Antifungal activity and possible mechanism of Streptomyces nojiriensis 9-13 against Mycogone sp., causing wet bubble disease on Agaricus bisporus.

Wet bubble disease (WBD) in Agaricus bisporus caused by Mycogone species imposes a substantial economic loss to mushroom production in China. Currently, fungicide application is the main method to control WBD. However, excessive use of fungicide is challenged by the appearance of resistance and food safety. Therefore, it is necessary to explore safe and efficient strategies to control WBD. Strain 9-13, isolated from the rhizosphere soil of Taxus chinensis, showed strong inhibitory activity against three Mycogone species. According to morphological and biochemical characteristics, and multilocus phylogenetic analysis, the strain was identified as Streptomyces nojiriensis. In addition, strain 9-13 extracts significantly inhibited mycelial growth and spore germination of M. perniciosa, M. rosea and M. xinjiangensis in vitro. Strain 9-13 and its extracts also exhibited broad-spectrum antifungal activities against 12 selected plant pathogenic fungi. Scanning electron microscopic observations showed that extracts destroyed mycelial structure, inducing mycelia to twist and shrink. Moreover, transmission electron microscopy revealed that extracts resulted in severe plasmolysis, rupture of cell membrane and a decrease in cell inclusions, and the cell wall appeared a rough and uneven surface. Notably, the extracts obviously reduced disease severity and incidence of WBD by from 83.85% to 87.32% in fruiting bodies and 77.36% in mushroom beds, and maintained fruiting time and color on harvested mushroom. Collectively, these results clearly indicate that S. nojiriensis 9-13 is a promising biocontrol agent to control WBD on A. bisporus.

Nondestructive detection of Pleurotus geesteranus strain degradation based on micro-hyperspectral imaging and machine learning.

In the production of edible fungi, the use of degraded strains in cultivation incurs significant economic losses. Based on micro-hyperspectral imaging and machine learning, this study proposes an early, nondestructive method for detecting different degradation degrees of Pleurotus geesteranus strains. In this study, an undegraded strain and three different degradation-level strains were used. During the mycelium growth, 600 micro-hyperspectral images were obtained. Based on the average transmittance spectra of the region of interest (ROI) in the range of 400-1000 nm and images at feature bands, feature spectra and images were extracted using the successive projections algorithm (SPA) and the deep residual network (ResNet50), respectively. Different feature input combinations were utilized to establish support vector machine (SVM) classification models. Based on the results, the spectra-input-based model performed better than the image-input-based model, and feature extraction improved the classification results for both models. The feature-fusion-based SPA+ResNet50-SVM model was the best; the accuracy rate of the test set was up to 90.8%, which was better than the accuracy rates of SPA-SVM (83.3%) and ResNet50-SVM (80.8%). This study proposes a nondestructive method to detect the degradation of Pleurotus geesteranus strains, which could further inspire new methods for the phenotypic identification of edible fungi.

Flower image classification based on an improved lightweight neural network with multi-scale feature fusion and attention mechanism.

In order to solve the problem that deep learning-based flower image classification methods lose more feature information in the early feature extraction process, and the model takes up more storage space, a new lightweight neural network model based on multi-scale feature fusion and attention mechanism is proposed in this paper. First, the AlexNet model is chosen as the basic framework. Second, a multi-scale feature fusion module (MFFM) is used to replace the shallow single-scale convolution. MFFM, which contains three depthwise separable convolution branches with different sizes, can fuse features with different scales and reduce the feature loss caused by single-scale convolution. Third, two layers of improved Inception module are first added to enhance the extraction of deep features, and a layer of hybrid attention module is added to strengthen the focus of the model on key information at a later stage. Finally, the flower image classification is completed using a combination of global average pooling and fully connected layers. The experimental results demonstrate that our lightweight model has fewer parameters, takes up less storage space and has higher classification accuracy than the baseline model, which helps to achieve more accurate flower image recognition on mobile devices.

Construction of prokaryotic nanocompartment in Yarrowia lipolytica to assist phloroglucinol production.

Phloroglucinol is an important chemical intermediate which has been tentatively produced by engineered bacteria. However, its biosynthesis in industry is limited due to its natural antibacterial activity. Our study firstly selected Yarrowia lipolytica as the chassis strain, which was verified to be tolerable to phloroglucinol. Then the gene of type III polyketone synthase PhlD (the key biosynthetic gene) was overexpressed to facilitate phloroglucinol production with a concentration of 107.4 mg/L. Furthermore, we introduced the prokaryotic nanocompartment to assist the intracellular catalytic activity. The results showed that the concentration of phloroglucinol was increased by about 2.5 times, indicating this multifunctional nanocompartment is orthogonal to the physiological activities of Y. lipolytica. Additionally, fermentations with xylose and lignocellulosic hydrolysates as the carbon source were performed with the engineered Y. lipolytica, resulting in a total concentration of 580.2 mg/L and 328.9 mg/L, respectively. These findings revealed the potential of Y. lipolytica in phloroglucinol production and provided an effective nanocompartment strategy to improve the catalytic activity of the enzyme for boosting phloroglucinol production. KEY POINTS: • The first time to select and use Y. lipolytica to produce phloroglucinol. • Successful construction of prokaryotic nanocompartment in Y. lipolytica to increase production of phloroglucinol. • Lignocellulose hydrolysate is used as a substrate in fermentation.

First report of cobweb disease of Auricularia heimuer caused by Hypomyces mycophilus in Fujian Province, China.

Auricularia heimuer is a gelatinous fungus with great edible and medicinal values. In September 2021, a suspected cobweb disease was found in some A. heimuer farms in Fujian Province, China. The disease caused white cottony mycelium to grow on the basal surface of the A. heimuer at the beginning of infection and gradually spread along the outer edge of the fruiting body, and eventually the white pathogen mycelium covered the entire fruiting body, which eventually led to the wilting and death of about 35% of A. heimuer . Two heavily infected tissues of A. heimuer were collected and two isolates were obtained by single spore isolation and purification technique. The pathogen colonies grew 10 to 12 mm per day on potato dextrose agar (PDA), and the colonies were initially white in color and gradually changed to yellowish brown with neat margins. Well-developed mycelium with septum, Conidiophores are bottle-stemmed and whorl-shaped branches, Conidia solitary, as ovoid, colorless singletons or doublets. The chlamydospores are yellowish, smooth surface, with 2-3 septa, size 9-22 µm × 30-38 µm. These morphological features are consistent with the Hypomyces mycophilus (Gea et al. 2019; Wang et al. 2021). For molecular identification, genomic DNA of the two isolates was obtained using an extraction kit (Biocolor, Shanghai, China), internal transcribed spacers (ITS) regions and 5SrRNA were amplified using ITS1 and ITS4 primers (White et al. 1990). A 590 bp DNA fragment was obtained and the sequences were deposited in GenBank (Accession Nos. OP715875 and OP782039), A BLAST search in GenBank revealed the highest similarity (≥99%) to H. mycophilus (GenBank Accession Nos. MH857567 and KU937111) . To fulfill Koch's postulates, the isolates cultured on PDA plates for 10 days were made into a spore suspension with sterile water at a concentration of 5 × 106 conidia/ml and sprayed onto twenty healthy fruiting bodies grown to about 2 cm in diameter, and another ten healthy fruiting bodies sprayed with sterile water as control, and incubated in an artificial climate chamber at 25℃ and relative humidity of 90%-95% (Back et al. 2012). After 4 days of inoculation, the pathogen started to germinate and slowly grew white mycelium, then the white mycelium multiplied at the base of the fruiting bodies and spread from the base to the periphery, and finally the fruiting bodies were completely covered by the pathogenic mycelium and gradually wilted. The symptoms were consistent with the natural disease symptoms under cultivation conditions, while the control group had normal growth of the seeds and no disease symptoms. H. mycophilus was reisolated and purified from symptomatic cotyledons and identified by the above method, and the results of the two experiments were consistent. To our knowledge, this is the first report of H. mycophilus causing cobweb disease in A. heimuer.

Expression profiling of circular RNA reveals a potential miR-145-5p sponge function of circ-AFF2 and circ-ASAP1 in renal cell carcinoma.

OBJECTIVES: Circular RNAs (circRNAs) are involved in carcinogenesis, though their expression profile in renal cell carcinoma (RCC) is uncharacterized. The tumor suppressor gene miR-145-5p is expressed in RCC tissues, but its relationship with circRNAs is unknown. Thus, we aimed to identify differentially expressed circRNAs in RCC tissues and to explore the interaction between these circRNAs and miR-145 in the development of RCC. METHODS: We performed high-throughput sequencing and bioinformatics analyses to examine the expression pattern of circRNAs in RCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to functionally annotate differentially expressed circRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was used for sequence verification. Small interfering RNAs were employed to investigate the function and mechanism of circRNAs in RCC. The relationship between miR-145-5p and circRNAs was confirmed using luciferase, RNA immunoprecipitation (RIP), and biotin-coupled probe RNA pull-down assays. RESULTS: Fifty-three circRNAs were significantly and differentially expressed in RCC compared to normal control tissue. Bioinformatic analyses indicated that two significantly upregulated circRNAs, circ-AFF2 and circ-ASAP1, had sequences corresponding to miR-145 response elements. Consistently, the luciferase reporter, RIP, and biotin-coupled probe RNA pull-down assays showed that circ-AFF2 and circ-ASAP1 may repress miR-145 by acting as sponges. circ-AFF2 and circ-ASAP1 were highly expressed in RCC patient-derived tumor samples; their overexpression correlated with poor prognosis and low miR-145 levels. Knockdown of circ-AFF2 or circ-ASAP1 in RCC cell lines inhibited proliferation, underscoring their oncogenic function. A circRNA-miRNA network was constructed for RCC using the differentially expressed circRNAs and projected miRNAs. Candidate genes were verified by RT-qPCR and western blot, indicating that circ-AFF2 and circ-ASAP1 may be connected to RCC proliferation and metastasis. CONCLUSION: circ-AFF2 and circ-ASAP1 were upregulated in RCC and likely promote tumor progression by sponging miR-145. Therefore, both circRNAs should be investigated further as potential diagnostic and therapeutic targets for RCC.

Recent advances in genetic technology development of oleaginous yeasts.

As important chemical raw materials and potential nutritional supplements, microbial lipids play an important role in ensuring economic development, food security, and energy security. Compared with non-natural hosts, oleaginous yeasts exhibit obvious advantages in lipid yield and productivity and have great potential to be genetically engineered into an oil cell factory. The main bottleneck in the current oleaginous yeasts engineering is the lack of genetic manipulation tools. Fortunately, the rapid development of synthetic biology has provided numerous new approaches, resources, and ideas for the field. Most importantly, gene editing technology mediated by CRISPR/Cas systems has been successfully applied to some oleaginous yeasts, almost completely rewriting the development pattern of genetic manipulation technology applicable. This paper reviews recent progress in genetic technology with regard to oleaginous yeasts, with a special focus on transformation methods and genome editing tools, discussing the effects of some important genetic parts. KEY POINTS: •Contribution of microbiotechnology in food safety and biofuel by oleaginous yeasts. •Advancement of genetic manipulation and transformation for oleaginous yeasts.

Risk factors for venoarterial-extracorporeal membrane oxygenation related nosocomial infection in children after cardiac surgery. / 儿童心脏术后静脉-åŠ¨è„‰ä½“å¤–è†œè‚ºæ°§åˆç›¸å ³åŒ»é™¢å† æ„ŸæŸ“çš„å±é™©å› ç´ .

OBJECTIVES: Extracorporeal membrane oxygenation (ECMO) is an extracorporeal life support strategy for the treatment of critically ill children with reversible heart and lung failure, increasingly being used in patients with low cardiac output after cardiac surgery. However, the mortality of patients is closely related to the complications of ECMO, especially bleeding, thrombosis, and infection, ECMO-related nosocomial infection has become a challenge to the success of ECMO. This study aims to analyze the incidence and risk factors for venoarterial-ECMO (VA-ECMO)-related nosocomial infections in children after cardiac surgery. METHODS: We retrospectively collected the data of patients who underwent VA-ECMO treatment after pediatric cardiac surgery in the Second Xiangya Hospital of Central South University from July 2015 to March 2021, and divided them into an infected group and a non-infected group. The clinical characteristics of the 2 groups of patients, VA-ECMO-related nosocomial infection factors, pathogenic microorganisms, and patient mortality were compared. Logistic regression was used to analyze the risk factors for nosocomial infection related to VA-ECMO after cardiac surgery. RESULTS: Of the 38 pediatric patients, 18 patients (47.37%) had VA-ECMO related nosocomial infection, served as the infected group, including 7 patients with blood infections and 11 respiratory tract infections. Gram-negative pathogens (16 strains, 88.9%) were the main bacteria, such as Acinetobacter baumannii (6 strains), Klebsiella pneumoniae (3 strains), and Stenotrophomonas maltophilia (3 strains). Compared with the non-infected group (n=20), the infection group had longer time of cardiopulmonary bypass, time of myocardial block, and time of VA-ECMO assistance (All P<0.05). Multivariate logistic regression analysis showed that time of cardiopulmonary bypass (OR=1.012, 95% CI 1.002 to 1.022; P=0.021) was an independent risk factor for ECMO-related nosocomial infection. The number of surviving discharges in the infected group was less than that in the non-infected group (1 vs 11, P<0.05). CONCLUSIONS: Cardiopulmonary bypass time is an independent risk factor for VA-ECMO-related nosocomial infection in children after cardiac surgery. Shortening the duration of extracorporeal circulation may reduce the incidence of VA-EMCO-related nosocomial infections in children after cardic surgery. The occurrence of VA-ECMO-related nosocomial infections affects the number of patient's discharge alive.

Nosocomial Infections During Extracorporeal Membrane Oxygenation in Pediatric Patients: A Multicenter Retrospective Study.

Objective: Extracorporeal membrane oxygenation (ECMO) is increasingly used in critically ill patients with respiratory and/or cardiac failure. This study aimed to investigate the epidemiology and risk factors of nosocomial infection (NI) in pediatric patients who underwent ECMO for respiratory and/or circulatory failure. Methods: Medical records for patients that were administered underwent ECMO support at Xiangya Second Hospital of Central South University, The Sixth Medical Center of PLA General Hospital, and Children's Hospital Affiliation of Zhengzhou University, from September 2012 to December 2019 were retrospectively reviewed. Clinical data of the patients who developed NI were collected and analyzed. Univariate and multivariate logistic regressions were performed to identify the independent predictive factors of NI during ECMO. Results: A total of 54 first episodes of NI were identified in the 190 patients on ECMO, including 32 cases of respiratory tract infections, 20 cases of bloodstream infections, and 2 cases of surgical site wound infections. Gram-negative pathogens were the dominant pathogens isolated, accounting for 92.6% of the NI. The incidence of ECMO-related NI was 47.6 cases per 1,000 ECMO days. In the univariate logistic regression, ECMO mode, ECMO duration, ICU duration, and peritoneal dialysis were associated with the development of NI in patients with ECMO support. However, in the multivariate analysis, only ECMO duration (OR = 2.46, 95%CI: 1.10, 5.51; P = 0.029), ICU duration (OR = 1.35, 95%CI: 1.05, 1.59; P = 0.017) and peritoneal dialysis (OR = 2.69, 95%CI: 1.08, 5.73; P = 0.031) were the independent predictive factors for NI during ECMO support. Conclusion: This study identified the significant correlation between ECMO-related NI and ECMO duration, ICU duration, and peritoneal dialysis. Appropriate preventive measures are needed for hospitals to reduce the incidence of ECMO in pediatric patients.

Rapid evolution and mechanism elucidation for efficient cellobiose-utilizing Saccharomyces cerevisiae through Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution.

Lack of cellobiose utilization capability for many microorganisms results in carbon source waste in lignocellulosic biorefinery. In this study, genes for cellobiose transport and hydrolysis were introduced to Saccharomyces cerevisiae synV, a semi-synthetic yeast with an inducible SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxPsym-mediated Evolution) system incorporated into its chromosome V, endowing cellobiose utilization capability to this strain. Thereafter, two evolved strains with 98.1% and 79.2% improvement, respectively, in cellobiose utilization rate were obtained through induced SCRaMbLE. Further studies suggested that the enhanced cellobiose utilization capability directly correlated with copy number increases of introduced genes and some chromosome structural variations. In particular, it was experimentally demonstrated for the first time that deletion of redox stress related gene MXR1 and ATP conversion related gene ADK2 contributed to enhanced cellobiose conversion. Thereafter, the effectiveness of MXR1 and ADK2 deletions was demonstrated in artificial hydrolysate and rice straw hydrolysate, respectively.

Genome Editing of Corynebacterium glutamicum Using CRISPR-Cpf1 System.

Corynebacterium glutamicum, as an important microbial chassis, has great potential in industrial application. However, complicated genetic modification is severely slowed by lack of efficient genome editing tools. The Streptococcus pyogenes (Sp) CRISPR-Cas9 system has been verified as a very powerful tool for mediating genome alteration in many microorganisms but cannot work well in C. glutamicum. We recently developed two Francisella novicida (Fn) CRISPR-Cpf1 assisted systems for genome editing via homologous recombination in C. glutamicum. Here, we describe the protocols and demonstrated that N iterative rounds of genome editing can be achieved in 3 N + 4 or 3 N + 2 days, respectively.

Bacterial mandelic acid degradation pathway and its application in biotechnology.

Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analysed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyse various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.

Oscillospira - a candidate for the next-generation probiotics.

Oscillospira is a class of organism that often appears in high-throughput sequencing data but has not been purely cultured and is widely present in the animal and human intestines. There is a strong association between variation in Oscillospira abundance and obesity, leanness, and human health. In addition, a growing body of studies has shown that Oscillospira is also implicated in other diseases, such as gallstones and chronic constipation, and has shown some correlation with the positive or negative changes in its course. Sequencing data combined with metabolic profiling indicate that Oscillospira is likely to be a genus capable of producing short-chain fatty acids (SCFAs) such as butyrate, which is an important reference indicator for screening "next-generation probiotics ". Considering the positive effects of Oscillospira in some specific diseases, such as obesity-related metabolic diseases, it has already been characterized as one of the next-generation probiotic candidates and therefore has great potential for development and application in the future food, health care, and biopharmaceutical products.

Dual-Frequency Polarized Reconfigurable Terahertz Antenna Based on Graphene Metasurface and TOPAS.

A hybrid dual-frequency polarized reconfigurable terahertz antenna is designed and studied. Graphene and TOPAS are employed as the polarization conversion metasurface and dielectric substrate, respectively, enabling tunable polarization conversion and circular polarization. TOPAS is a good substrate material for broadband THz components due to its low absorption. By adjusting the chemical potential of graphene between 0 eV and 0.5 eV, the polarization state in the band of 1 THz (0.76-1.02 THz) and 2.5 THz (2.43-2.6 THz) can be reconstructed. Thanks to the multilayer graphene structure and low absorption TOPAS, the graphene metasurface exhibits a broad bandwidth of 0.26 and 0.17 THz, respectively, in the band of 1 THz and 2.5 THz. The working state of the circularly polarized antenna and linearly polarized antenna can be switched in the bands around 1 THz (0.7-0.75 THz, 0.96-1.04 THz) and 2.5 THz (2.42-2.52 THz), respectively, without changing the physical geometry. Moreover, the graphene antenna, metasurface, and hybrid structure are tested, respectively, to verify that the components do not interfere with each other in performance. The hybrid antenna shows great potential in tunable terahertz devices and related applications.

Precision strategies for cancer treatment by modifying the tumor-related bacteria.

Research on the roles of the bacteria in tumor development and progression is a rapidly emerging field. Increasing evidence links bacteria with the modification of the tumor immune microenvironment, which greatly influences the antitumor response. In view of the individual immune effects of various bacteria in various tumors, developing personalized bacteria-modulating therapy may be a key to successful antitumor treatment. This review emphasizes the critical role of the bacteria in immune regulation, including both the tumor bacteria and gut bacteria. Aiming at tumor-related bacteria, we focus on various precise modulation strategies and discuss their impact and potential for tumor suppression. Finally, engineered bacteria with tumor-targeting ability could achieve precise delivery of various payloads into tumors, acting as a precision tool. Therefore, a precise tumor-related bacteria therapy may be a promising approach to suppress the development of tumors, as well as an adjuvant therapy to improve the antitumor efficacy of other approaches. KEY POINTS: • The mini-review updates the knowledge on complex effect of bacteria in TME. • Insight into the interaction and adjustment of bacteria in gut for TME. • Prospects and limitations of bacteria-related personalized therapy in the clinical anticancer therapy.

Steroidobacter gossypii sp. nov., isolated from cotton field soil.

A Gram-negative bacterium, designated S1-65T, was isolated from soil samples collected from a cotton field located in the Xinjiang region of PR China. Results of 16S rRNA gene sequence analysis revealed that strain S1-65T was affiliated to the genus Steroidobacter with its closest phylogenetic relatives being 'Steroidobacter cummioxidans' 35Y (98.4 %), 'Steroidobacter agaridevorans' SA29-B (98.3 %) and Steroidobacter agariperforans KA5-BT (98.3 %). 16S rRNA-directed phylogenetic analysis showed that strain S1-65T formed a unique phylogenetic subclade next to 'S. agaridevorans' SA29-B and S. agariperforans KA5-BT, suggesting that strain S1-65T should be identified as a member of the genus Steroidobacter. Further, substantial differences between the genotypic properties of strain S1-65T and the members of the genus Steroidobacter, including average nucleotide identity and digital DNA-DNA hybridization, resolved the taxonomic position of strain S1-65T and suggested its positioning as representing a novel species of the genus Steroidobacter. The DNA G+C content of strain S1-65T was 62.5 mol%, based on its draft genome sequence. The predominant respiratory quinone was ubiquinone-8. The main fatty acids were identified as summed feature 3 (C16:1ω6c/C16:1ω7c), C16 : 0 and iso-C15 : 0. In addition, its polar lipid profile was composed of aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Here, we propose a novel species of the genus Steroidobacter: Steroidobacter gossypii sp. nov. with the type strain S1-65T (=JCM 34287T=CGMCC 1.18736T).

Genomic molecular signatures determined characterization of Mycolicibacterium gossypii sp. nov., a fast-growing mycobacterial species isolated from cotton field soil.

A Gram-positive, acid-fast and rapidly growing rod, designated S2-37 T, that could form yellowish colonies was isolated from one soil sample collected from cotton cropping field located in the Xinjiang region of China. Genomic analyses indicated that strain S2-37 T harbored T7SS secretion system and was very likely able to produce mycolic acid, which were typical features of pathogenetic mycobacterial species. 16S rRNA-directed phylogenetic analysis referred that strain S2-37 T was closely related to bacterial species belonging to the genus Mycolicibacterium, which was further confirmed by pan-genome phylogenetic analysis. Digital DNA-DNA hybridization and the average nucleotide identity presented that strain S2-37 T displayed the highest values of 39.1% (35.7-42.6%) and 81.28% with M. litorale CGMCC 4.5724 T, respectively. And characterization of conserved molecular signatures further supported the taxonomic position of strain S2-37 T belonging to the genus Mycolicibacterium. The main fatty acids were identified as C16:0, C18:0, C20:3ω3 and C22:6ω3. In addition, polar lipids profile was mainly composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Phylogenetic analyses, distinct fatty aids and antimicrobial resistance profiles indicated that strain S2-37 T represented genetically and phenotypically distinct from its closest phylogenetic neighbour, M. litorale CGMCC 4.5724 T. Here, we propose a novel species of the genus Mycolicibacterium: Mycolicibacterium gossypii sp. nov. with the type strain S2-37 T (= JCM 34327 T = CGMCC 1.18817 T).

Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production.

Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.

Advances and Perspectives for Genome Editing Tools of Corynebacterium glutamicum.

Corynebacterium glutamicum has been considered a promising synthetic biological platform for biomanufacturing and bioremediation. However, there are still some challenges in genetic manipulation of C. glutamicum. Recently, more and more genetic parts or elements (replicons, promoters, reporter genes, and selectable markers) have been mined, characterized, and applied. In addition, continuous improvement of classic molecular genetic manipulation techniques, such as allelic exchange via single/double-crossover, nuclease-mediated site-specific recombination, RecT-mediated single-chain recombination, actinophages integrase-mediated integration, and transposition mutation, has accelerated the molecular study of C. glutamicum. More importantly, emerging gene editing tools based on the CRISPR/Cas system is revolutionarily rewriting the pattern of genetic manipulation technology development for C. glutamicum, which made gene reprogramming, such as insertion, deletion, replacement, and point mutation, much more efficient and simpler. This review summarized the recent progress in molecular genetic manipulation technology development of C. glutamicum and discussed the bottlenecks and perspectives for future research of C. glutamicum as a distinctive microbial chassis.

Combined adaptive evolution and transcriptomic profiles reveal aromatic aldehydes tolerance mechanisms in Yarrowia lipolytica.

Yarrowia lipolytica is an efficient oleaginous yeast, whereas its activity is typically reduced by inhibitors present in lignocellulosic hydrolysate. Understanding the response mechanism of Y. lipolytica to hydrolysate inhibitors and developing inhibitor tolerant strains are vital to lignocellulose valorization by this promising species. In this study, through adaptive laboratory evolution on three representative aromatic aldehyde inhibitors, evolved strains were obtained. Fermentation phenotype suggested that aromatic aldehydes conversion was one main reason for high tolerance of adapted strains. Transcriptome profiling analysis and reverse metabolic engineering confirmed that overexpressing the aldehyde ketone reductase gene YALI0_B07117g and aldehyde dehydrogenase gene YALI0_B01298g effectively converted aromatic aldehyde to corresponding alcohols and acids. The potential degradation pathways for aromatic aldehyde inhibitors in Y. lipolytica XYL+ were then discussed. This study provided insights to the aromatic aldehyde degradation in Y. lipolytica and a reliable basis for the development of aromatic aldehyde tolerant strains.