and is exothermic by 0.73 eV. Our Bader charge analyses revealed that the addition of the Cu component enhances the electrostatic interaction between the CHO intermediate and the γ-AlOOH(001) surface with the aid of the formed CuOx species; as a result, the initial C-C chain forms in a different way. Moreover, the rate constant results manifest that the formation of the OHCCHO key intermediate can be facilitated by increasing the reaction temperature. We expect the obtained results will be useful for future experimental studies to improve the selectivity of C2 oxygenates in syngas conversion.

Influence of global gene regulatory networks on single cell heterogeneity of green fluorescent protein production in Bacillus subtilis.

BACKGROUND: Gram-positive bacterium Bacillus subtilis has been extensively studied as a microbial cell factory for high-level producing a wide range of interesting products. Green fluorescent protein (GFP) is commonly used as a marker for determining the strength of a given promoter or for the subcellular localization of a fusion protein. However, the inherent heterogeneity of GFP expression among individual cells that can arise from global regulation differences in the expression host, has not yet been systematically assessed. B. subtilis strains with single mutation(s) in the two major transcriptional regulators CcpA and/or CodY were earlier found to improve overall heterologous protein production levels. Here, we investigate the dynamic production performance of GFP in the reporter strains with chromosomally integrated Physpank-sfGFP(Sp). RESULTS: The mutation R214C in the DNA-binding domain of CodY effectively enhances GFP production at the population level relative to two other strains, i.e. wildtype (WT) and CcpAT19S. During the late stationary phase, the high- and low-level GFP-producing cells coexist in the WT population, while the CodYR214C population at the single-cell level shows higher phenotypic homogeneity of fluorescence signals. CONCLUSION: Expression of GFP is prominently heterogeneous in the WT B. subtilis cells, and this phenotypic heterogeneity can be significantly reduced by CodYR214C mutation. The rates of production heterogeneity show a high correlation to the overall GFP yields. Moreover, the toolkit of flow cytometry and fluorescence microscopy that can achieve real-time profiles of GFP production performance in various strains may facilitate the further use of B. subtilis as a cell factory.

Boosting heterologous protein production yield by adjusting global nitrogen and carbon metabolic regulatory networks in Bacillus subtilis.

Bacillus subtilis is extensively applied as a microorganism for the high-level production of heterologous proteins. Traditional strategies for increasing the productivity of this microbial cell factory generally focused on the targeted modification of rate-limiting components or steps. However, the longstanding problems of limited productivity of the expression host, metabolic burden and non-optimal nutrient intake, have not yet been completely solved to achieve significant production-strain improvements. To tackle this problem, we systematically rewired the regulatory networks of the global nitrogen and carbon metabolism by random mutagenesis of the pleiotropic transcriptional regulators CodY and CcpA, to allow for optimal nutrient intake, translating into significantly higher heterologous protein production yields. Using a ß-galactosidase expression and screening system and consecutive rounds of mutagenesis, we identified mutant variants of both CodY and CcpA that in conjunction increased production levels up to 290%. RNA-Seq and electrophoretic mobility shift assay (EMSA) showed that amino acid substitutions within the DNA-binding domains altered the overall binding specificity and regulatory activity of the two transcription factors. Consequently, fine-tuning of the central metabolic pathways allowed for enhanced protein production levels. The improved cell factory capacity was further demonstrated by the successfully increased overexpression of GFP, xylanase and a peptidase in the double mutant strain.

Insight into the mechanism of methanol assistance with syngas conversion over partially hydroxylated γ-Al2O3(110D) surface in slurry bed.

Despite numerous studies devoted to the various properties of γ-Al2O3, the explorations of its catalytic activity remain scarce. In this study, density functional theory calculations are performed to study the elementary adsorption and reaction mechanisms for syngas conversion on partially hydroxylated γ-Al2O3(110D) surface in liquid paraffin. It is found that the partially hydroxylated γ-Al2O3(110D) surface with the hydroxyl coverage of 8.9 OH nm-2 is formed by two dissociative adsorptions of H2O on the dry γ-Al2O3(110D) surface. The hydroxyl coverage conditions play a key role in determining the dominant reaction mechanism on account of the existence of strong hydrogen bonds. The preferential pathway for syngas conversion with assistance of methanol over the partially hydroxylated γ-Al2O3(110D) surface in liquid paraffin has been proven to be CH3OH → CH3O + H → CH3 + OH, CH3 + CO → CH3CO. C2H5OH is then formed by successive hydrogenation via the pathway CH3CO + 3H → CH3CHO + 2H → CH3CH2O + H → C2H5OH. Here, CH3CHO formation by CH3CO hydrogenation is not inhibited. Actually, with the assistance of partially hydroxylated γ-Al2O3, CH3CHO has been synthesized with high selectivity in our previous experiment by the reaction of methanol and syngas, which provides favorable evidence for our results. The rate-limiting step is the formation of CH3O from CH3OH dehydrogenation with an activation barrier of 122.2 kJ mol-1. Moreover, the reaction barrier of CO insertion into the adsorbed CH3 group is at least 89.4 kJ mol-1, lower than those of CH4, C2H6, and CH3OCH3 formations. ADCH charge and ESP analyses indicate that the typical (Al, O) Lewis acid-base pair may have a significant effect upon the initial C-C chain formation. Thus, the present study provides a new approach for the rational tailoring and designing of new catalysts with superior reactivity involved in syngas conversion.

Cell surface engineering of Bacillus subtilis improves production yields of heterologously expressed α-amylases.

BACKGROUND: Bacillus subtilis is widely used as a cell factory for numerous heterologous proteins of commercial value and medical interest. To explore the possibility of further enhancing the secretion potential of this model bacterium, a library of engineered strains with modified cell surface components was constructed, and the corresponding influences on protein secretion were investigated by analyzing the secretion of α-amylase variants with either low-, neutral- or high- isoelectric points (pI). RESULTS: Relative to the wild-type strain, the presence of overall anionic membrane phospholipids (phosphatidylglycerol and cardiolipin) increased dramatically in the PssA-, ClsA- and double KO mutants, which resulted in an up to 47% higher secretion of α-amylase. Additionally, we demonstrated that the appropriate net charge of secreted targets (AmyTS-23, AmyBs and AmyBm) was beneficial for secretion efficiency as well. CONCLUSIONS: In B. subtilis, the characteristics of cell membrane phospholipid bilayer and the pIs of heterologous α-amylases appear to be important for their secretion efficiency. These two factors can be engineered to reduce the electrostatic interaction between each other during the secretion process, which finally leads to a better secretion yield of α-amylases.

Identification of the protopanaxatriol synthase gene CYP6H for ginsenoside biosynthesis in Panax quinquefolius.

Panax quinquefolius is one of perennial herbs and well known for its outstanding pharmacological activity. Ginsenosides are thought to be the main active ingredients in P. quinquefolius and exist in many kinds of plant genus Panax (ginseng). Protopanaxatriol synthase, which is considered cytochrome P450 (CYP450) in ginsenoside biosynthesis pathway can convert protopanaxadiol into protopanaxatriol. However, the protopanaxatriol synthase gene in P. quinquefolius has not been identified. Here, we cloned and identified a protopanaxatriol synthase gene from P. quinquefolius (CYP6H, GenBank accession no. KC190491) at the first time, reverse transcription-PCR (RT-PCR) analysis showed no obvious transcription change of CYP6H in methyl jasmonate (MeJA)-induced hairy roots. Ectopic expression of CYP6H in Saccharomyces cerevisiae resulted in the production of protopanaxatriol with added exogenous protopanaxadiol and confirmed by liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (LC/APCIMS). Moreover, high-performance liquid chromatography (HPLC) analysis shows that RNA interferences of CYP6H in transgenic hairy roots could increase the accumulation of protopanaxadiol-type ginsenosides and decrease the accumulation of protopanaxatriol-type ginsenosides, whereas the effect of overexpression CYP6H in transgenic hairy roots was contrary. Our study indicated that CYP6H is a gene encoding protopanaxadiol 6-hydroxylase which could convert protopanaxadiol into protopanaxatriol in P. quinquefolius ginsenoside biosynthesis, we also have confirmed the function of CYP6H on effect accumulation of ginsenosides.

The isolation and characterization of dammarenediol synthase gene from Panax quinquefolius and its heterologous co-expression with cytochrome P450 gene PqD12H in yeast.

Panax quinquefolius is one of perennial herbs and well known for its outstanding pharmacological activity. Ginsenosides are thought to be the main active ingredients in Panax quinquefolius and exist in many kinds of plant genus Panax (ginseng). Dammarenediol synthase, which is considered as a key enzyme in ginsenoside biosynthesis pathway can convert 2, 3-oxidosqualene into dammarenediol-II. However, the dammarenediol synthase gene in Panax quinquefolius has not been identified. Here, we cloned and identified a dammarenediol synthase gene from Panax quinquefolius (PqDS, GenBank accession No. KC316048) at the first time, and reverse transcription-PCR (RT-PCR) analysis also showed an obvious transcription increase of PqDS in the methyl jasmonate (MeJA)-induced hairy roots. Ectopic expression of PqDS in yeast resulted in the production of dammarenediol-II was confirmed by liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (LC/APCIMS). Moreover, overexpression of PqDS in transgenic hairy roots could increase the transcription of gene PqDS and another P450 gene PqD12H (encoding protopanaxadiol synthase in Panax quinquefolius), the accumulation of ginsenosides also increased at the same time. In addition, both PqDS and PqD12H gene co-expressed in recombinant yeast result in the production of protopanaxadiol was detected by LC/APCIMS; this result also provides a new strategy for the abundant production of protopanaxadiol in vitro.