Abstract:The skin is the largest organ and the carrier of the second largest microbiota in the human body, playing a role in defending against the stimuli from the external environment. External stimuli such as UV rays and fog and haze can cause injuries in the skin, resulting in skin aging or barrier damage. Postbiotics are defined as preparations of inanimate microorganisms or their components that confer health benefits on the host. Recent studies have shown that postbiotics have the potential for maintaining skin health. This article introduces the concept and types of postbiotics and describes the potential role of postbiotics in repairing the skin barrier, promoting wound healing, protecting the skin from photoaging, and regulating the skin microbiota, with the aim of providing a reference for in-depth research on the benefits of postbiotics in skin health and the development of raw materials.

Abstract:Streptomyces is a genus of Gram-positive soil bacteria with complex morphological differentiation and life cycle. It has strong secondary metabolic capacity and can produces a variety of antibiotics. The growth of Streptomyces is often associated with morphological differentiation and secondary metabolism, which involve complex regulatory mechanisms, including pathway-specific regulation, pleiotropic regulation, and global regulation. The bld gene family is essential for the normal morphological development of Streptomyces and named since its deletion causes the “blad” phenotype. BldD, a global regulator encoded by a member of the bld family, can significantly regulate the morphological differentiation and secondary metabolism of Streptomyces. This review introduces the structure of BldD and the effects of BldD on the morphological differentiation and secondary metabolism of representative strains of Streptomyces, providing a reference for revealing the molecular regulatory mechanism of BldD in Streptomyces.

Abstract:Yarrowia lipolytica is a species of unconventional lipid-producing yeast with a well-defined genetic background and a comprehensive suite of gene editing tools. Terpenoids are natural secondary metabolites with isoprene as the basic structural unit and are ubiquitous in nature. In recent years, with the rapid development of synthetic biology, the synthesis of terpenoids by metabolic engineering has attracted increasing attention. In this paper, we reviewed the metabolic engineering in Y. lipolytica for the synthesis of terpenoids from enhanced precursor supply, subcellular organelle synthesis, and carbon source utilization. In addition, this paper envisions the potential research directions, with a view to providing guidance for the following research.

Abstract:Natural products with biological activity derived from microbes have been widely used in agriculture, health care, and other fields due to their diverse biological activities, being the main source of natural drug precursors. The discovery of novel active natural products has slowed down sharply since the 21st century, while the demand for active natural products is increasing. Therefore, it is urgent to develop new active natural products. The desert is the largest terrestrial ecosystem on Earth, with diurnal temperature variation, low water activity, nutrient scarcity, and high intensity of ultraviolet radiation and other abiotic factors. Accordingly, the microorganisms living in such environment have evolved special physiological and biochemical pathways to adapt to the environment, producing structurally novel active natural products. This paper reviews the research progress in the natural products with antimicrobial, anti-radiation, antioxidant, anti-tumor and anti-cancer activities from desert microorganisms in recent years, aiming to provide guidance for the development and application of such natural products.

Abstract:Klebsiella pneumoniae is a prevalent clinical conditional pathogen. K. pneumoniae infection involves a complicated network of pathogen-host interactions. Despite the profound knowledge about the molecular and cellular mechanisms of this bacterium, studies remain to be carried out regarding the outer membrane vesicles (OMVs) derived from K. pneumoniae and their role in bacterial pathogenesis. We summarized the current knowledge on the components of OMVs derived from K. pneumoniae and reviewed the research progress in the roles of OMVs in the survival and pathogenicity of K. pneumoniae.

Abstract:Polybrominated diphenyl ethers (PBDEs) are frequently used flame retardants. They are widely distributed in the global environment and difficult to be degraded, causing serious harm to the environment. Due to their potential toxicity, durability, and bioaccumulation, more and more attention has been paid to degrading PBDEs with high efficiency. The microbial degradation method has become a research hotspot because of the low cost, high efficiency, and low secondary pollution. This paper first introduces the pollution status of PBDEs in water, atmosphere, and soil and the toxicity of PBDEs to biological health. Then, it elaborates on the key factors influencing microbial degradation, the different pathways of anaerobic and aerobic degradation, and the intensifying approaches and mechanism of degradation. Finally, we prospect the application of new materials, density functional theory, and new research methods in the in-situ degradation of PBDEs, aiming to provide a theoretical foundation and technical support for treating the pollution of PBDEs.

Abstract:Clubroot caused by Plasmodiophora brassicae Woronin is a globally prevalent soil-borne disease posing a severe threat to the yield and quality of Brassica crops. Due to the violent physiological differentiation and biotrophic characteristics exhibited by P. brassicae, evaluating the pathotypes of P. brassicae in different regions is crucial for breeding Brassica crops with disease resistance and planning the crop cultivation pattern. Accurately assessing the number of P. brassicae resting spores in the soil is instrumental in predicting the risk levels of clubroot in the fields, laying a foundation for subsequent selection of control methods and evaluation of their effectiveness. This paper briefs the methods for identifying P. brassicae pathotypes and detecting and quantifying the resting spores in the soil. Additionally, we propose a single-cell sequencing technique with potential application in the study of P. brassicae pathotypes and analyze the feasibility of recombinase polymerase amplification (RPA) in the detection and quantification of P. brassicae. The aim of this paper is to offer a theoretical foundation and methodological reference for the effective control of clubroot while providing new insights and solutions for the identification and detection of P. brassicae.

Abstract:Insect symbionts and their metabolites are complex and diverse and have potential medical values. Some culturable symbionts in insects can be used to accelerate wound healing and treat the irritable bowel syndrome. The culturable symbionts in insects can produce a variety of active compounds. Among them, organic acids, antimicrobial peptides, and alkaloids can inhibit the pathogens of humans; lipases, yeast killer toxin (KT), and reactive oxygen species can kill malaria parasites; peptides, polyketides, and esters can inhibit human tumors. However, due to the limitations from immature isolation and culture methods, insufficient clinical trials, and clinical adverse reactions caused by their secondary metabolites, the application of insect symbionts in the medical field is still in its infancy. This paper reviewed the medical functions of insect symbionts and their metabolites and summarized the status, problems, and solutions in the application of insect symbionts and their metabolites in the medical field, aiming to give insights into the study and application of functional symbionts.

Abstract:Ulcerative colitis (UC) is an inflammatory bowel disease with unknown pathogenesis and increasing incidence. An intact intestinal barrier is essential for maintaining intestinal homeostasis and preventing diseases. The gut microbiota plays a crucial role in constituting the intestinal barrier, enhancing the immune response of the intestinal mucosa, and maintaining the intestinal environment. The gut microbiota imbalance can lead to intestinal barrier damage, and both intestinal barrier damage and gut microbiota imbalance are involved in the development of UC. In recent years, increasing studies of UC focused on the intestinal barrier and regulation of gut microbiota have been carried out. This article reviews the components of the intestinal barrier and the role of gut microbiota in UC, aiming to provide a theoretical basis for the future research in this field.

Abstract:[Background] Lactosucrose, a novel functional oligosaccharide, has been demonstrated capable of improving the gut microbiota and boosting the immunity of humans and animals. Since it is increasingly utilized in food and feed industries, the market demand for lactosucrose has been increasing year by year. The industrial production of lactosucrose mainly uses β-fructofuranosidases due to the high product specificity. However, the conversion rates of existing enzymes were generally low, which made the production cost remaining high. [Objective] To identify new β-fructofuranosidases for the enzymatic properties and industrial production of lactosucrose. [Methods] We identified a β-fructofuranosidase gene from Arthrobacter sp. EpRS66 and expressed it in Escherichia coli. Furthermore, we characterized the enzymatic properties of the recombinant β-fructofuranosidase and optimized the optimum reaction conditions for the production of lactosucrose. [Results] The recombinant enzyme showed the optimal performance at 40 ℃ and pH 6.0. It maintained good stability within the range of pH 5.0-8.0 and had a half-life of 20 min at 40 ℃. Under the reaction conditions of 40 ℃ and pH 6.0, the conversion rate of lactosucrose reached 32.2% at the time point of 3 h with substrates of 15% sucrose and 15% lactose and an enzyme addition of 25 μg/mL. Moreover, with high concentrations of substrates (30% sucrose and 30% lactose), the conversion rate reached 30.8%. [Conclusion] This study provides a novel β-fructofuranosidase that can effectively catalyze the formation of lactosucrose, offering a new choice for industrial production of lactosucrose.

Abstract:[Background] Plant essential oils are secondary metabolites with a volatile odor, which are environmentally friendly, natural, and residue-free, and it is widely used in food, gariculture and medicene, play an important role in people’s live. [Objective] To study the volatile components in the essential oils from Perilla frutescens (L.) Britt and Salvia digitaloides Diels and examine the anti-fungal and cytotoxic effects of the essential oils. [Methods] Essential oils were extracted by the steam distillation method, and the chemical components in the essential oils were analyzed by gas chromatography-mass spectrometry (GC-MS). The anti-fungal and cytotoxic effects of the essential oils were evaluated by the mycelial growth rate and the methyl thiazolyl tetrazolium (MTT) colorimetric assay. [Results] The main chemical components in the essential oil of P. frutescens were perillaketone (67.84%) and isoegomaketone (14.95%), while those of S. digitaloides Diels were caryophyllene oxide (9.59%), α-cadinol (8.84%), and palmitic acid (7.24%). The essential oils had varying degrees of antimicrobial effects. Specifically, the essential oil of P. frutescens had the strongest activity, with the median effective concentration (EC₅₀) of 32.78, 43.34 and 45.19 µg/mL against Alternaria tenuissima, Sclerotinia sclerotiorum, and Cylindrocarpon destructans, respectively. The EC₅₀ of the essential oil of S. digitaloides Diels against Fusarium solani was 97.68 µg/mL. The median inhibitory concentration (IC₅₀) of the essential oils of S. digitaloides Diels and P. frutescens against K562 cells were 282.69 µg/mL and 352.79 µg/mL, respectively. [Conclusion] The essential oils of S. digitaloides Diels and P. frutescens have strong biological activities.

Abstract:[Background] Biofilms as the main existing form of marine bacteria are related to the settlement and metamorphosis of marine invertebrates and regulated by quorum sensing, and thus it is of great significance to understand the relationship between quorum sensing, biofilm formation, and marine invertebrate metamorphosis. [Objective] To explore the relationship between quorum sensing, biofilm formation, and settlement and metamorphosis of Mytilus coruscus by adding quorum sensing inhibitors. [Methods] Different quorum sensing inhibitors (2-5H-furanone, 2-4-thiazolidinedione, pyrogallol, furanone C-30, and coumarin) were applied to Shewanella marisflavi, and the extracellular polymeric substance content of the biofilm was observed by confocal laser scanning microscopy (CLSM). With M. coruscus as the model, the effects of bacterial biofilms interfered by quorum sensing inhibitors on the settlement and metamorphosis of M. coruscus were studied. [Results] Quorum sensing inhibitors decreased the content of extracellular α-polysaccharide and protein in the biofilm of Shewanella. Furthermore, the post-larval rate of M. coruscus was decreased. [Conclusion] The quorum sensing system of S. marisflavi can regulate the extracellular polymeric substance content of the biofilm, thus indirectly influencing the settlement and metamorphosis of M. coruscus.

Abstract:[Background] Turpan Basin presents a dry climate with little rain, high temperatures in summer, and strong ultraviolet radiation, which make it difficult for common microorganisms to survive. Therefore, it is a precious place to explore thermophilic microbial resources. [Objective] To obtain thermophilic microbial resources in Turpan Basin, explore their ability to produce thermostable enzymes, and promote the development and application of thermophilic microbial resources in Xinjiang. [Methods] Six medium with different nutrient levels were used to isolate thermophilic strains from the surface sand samples of the Gobi Desert in Turpan at 50 ℃. After the isolates were identified, the capacity of the isolates in producing amylase, cellulase, xylanase, glucanase, and protease at high temperatures was measured. [Results] A total of 41 strains of thermophilic bacteria were isolated, belonging to 6 genera (Bacillus, Paenibacillus, Brevibacillus, Anoxybacillus, Aeribacillus, and Caldibacillus) of Bacillaceae. Among the 41 strains, 29, 29, 33, 37, and 37 strains produced amylase, cellulase, xylanase, glucanase, and protease, respectively. Strains TRM81951, TRM81961, and TRM81969 were capable of producing multiple enzymes. Strains TRM81953, TRM81988, TRM81972, and TRM81957 had strong capacity to produce amylase, xylanase, glucanase, and protease, respectively. [Conclusion] The Gobi Desert in Turpan harbors multiple thermophilic strains of Bacillaceae, and most of these strains have strong capacity to produce hydrolases, which are conducive to the utilization of nutrients in the barren environment.

Abstract:[Background] The prevalence of secondary salinization in soil poses a significant constraint on the sustainable development of protected vegetable production. [Objective] To screen out the salt-tolerant growth-promoting microbial strains and provide bacterial resources for remediating secondary salinized soils in greenhouses. [Methods] The LB medium with 5% salt was used to screen out the salt-tolerant strains from the soil samples of vegetable greenhouses by the dilution-plate coating method. The growth-promoting ability of each strain was determined by the seed immersion method. The morphological characteristics, physiological and biochemical properties, and 16S rRNA gene sequence were used to identify the strains. The salt tolerance and growth-promoting effect of each strain were measured by quantitative and qualitative methods. Pot experiments were carried out to examine the remediation effect of each strain on salinized soil samples and the cucumber growth-promoting effect. [Results] Fifty-eight strains of salt-tolerant bacteria were isolated from 37 salinized soil samples. Among them, five strains, YQ-1-8, SN-1-4, 3A-2, L1-2, and L3-3, increased the simplified activity index of cucumber by more than 15%, and all of them had growth-promoting effects on cucumber seedlings exposed to 0.3% salt. However, the growth-promoting effect decreased with the increasement of the salt concentration. YQ-1-8 was identified as B acillus velezensis, SN-1-4 as Arthrobacter arilaiti, 3A-2 as B. marisflavi, L1-2 as B. cereus, and L3-3 as B. aryabhattai. Strain 3A-2 was capable of solubilizing organophosphorus and producing IAA and exopolysaccharide. The results of pot experiments showed that 3A-2 at 1×10⁷ cfu/g increased the stem thickness, plant height, aboveground fresh weight, aboveground dry weight, and chlorophyll by 12.39%, 14.31%, 30.92%, 38.46%, and 9.06%, respectively. In addition, the strain increased the content of available nitrogen and available potassium and decreased the pH, electrical conductivity, and total salt content in soil (P<0.05). [Conclusion] Strain 3A-2 with salt tolerance and growth-promoting effect can serve as a candidate for the development of microbial agents for the recommendation of secondary salinized soils.

Abstract:[Background] Longyangxia valley is one of the most important lake wetlands in the source region of the Yellow River, demonstrating great potential in water regulation. [Objective] To explore the soil fungal diversity and screen biocontrol isolates from Longyangxia valley, enrich the fungal resources of lake wetlands in alpine regions, and provide basic materials for subsequent development of biocontrol agents. [Methods] Ten soil samples were collected from the shoreside of Longyangxia reservoir in Longyangxia valley, and fungi were isolated by the dilution coating method. The isolates were identified by morphological observation and methods of molecular biology, and the biocontrol isolates were screened by the plate confrontation method. [Results] One hundred and four fungal strains belonging to 23 genera were isolated, including Preussia, Trichoderma, Alternaria, Cladosporium, Bipolaris, Pseudogymnoascus, and Penicillium. The isolates belonging to Preussia and Trichoderma were the most, with the number of 21 and 19 and the isolation frequency of 20.19% and 18.27%, respectively. The isolates of Botryotrichum, Westerdykella, Leptosphaeria, Arthrinium, Scolecobasidium, Sporothrix, Tetracladium, and Aphanoascus were the fewest, and all these genera had only one isolate, with the isolation frequency of 0.96%. Nineteen isolates of Trichoderma were screened out from the 104 fungal isolates, and these isolates had great biocontrol effects on eight fungal pathogens isolated from the main crops of Qinghai Province, with the inhibition rates between 51.6%–73.5%. Ten Preussia isolates, 4 Pseudogymnoascus isolates, 3 Cladosporium isolates, 2 Bipolaris isolates, and 1 isolate each of Arthrinium, Leptosphaeria, Westerdykella, Penicillium, and Emericellopsis also exerted strong inhibitory effects on the eight pathogens, with the largest inhibition zone ≥10 mm. [Conclusion] The soil of Longyangxia valley harbors abundant fungal resources and demonstrates high potential of exploitation and utilization.

Abstract:[Background] Wheat scab and Fusarium toxin pollution caused by Fusarium graminearum complex seriously affect the yield and quality of wheat. Volatile organic compounds (VOC) produced by biocontrol strains can be used for the biocontrol of plant diseases. [Objective] To provide a theoretical basis for the full application of biocontrol strains. [Methods] We collected VOC from Bacillus velezensis 6W1, an antagonistic strain isolated in the previous study. The two-tier culture dish was employed to study the effects of VOC on the mycelial growth of F. graminearum. The plate confrontation-fumigation assay was employed to examine the effects of VOC on the spore germination and deoxynivalenol (DON) production of F. graminearum. The components of VOC were qualitatively analyzed by gas chromatography-ion mobility spectrometry (GC-IMS). [Results] The VOC produced by B. velezensis 6W1 inhibited the growth and DON production but had no effect on the spore germination of F. graminearum. The results of GC-IMS showed that the VOC produced by the strain mainly included esters, alcohols, aldehydes, alkenes, and ketones. The inhibitory effect of the standard substance of each component was tested. The results showed that these substances inhibited the growth and DON production of F. graminearum. [Conclusion] In summary, B. velezensis 6W1 can produce VOC capable of inhibiting the growth and toxin production of F. graminearum. This strain demonstrates great potential in the development of biocontrol products, and its VOC also have high research and application values in the prevention and control of plant diseases.

Abstract:[Background] Dolycoris baccarum L. is a herbivorous pest that harms sorghum, maize, soybean and other crops and fruit plants. Studying its gut bacteria is essential for the control of D. baccarum L. and the exploration of functional bacterial resources from the gut. [Objective] This study aims to gain insights into the culturable bacteria in the gut of D. baccarum L. and screen out cellulase-producing strains. The cellulase activities of the strains screened out were determined. The enzyme production conditions of several strains were explored. [Methods] The gut bacteria of D. baccarum L. were isolated by the culture method and identified by morphological observation and 16S rRNA gene sequencing. The inhibition zone method was employed to screen out the strains capable of producing cellulase. The cellulase activities of the strains were determined by the 3,5-dinitrosalicylic acid (DNS) method. [Results] A total of 35 strains were isolated from the gut of D. baccarum L., they are 10 species of bacteria belonging to 5 genera, including 3 species of Enterococcus, 4 species of Bacillus, and 1 species of Lactococcus, Serratia, and Pantoea, respectively. A total of 13 strains capable of producing cellulase were screened out. Strains B8, B22, B23, and B25 had strong cellulase-producing capacity, among which B22 had the most prominent cellulase-producing ability (D/d=7.01). The cellulase-producing capacity was the strongest in the medium with pH 5.0, culture with B8, B23, and B25 for 24 h, or culture with B22 for 36 h. [Conclusion] The gut of D. baccarum L. harbors rich culturable bacteria and 37% of the isolates can produce cellulose, which can assist in food digestion and influence the host health. Both fermentation time and medium pH influence the cellulase production of functional strains. Strain B22 with strong cellulase-producing ability should be further developed and utilized.

Abstract:[Background] To successfully infect and colonize the host tissue, phytopathogenic fungi need to detoxify the antifungal secondary metabolites such as phenolic compounds in the host. Studies have shown some pathogenic fungi can degrade phenolic compounds in the host by synthesizing catechol 1,2-dioxygenase (CHD). However, whether the Alternaria alternata can degrade phenols in pear fruit peel and the mechanism remain unclear. [Objective] To clone CHD from A. alternata, conduct bioinformatics analysis of CHD, and study the degradation performance of phenolic acids in pear fruit peel by CHD, thus providing support for further clarifying the molecular mechanism of this enzyme. [Methods] CHD was cloned from A. alternata by homologous cloning. Smart and SOPMA were used for bioinformatics analysis. The changes in phenolic acid content after metabolism of A. alternata were determined by quaternary ultra-fast liquid chromatography, and the expression level of CHD during the metabolism of phenolic acids was analyzed by RT-qPCR. [Results] Two CHD genes were cloned from A. alternata and designated as AaCHD1 and AaCHD2. The proteins encoded by the two genes both contained C-terminal and N-terminal conserved domains of dioxygenases. The phylogenetic analysis showed that AaCHD1 and AaCHD2 were highly homologous to the CHD amino acid sequences in Stemphylium lycopersici and Cochliobolus heterostrophus, respectively. Furthermore, A. alternata can grow with phenolic acids as the sole carbon source and differentially metabolize phenolic acids in pear fruit peel. Specifically, it showed stronger degradation effects on ferulic acid, chlorogenic acid, and caffeic acid than on p-coumaric acid. At the same time, exogenous phenolic acids up-regulated the expression of AaCHD1 and AaCHD2, and exogenous caffeic acid had the strongest up-regulatory effect, followed by ferulic acid and p-coumaric acid. [Conclusion] AaCHD in A. alternata played a role in degrading phenolic acids in pear fruit peel, and the degradation effects vary with different phenolic acids, which provides a theoretical basis for comprehensively revealing the molecular mechanism of AaCHD in overcoming the defense effect of phenolic acids in pear peel.

Abstract:[Background] The recent studies have shown that Metarhizium spp., major entomopathogenic fungi, can colonize plant roots and promote plant growth. However, the effects and mechanisms of Metarhizium in promoting rice growth remain unclear. In addition, the colonization abilities and growth-promoting effects of different Metarhizium strains remain to be studied. [Objective] To clarify the colonization abilities and rice growth-promoting effects of M. robertsii and M. acridum. [Methods] The colonization abilities of M. robertsii and M. acridum were determined by selective culture, microscopic observation, and molecular methods. At the same time, the growth and physiological indexes of rice treated the two strains under soil cultivation and hydroponic cultivation conditions were compared, including the seed germination rate, plant height, taproot length, fresh weight, dry weight, chlorophyll content, and root vitality. [Results] Only M. robertsii colonized rice roots, accelerated the germination of rice seeds, and promoted the growth of rice. Under soil cultivation conditions, M. robertsii increased the height, taproot length, fresh weight, dry weight, chlorophyll content, and root vitality of rice plants by a maximum of 45.2%, 72.3%, 30.5%, 72.6%, 92.3% and 63.7%, respectively. Under hydroponic cultivation conditions, it increased the plant height, taproot length, fresh weight, dry weight, and chlorophyll content by a maximum of 59.3%, 17.9%, 90.9%, 28.4%, and 64.8%, respectively. M. robertsii exerted stronger promoting effects on the root length, dry weight and chlorophyll content of rice plants in soil cultivation than in hydroponic cultivation, while it demonstrated stronger promoting effects on the plant height and fresh weight of rice plants in hydroponic cultivation than in soil cultivation. [Conclusion] M. robertsii could colonize rice roots and promote the growth of rice, whereas M. acridum had no significant effect on the growth of rice. The findings provide a theoretical basis for deciphering the rice growth-promoting mechanism of Metarhizium.

Abstract:[Background] Free gossypol in cottonseed meal limits the release of nutrients and the application of cottonseed meal as protein feed, and microbial fermentation is an effective approach for the removal of gossypol from cottonseed meal. [Objective] To screen a strain capable of degrading gossypol and decipher the mechanism of gossypol degradation by the strain. [Methods] The strain capable of degrading gossypol was screened with the degradation rate of gossypol as the indicator and identified by morphological observation, physiological and biochemical tests, and phylogenetic analysis based on 16S rRNA sequences. The possible intermediates of gossypol metabolism by the selected strain were analyzed and the utilization capability of the strain for the key intermediates of polycyclic aromatic hydrocarbons was determined. Furthermore, whole genome sequencing of the strain was carried out to mine the genes encoding the enzymes involved in the degradation of gossypol. [Results] A strain capable of degrading gossypol was isolated from a soil sample in the outskirts of Baoding and named M-15. After fermentation by strain M-15, the content of free gossypol in cottonseed meal decreased from 882.07 mg/kg to 32.38 mg/kg, which indicated a degradation rate as high as 96.33%. The strain was identified as Bacillus subtilis. Salicylic acid, catechol, and gentianic acid were the major intermediates in the degradation of gossypol by strain M-15. According to the utilization capacity of the intermediates in the metabolism of polycyclic aromatic hydrocarbons, the possible degradation pathway of gossypol in the fermentation of cottonseed meal by strain M-15 was deduced as follows. Naphthalenes were produced from gossypol with the binaphthalene structure and then formed catechol or gentianic acid via the salicylic acid pathway. Catechol and gentianic acid underwent ring opening at the meta position, and the products entered the tricarboxylic acid cycle to complete the degradation. [Conclusion] The strain M-15 highly effective in degrading gossypol was screened out. It may degrade gossypol via the salicylic acid pathway. The findings provided a theoretical basis for the development and application of microbial fermentation for detoxification of cottonseed meal.

Abstract:[Background] d-allulose is an excellent sugar substitute with high sweetness and low calories. d-allulose 3-epimerase (DPEase) catalyzes the epimerization of d-fructose to produce d-allulose, being an essential enzyme in the enzymatic production of d-allulose. [Objective] To improve the potential of DPEase for industrial application, we realized heterologous expression of this enzyme and characterized the enzymatic properties. [Methods] A DPEase (NtDPEase) from Novibacillus thermophilus was expressed in Komagataella phaffii under the regulation of the glyceraldehyde-3-phosphatedehydrogenase (GAP) constitutive promoter. The enzymatic properties of the recombinant protein were then characterized. [Results] The transformant was incubated in a 5 L fermenter for high cell density fermentation (108 h), with the highest enzyme activity of 201.3 U/mL. The recombinant enzyme was purified to reach the electrophoretic purity, with a molecular weight of 35 kDa. This enzyme showed the best performance at pH 7.0 and 60 ℃ and good stability within the ranges of pH 6.0-8.0 and temperatures below 45 ℃. Furthermore, the enzyme was used to convert d-fructose with different concentrations (100-500 g/L) to produce d-allulose, which scored the highest conversion rate of 29.0%. [Conclusion] This study achieves the efficient expression of NtDPEase in K. phaffii for the first time, providing a theoretical and practical basis for the enzymatic production of d-allulose.

Abstract:[Background] Staphylococcus aureus is a key reason for the increase in the global drug resistance burden. Bacteriocins produced by lactic acid bacteria are a new method to treat pathogenic bacterial infections and has broad application prospects. [Objective] To screen the bacteriocins of lactic acid bacteria that inhibit S. aureus. [Methods] The agar diffusion method was used to screen the bacteriocin-producing lactic acid bacteria. Strains were identified by 16S rRNA gene sequencing and a phylogenetic tree was constructed using MEGA 11. After the effects of acids and hydrogen peroxide were excluded, the anti-enzymolysis property, pH stability, and thermostability of the bacteriocin produced by this strain were characterized. The growth curve, acid production capacity, and tolerance to simulated gastric fluid of the strain were studied. [Results] A strain named Leuconostoc mesenteroides WJY-6 was isolated from pumpkin in Yanji. It secreted a bacteriocin showing inhibitory effects on S. aureus from different sources. The bacteriocin exhibited a good anti-enzymolysis property and maintained over 35% of the inhibitory effect after being treated at 100 ℃ and 121 ℃. The bacteriocin showcased the strongest inhibitory activity at pH 3.0-5.0. The strain entered a stable growth phase after 18 h, with the pH dropping below 5.0 after 8 h, which steadily improved the inhibitory effect. The strain showed strong survival ability and proliferated actively in the simulated gastric fluid. [Conclusion] L. mesenteroides WJY-6 has a strong acid production ability and good tolerance to simulated gastric fluid. Moreover, it secretes a bacteriocin with excellent physical and chemical properties and inhibitory effect on S. aureus. The bacteriocin is expected to become a new alternative of antibiotics for the prevention and treatment of S. aureus.

Abstract:[Background] Porcine epidemic diarrhea virus (PEDV) is one of the major pathogens causing diarrhea in piglets. The rapid onset makes it difficult to document the cases, and few studies have reported the dynamics of PEDV distribution in pig farms after PEDV infection in piglets. [Objective] To explore the transmission dynamics of PEDV in large swine farms and improve the strategy for the prevention and control of porcine epidemic diarrhea (PED). [Methods] The transmission process of PEDV after infection in piglets in a closed large farm was simulated and the virus abundance in piglets and different areas of the farm was determined. [Results] The virus abundance of anal swabs and air samples presented consistent changes in the early stage of PEDV infection in piglets. The spread of PEDV in the farm was closely related to the movement of employees, and the bathing room might be a major hiding place of PEDV. [Conclusion] The virus abundance in the air of swine barns has the potential to be used as a monitoring indicator in the early stage of PED, and employee-associated media and sites are key targets for the prevention and control of PEDV. This study provides a reference for improving the control of PED and lays a foundation for research on the spread of similar viruses in large pig farms.

Abstract:[Background] Pale liver disease caused by duck adenovirus B2 (DAdV B2) infection has been widely prevalent in Muscovy duck flocks in China since 2014, and no incidence has been observed in other duck breeds. In this study, two suspected cases of pale liver disease were reported in Cherry Valley ducks. [Objective] To identify the causative agent of pale liver disease in Cherry Valley ducks. [Methods] PCR or RT-PCR and pathogen isolation were carried out with the internal organ samples of diseases ducks. The isolate was identified, sequenced, and used for the challenge in ducklings. [Results] The internal organ samples were DAdV B2 positive, and a strain named DAdV B2/BG19 was successfully isolated. The LMH cells infected with BG19 developed a characteristic cytopathic effect (CPE) with cell enlargement, rounding, and final disintegration. The isolate BG19 carried two fiber genes, and its sequences of hexon, fiber-1, fiber 2, and DNA polymerase gene shared the sequence identity above 98.26% with those of the DAdV B2 isolates submitted in GenBank, whereas these genes had the sequence identity of 77.12%, 30.8%, 34%, and 99.78%, respectively, with those of the DAdV B1 isolate GR. All the strains of DAdV B1 and DAdV B2 shared the same clade in the phylogenetic tree built based on DNA polymerase gene. The mutation G133T in the ORF67 gene of BG19 resulted in a premature stop codon, which led to a truncated ORF67 protein 14 residues shorter than that of previous prevalent strain CH-GD-12-2014. BG19 was pathogenic to 2-day-old Cherry Valley ducklings and Muscovy ducklings, with the morbidities of 50.0% and 87.5% and the mortalities of 12.5% and 37.5%, respectively. The clinical symptoms and pathological changes of dead ducks were similar to those of clinical cases. [Conclusion] A highly virulent strain of DAdV B2 with truncated ORF67 protein expression was successfully isolated and identified from a case of pale liver disease in Cherry Valley ducks. This was the first report about the pathogenicity of DAdV B2 in Cherry Valley ducks.

Abstract:[Background] Kirromycin is a complex linear polyketide-nonribosomal peptide compound produced by Streptomyces collinus Tü 365, which interacts with the bacterial elongation factor EF-Tu, thereby inhibiting protein synthesis and exhibiting narrow-spectrum antibacterial activity. Currently, kirromycin is widely used as an experimental reagent in studying ribosomal structure and function. Recent studies have reported that kirromycin and its analogs exhibit superior activity against Wolbachia compared to the registered drug doxycycline, making them potential lead compounds for treating filarial worm infections. [Objective] Combinatorial metabolic engineering methods were used to construct high-production strains of kirromycin to enhance kirromycin production and lay the foundation for further applications. [Methods] Based on the kirromycin biosynthetic gene cluster and biosynthetic pathways analysis, overexpression or co-overexpression of the genes encoding crotonyl CoA reductase (kirN), aspartate-1-decarboxylase (kirD), phosphopantetheinyl transferase (kirP), efflux pump proteins of the major facilitator superfamily (kirTI and kirTII), and acetyl-CoA carboxylase (acc) from Streptomyces coelicolor A3(2) under the control of constitutive promoter kasOp* were performed to increase kirromycin production in S. collinus. [Results] Overexpression or co-overexpression of the aforementioned genes had a certain effect on increasing kirromycin production. Better results were observed from the overexpression of the acc gene and co-overexpression of kirD, kirN, kirP, kirTI, and kirTII genes. Compared to the wild-type strain, kirromycin production increased by 57.8% and 65.6%, reaching 198.3 mg/L and 208.1 mg/L, respectively. A systematic search for homologous proteins-coding genes of kirromycin biosynthetic enzymes in publicly available bacterial genome databases revealed 31 biosynthetic gene clusters potentially synthesizing kirromycin-like natural products. [Conclusion] This study effectively increased kirromycin production in S. collinus using metabolic engineering methods, laying a solid foundation for further applications and development of kirromycin.

Abstract:[Background] The Chinese medicine Sanghuang contains active components such as polysaccharides, sterols, triterpenoids, and total phenols, exhibiting exceptional medicinal values including antioxidant, free radical-scavenging, immune-enhancing, and anti-tumor properties. Inonotus hispidus is a type of Sanghuang. Currently, there are limited research reports on the nutrient composition of I. hispidus. [Objective] To explore the nutritional value and content of active components in I. hispidus. [Methods] The levels of basic nutrients, active components, and pesticide and heavy metal residues were measured in the golden-colored MS-5 fruiting bodies, black MS-5 fruiting bodies, and golden-colored MS-9 fruiting bodies of I. hispidus and compared the measured results with those in the fruiting bodies of Ganoderma lucidum. [Results] The protein content and ash content in the three types of I. hispidus fruiting bodies increased by 1.96–2.20 times and 3.69–5.66 times compared with that of G. lucidum, respectively. The fruiting bodies of I. hispidus contained seven essential amino acids required by the human body. Moreover, the MS-9 (golden) fruiting bodies had the highest level of essential amino acids, which was 2.28 times and 1.62 times of that in G. lucidum and eggs, respectively. The content of polysaccharides, total phenols, and total flavonoids in the three types of I. hispidus fruiting bodies was 1.48–1.56, 3.42–5.70, and 3.67–4.83 times of that in G. lucidum, respectively. Furthermore, the levels of pesticide and heavy metal residues in I. hispidus fruiting bodies were below the national standards. [Conclusion] This study demonstrates that I. hispidus has a remarkable nutritional value and and promising medicinal value, as well as being safe and environmentally friendly, providing a scientific basis for its medicinal development.

Abstract:[Background] PDA is widely used in the production of wood-decay fungi, while the lack of wood components can easily lead to the degradation of the fungal strains. Therefore, it is urgent to improve the formula of PDA. [Objective] To overcome the shortcomings of routine PDA in the production of wood-decay fungi and achieve efficient and economical production. [Methods] According to the nutrient requirements of mycelial growth and the principle of saving costs, we treated agricultural wastes such as fresh mushroom stem residues and apple plant twigs and then supplemented them into routine PDA to design improved PDA. The formulas of improved PDA were screened with the mycelial growth rate (S) and dehydrogenase activity (K) of Lentinus edodes 808 and white Hypsizygus marmoreus as indicators. Furthermore, the formula of improved PDA was optimized, and the mycelial growth rate (S), mycelial weight increase (W), and mycelial fresh weight (G) were determined to evaluate the mycelial culture effect and benefit of the optimized formula of improved PDA. The correlations and differences of S, W, and G with K and cellulase activity (N) were analyzed to explore the correlation between mycelial growth and enzyme activity. [Results] The improved PDA formula with 1%-2% glucose, stem residues of white H. marmoreus or Pleurotus ostreatus, and apple plant twigs improved S and K. Among the 26 optimized formulas of improved PDA, B11 (twig extract 30 mL, fresh white H. marmoreus stem residue extract 10.0 mL, glucose 5.0 mL, potato extract 50.0 mL, and water 5.0 mL) demonstrated the best performance in improving the mycelial growth of L. edodes 808, increasing the S, W, and G by 7%, 106%, and 84%, respectively, while halving the glucose usage. The formula P16 (twig extract 30 mL, fresh P leurotus ostreatus stem residue extract 20.0 mL, glucose 5.0 mL, potato extract 40.0 mL, and water 5.0 mL) showed the best performance in improving the mycelial growth of white H. marmoreus, increasing the S, W, and G by 29%, 47%, and 129%, respectively. It not only decreased the glucose application by 50% and potato extract application by 20% but also reduced the overall costs by 10%, with outstanding economic and social benefits. There was no significant difference or correlation of K and N with S, W, and G. [Conclusion] Adding fresh mushroom stem residues (P. ostreatus or white H. marmoreus) and apple plant twigs to PDA can improve the mycelial growth and weight of L. edodes 808 and white H. marmoreus. Moreover, it can significantly reduce the usage of glucose and potato extract, decrease costs, and improve economic and social benefits. The mycelial growth showcases no correlation with dehydrogenase or cellulase activity.

Abstract:[Background] Mycoplasma synoviae (MS) is a common pathogen in poultry, posing a serious threat to the development of the poultry industry. The co-infection of MS with other pathogens makes it difficult to diagnose based on clinical symptoms. Therefore, it is urgent to establish a rapid, accurate, and sensitive method for rapid diagnosis of suspected sick birds to reduce economic losses. [Objective] To establish a TaqMan fluorescence quantitative PCR method for determining the load of MS in the blood of infected chicken, and to provide technical support for the clinical detection of MS infection. [Methods] A pair of specific primers and a probe were designed according to the conserved sequence of MS gene in GenBank. The optimal annealing temperature was determined by temperature gradient qPCR, and the amounts of primers and the probe were optimized by the matrix method. The standard curve was established with the genome of MS 0801 as a template, and the specificity, sensitivity, and repeatability of the established method were evaluated. Furthermore, the established method was used to measure the MS load in the blood of chicken samples infected via nasal drip or footpad challenge. [Results] The optimal annealing temperature of the established method was 55 ℃, and the amounts of primers and the probe (10 mol/L) were 0.8 mL and 0.4 mL, respectively. The amplification curve had a good linear relationship, with R²>0.99. The method had strong specificity since it had specific reaction only to MS and no reaction to other pathogens. In addition, the method had high sensitivity, with the lower limit of detection being 25 copies/μL blood. The coefficients of variation of inter-batch and intra-batch experiments were less than 2%, which indicated that the method had high repeatability. There was no significant difference in the peak or overall fluctuations of MS load in the chicken samples infected via nasal drip or footpad challenge, while the proliferation of MS in the blood of footpad challenge was faster than that of nasal drip challenge. [Conclusion] A TaqMan fluorescence quantitative PCR method for rapid detection of MS was established and used to detect the dynamic changes of MS in the blood of infected chicken. This method provided technical support for clinical detection of MS infection and new ideas for evaluation of vaccination performance.

Abstract:[Background] Phytophthora cryptogea P. is a quarantine pathogen causing serious symptoms in a variety of plants in the global range. [Objective] To establish a specific, sensitive, and quantitative assay for the detection of P. cryptogea. [Methods] Specific primers and probes for real-time fluorescence quantitative PCR were designed and screened according to the conserved sequence of Ypt1 in P. cryptogea. The reaction system and procedure were optimized in terms of primer concentration, probe concentration, and annealing temperature, and the standard curve and detection system were established under the optimal reaction conditions. The specificity, sensitivity, and repeatability of the established detection system were evaluated. [Results] Considering C_q, RFU, and cost, the optimal PCR conditions were determined as the primer concentration of 20 μmol/L, the probe concentration of 10 μmol/L, and annealing at 60 ℃. The linear equation of the established standard curve was y=−3.323x+40.767, with R²=0.998 and E=99.9%, which indicated the established system had good correlation and high amplification efficiency. No amplification curve appeared for the other eight common species of oomycetes and fungi, which indicated that the designed primers and probe had strong specificity. The established method showed the minimum limit of detection being only 1 copy and the minimum limit of stable detection being 10 copies. Compared with conventional PCR, the method established in this study increased the detection sensitivity by 10−100 times. The intra-batch and inter-batch tests with the established method showed the standard deviation (SD) of C_q ranging from 0.04 to 0.13 and the coefficient of variation (CV) ranging from 0.20% to 0.58%, indicating that the method had good repeatability, stability, and reliability. [Conclusion] We established a Ypt1-targeted TaqMan real-time fluorescence quantitative PCR method for the detection of P. cryptogea. This method can efficiently and specifically identify P. cryptogea infecting Gerbera jamesonii, serving the rapid and efficient detection of this pathogen at port clearance and in the field, particularly for the detection and identification of trace pathogens in core materials such as breeder’s seed and original species. It is essential for the early diagnosis and effective prevention and control of diseases, demonstrating a broad application prospect.

Abstract:[Background] With the rapid development of new types of stations and sequencing methods, the data in microbial ecology has experienced explosive growth, providing rich resources for revealing the role of microorganisms in global ecosystems. However, the processing and analysis of these large datasets pose challenges to conventional methods. Machine learning, with unique advantages in handling big data, has become a key technology to address these challenges. [Objective] This study comprehensively explored the developmental trends, current status, and hotspots in the application of machine learning in microbial ecology through bibliometric analysis, aiming to guide the future integration of machine learning with the research of microbial ecology. [Methods] The relevant articles published between 1991 and 2023 in the Web of Science (WOS) Core Collection were collected and analyzed. CiteSpace was used to visualize the evolution of the number of publications, international collaboration, and interdisciplinary status. Carrot2 was employed to mine textual data and build knowledge maps. [Results] The application of machine learning in the research of microbial ecology has undergone two distinct phases: stable growth followed by explosive growth, with 2018 marking a turning point. This research field has gained increasing attention, which led to continuous growth in the research output. The integration of machine learning with other disciplines, especially chemistry, physics, environmental sciences, and computer science, has become increasingly tight-knit, providing new perspectives for the advancement of scientific research. The application of machine learning in microbial ecology is extensive. The early studies primarily focused on sequence recognition and species identification. However, as deep learning and computer vision technologies have kept advancing since 2018, the research focus shifted towards predicting complex systems. The comparison of keywords between the two phases highlighted the evolution of machine learning in microbial ecology from basic data processing and analysis to complex and advanced prediction models. [Conclusion] According to the results of bibliometric analysis and considering challenges like data scarcity, difficulties in model selection, and poor interpretability in applying machine learning in microbial ecology, we suggest that international collaboration, data sharing, and interdisciplinary exchange should be emphasized in the future to promote the development of interpretable machine learning.

Abstract:[Background] Endophytes exist in almost all plants that have been studied so far, and plant hosts infected with endophytes often experience rapid growth and develop resistance to stress, diseases, and natural enemies. Studies have been conducted regarding the endophyte diversity, while few studies involve quantitative statistics and analysis. [Objective] To study the current research status and hotspots of endophytic fungal diversity by bibliometrics. [Methods] The relevant articles were retrieved from the Web of Science (WOS) Core Collection with the keywords of “endophytic fungal diversity and plant” and the time interval of 1992-2022. The number of articles, journals, research institutions, main authors, and keywords were analyzed and the distribution was visualized by CiteSpace. [Results] The keyword burst analysis showed that biodiversity, symbiosis, and soil were closely related to the period of article surging in this field. The cluster analysis of keywords yielded 9 keyword tags in 3 hot research directions. [Conclusion] The number of articles published in English about endophytic fungal diversity and plant has grown rapidly since 2019. Endophytic fungal diversity, promotion of host growth by endophytic fungi, and medicinal properties of secondary metabolites of endophytic fungi are currently the focuses of research in this field. In the future, high-impact authors and institutions should enhance collaboration and carry out in-depth and systematic research on the three hot spots and shortcomings in this field.

Abstract:[Background] The role of gut microbiota in the occurrence and development of sepsis has been extensively reported. Considering the important role of gut microbiota in sepsis, it may be a new way to treat sepsis by regulating the structure or products of gut microbiota. However, the safety issue has been a main factor limiting the large-scale application of the microbial therapy. China has a number of sepsis patients, while the research on the microbial therapy for sepsis starts late. Reviewing the international studies about sepsis and gut microbial therapy is of great significance for promoting China’s research in this field. [Objective] To analyze the research status, hotspots, and frontiers of sepsis and gut microbial therapy. [Methods] We retrieved the articles about gut microbial therapy and sepsis from Web of Science (WOS) core collection and China National Knowledge Infrastructure (CNKI) with the time interval from January 2001 to November 2023. CiteSpace was used to perform visual analysis of the number of publications, publishing countries, publishing institutions, authors, journals, and keywords and establish the visual diagrams. [Results] After data retrieval and screening, 807 articles from WOS and 49 articles from CNKI were included for analysis. Within the global range, the country with the largest number of publications about sepsis and gut microbial therapy was the United States, and the country with the highest centrality was Sweden; the most prolific institution was the University of Western Australia, while the institution with the highest centrality was the University of London; the highly productive authors included PATOLES, RAOS, ATHALYEJAPE G, and FANG H; the high-frequency keywords included necrotizing enterocolitis, sepsis, double blind, preterm infants, and gut microbiota; the main clusters were #0 necrotizing enterocolitis, #1 enteral nutrition, #2 preterm infants, #3 fecal microbiota transplantion, #4 critical care, #5 Escherichia coli, #6 sepsis, #7 acute pancreatitis, etc. In China, the main research institutions in this field included Southern Medical University, Zhengzhou University, and Hebei Medical University; the keywords included sepsis, probiotics, gut microbiota, and enteral nutrition; the main clusters were #0 immune function, #1 gut microbiota, #2 enteral nutrition, #3 sepsis, #4 infection, #5 fecal microbiota transplantation, etc. [Conclusion] CiteSpace was used to conduct bibliometric and visual analyses of the research on gut microbial therapy and sepsis. The research in this field continued to attract the attention of research institutions and researchers around the world. Sepsis and necrotizing enterocolitis represent the hot words in the research of gut microbial therapy and sepsis in China and the world, respectively. The research in this field is evolving from basic exploration to clinical application.

Abstract:[Background] Since no effective method is available in clinical practice to cure inflammatory bowel disease (IBD), an increasing number of researchers are applying fecal microbiota transplantation (FMT) to the treatment of IBD, hoping to develop safe and effective supplementary therapies. [Objective] To present innovative research concepts and avenues for clinical medical practitioners by reviewing the research hotspots and frontiers concerning FMT for IBD. [Methods] We employed CiteSpace 6.2.R6 to visually analyze the publications about FMT for IBD. The data were gathered from the China National Knowledge Infrastructure and Web of Science, spanning the period from January 2003 to January 2024. [Results] A total of 882 publications were included in this study, encompassing 664 publications in the English language and 218 in Chinese. The results unveiled that the publications in the English language principally focused on the interplay between post-FMT alterations in gut microbiota and resultant clinical outcomes, safety evaluation, and mechanisms of action. The publications in Chinese centered predominantly on the therapeutic protocols involving FMT, safety evaluation, and mechanisms of action. [Conclusion] Both domestic and overseas researchers have augmented their attention toward FMT for IBD. Nonetheless, discernible disparities persist between China and other countries in this realm. There exists a vital need for enhanced collaboration among domestic institutions, which can foster collective impetus to propel the advances in FMT for IBD patients in China. In addition, the pivotal engagement of nurses is imperative for the establishment of a robust medical care framework within this sphere.

Abstract:Microbiology Experiment was redesigned and set as several scientific research projects. The modules of this course included environmental microbial diversity, screening, identification, cultivation, and enzyme production of enzyme-producing strains, and microbial test of water quality. Each module aimed to solve a scientific problem. At the same time, the basic experiment techniques and methods of microbiology were integrated in the research-oriented experiments. Thus, a comprehensive, research-oriented teaching mode was constructed for Microbiology Experiment. Furthermore, the staff, textbook, and materials supporting the teaching were provided. The teaching quality was evaluated by operation examinations and questionnaire survey. Such a modular teaching mode paves a new way for the reform of Microbiology Experiment teaching.

Abstract:With rich connotation and wide extension, Microbiology provides the theoretical basis and practical guidance in the cultivation of talents majoring in biological, food, and pharmaceutical sciences in colleges and universities. However, the current teaching mode of Microbiology is not suitable for the training goals of talents targeted at the development needs of national and regional industries. This study incorporated the concept of artificial intelligence, which has developed rapidly in recent years, into the teaching of Microbiology, creating an intelligent teaching mode characterized by “trinity of intelligence” (integration of intelligence into the teaching contents, evaluation of whole-process intelligent teaching, and progressive cultivation of intelligent thinking) of Microbiology. This teaching mode gradually improves students’ intelligent thinking and helps to achieve the goal of fostering innovative and application-oriented talents.

Abstract:Microbial Physiology is a basic course for the undergraduates majoring in microbiology. With the advances of science and technology, the research field of Microbial Physiology is expanding. Accordingly, the teaching contents and mode of Microbial Physiology should be updated to reflect the state-of-the-art research achievements and adapt to the requirements of agricultural universities and colleges. Taking the teaching of myxobacteria as an example, we built the teaching and evaluation system composed of interest guidance, theory impartation, social practice, and comprehensive evaluation by two years of course development. Furthermore, we organized the field investigation and discussion on the topic of myxobacteria and agricultural applications. The teaching content innovation and teaching mode exploration of Microbial Physiology by combining the basic theory with agricultural practice improves the ability of undergraduates to think independently and apply what they have learned, providing support for training high-quality scientific and technological talents in agriculture.