Interferon gamma-inducible protein 16 (IFI16), a pivotal member of the pyrin and hematopoietic expression, interferon-inducible nature, and nuclear localization (HIN) domain-containing protein (PYHIN) family, possesses a unique molecular structure that enables it to recognize diverse nucleic acid molecules within cells. As a key immunoregulatory factor, IFI16 participates in the transduction of innate immune signaling through multiple pathways and plays a significant role in host antiviral defense. This review systematically summarized the molecular characteristics of IFI16 and its regulatory mechanisms in innate immunity and viral infection, aiming to provide a theoretical basis for the development of therapeutic targets and antiviral drugs.

Soil-borne diseases are currently the most significant type of plant disease restricting crop production and threatening food safety. The rhizosphere microbiome, often regarded as the “second genome of plants”, has shown considerable potential in controlling soil-borne crop diseases. The use of rhizosphere microbes to control soil-borne diseases offers many advantages, such as being environmentally friendly, efficient, and broadly applicable, which makes it a hot topic in rhizosphere microbe research. In this review, we first introduced rhizosphere microbes and their potential for controlling soil-borne crop diseases. Subsequently, by integrating the latest research advances, we systematically summarized seven mechanisms of microbial control against soil-borne diseases and categorized them into three pathways: (1) direct interactions between microbes and pathogens; (2) direct and indirect interactions between microbes and plants; (3) indirect interactions among microbes. Furthermore, we reviewed the current applications of the rhizosphere microbes in controlling soil-borne crop diseases. Finally, we analyzed the key research challenges in using rhizosphere microbes for soil-borne disease control and discussed potential solutions, aiming to provide references for advancing the green control of soil-borne diseases.

Peptidoglycan as a key component of the bacterial cell wall is essential for maintaining bacterial morphology and osmotic stability. During normal bacterial growth, peptidoglycan is continuously remodeled through synthesis and hydrolysis, achieving a dynamic equilibrium. Peptidoglycan hydrolases play a central role in regulating peptidoglycan homeostasis, and the hydrolysis products (peptidoglycan fragments) are recycled for biosynthesis via the peptidoglycan recycling pathway. Growing evidence indicates that peptidoglycan fragments function as important signaling molecules to regulate critical physiological processes such as antibiotic resistance, endospore germination, and interspecies interactions, greatly expanding our understanding of bacterial physiological regulation. This review summarizes the major classes of bacterial peptidoglycan hydrolases and highlights recent advances in the role of peptidoglycan fragments as signaling molecules in regulating cellular processes, providing a theoretical foundation for further exploration of the multifaceted physiological functions of bacterial peptidoglycan.

Soil colloidal phosphorus (CP) is an active component that cannot be overlooked in the soil phosphorus cycle. Its occurrence forms and migration behavior significantly influence phosphorus bioavailability and environmental risks. This paper systematically reviews the multiscale regulatory mechanisms of microbial actions in CP transformation and migration. It focuses on chemical effects (e.g., proton secretion, iron reduction, and organic acid coordination), physical effects (e.g., extracellular polymer trapping and biofilm pore remodeling), and microbial community dynamics and molecular ecology three dimensions to elucidate how microbes drive CP activation, immobilization, and migration through interfacial reactions, functional gene expression, and community interactions. The paper further explores the synergistic effects of multiple factors on microbial regulation processes, including soil physicochemical properties, agricultural management practices, and emerging pollutants. It identifies current research gaps in cross-scale coupling, in situ characterization, and mechanism modeling, while providing theoretical foundations and research directions for enhancing soil phosphorus utilization and pollution control.

Hyperuricemia is a pathological phenomenon in which the metabolism of uric acid in the human body is disrupted and blood uric acid levels remain above normal. In recent years, gut microbiota has become a research hotspot for various metabolic diseases, serving as a potential new target for the prevention and treatment of hyperuricemia. This article reviews the metabolic pathways and physiological effects of uric acid in the human body and elucidates the regulatory mechanisms of gut microbiota on hyperuricemia. Such mechanisms include inhibiting uric acid synthesis by the breakdown and internalization of purines, degrading uric acid and promoting uric acid excretion, repairing intestinal barriers, influencing intestinal metabolites, and regulating intestinal immunity. In addition, this article summarizes the potential applications of optimizing dietary structure, taking probiotics and prebiotics, and fecal microbiota transplantation in the treatment of hyperuricemia, providing new ideas and references for the prevention and treatment of hyperuricemia.

The gut structure and functional performance rely on the stable type and quantity of gut mucosal epithelial cells, whose stability depends on continuous proliferation, differentiation, and migration of intestinal stem cells (ISCs) located in the crypts. Interactions between gut microbiota and ISCs support the homeostasis of the gut ecosystem. Intestinal epithelial cells (IECs) differentiated from ISCs influence the composition and function of gut microbiota through secreting immunoglobulins, mucins, etc. Meanwhile, the microorganism-associated molecular patterns (such as lipoteichoic acid and lipopolysaccharides) and metabolites (such as short-chain fatty acids and bile acids) from gut microbiota form the unique gut microenvironment to regulate the activity of ISCs and the homeostasis of IECs. Regulating the activity of ISCs and gut health by modifying gut microbiota has become a focus of current research. Thus, this review elaborates on the impact of ISCs on the gut microbiota as well as the regulatory roles of gut microbiota and related metabolites on the proliferation and differentiation fate of ISCs, aiming to broaden the understanding of the interaction between gut microbiota and ISCs. It is expected to provide strategies and targets for the regulation on gut health.

In recent years, microbially mediated mineralization, a widespread form of biomineralization in nature, has emerged as a research hotspot. This process not only exerts profound influences on mineral formation and global biogeochemical cycling but also contributes to mineral deposition within living organisms, thereby holding significant ecological and biological importance. Among microorganisms, bacteria—characterized by high metabolic activity and remarkable environmental adaptability—represent the most prominent agents in microbial mineralization. This review summarizes the mechanisms of bacteria-mediated mineralization and their applications in the biomedical field, with a particular emphasis on three principal mechanisms: bacteria-controlled mineralization, bacteria-induced mineralization, and bacteria-influenced mineralization. Furthermore, the potential applications of these processes in medical imaging, targeted therapy, and tissue engineering are discussed. The overarching aim is to provide valuable references and scientific insights to inform future research and facilitate their translation into practical applications.

Antibiotic resistance (AR) in microorganisms has become a crucial challenge to global public health security. The acquirement of AR in microorganisms is often accompanied by a fitness cost. Typically, in an environment without antibiotics, the bacterial community with AR shows weaker competitiveness than susceptible bacteria, which makes antibiotic resistance genes (ARGs) a burden for bacteria. This article elaborates on the mechanisms underlying the generation of fitness costs and the corresponding measurement methods, provides examples to illustrate the fitness costs mediated by ARGs under different acquisition methods, and introduces the differences in fitness costs between chromosome-mediated and plasmid-mediated ARGs as well as their molecular mechanisms. Finally, it proposes prevention and control strategies for antibiotic resistant bacteria (ARB) based on fitness costs. This article reveals the biological law of the trade-off between antibiotic resistance and bacterial fitness and provides ideas for preventing and controlling the global public health security issues caused by ARB and ARGs.

[Objective] To explore the changes and differences of gut microbiota of worker bee larvae of Apis cerana cerana and Apis mellifera ligustica after infection with Chinese sacbrood virus (CSBV) and evaluate the antiviral activity of Bacillus subtilis against CSBV. [Methods] Two-day-old larvae of A. c. cerana and A. m. ligustica were collected from colonies and artificially reared in an incubator (34 ℃, RH 85%). The 3-day-old larvae were inoculated with CSBV and samples were collected when the larvae were 4 and 7 days old for 16S rRNA gene sequencing. In addition, the 3-day-old larvae of A. c. cerana were fed with different concentrations of B. subtilis suspensions during CSBV inoculation. When the larvae were 7 days old, the antioxidant capacity indicators malondialdehyde (MDA) content and superoxide dismutase (SOD) activity were determined. Additionally, the relative expression levels of four antimicrobial peptide genes (Abaecin, Apidaecin, Hymenoptaecin, and Defensin) and the CSBV gene were determined by real-time fluorescence quantitative PCR. [Results] The number of gut microorganisms in bee larvae significantly decreased after CSBV infection. The abundance of Bacillus in the gut of 7-day-old A. c. cerana larvae significantly decreased. The gut of A. m. ligustica larvae showed significantly decreased abundance of Streptomyces and significantly increased abundance of Brevundimonas. At 4 days old, CSBV-infected A. c. cerana larvae had significantly higher abundance of Melissococcus in the gut than the infected A. m. ligustica larvae. At 7 days old, CSBV-infected A. c. cerana larvae had significantly lower Chao1 index than the control group and the infected A. m. ligustica larvae, which indicated that the gut microbiota diversity of A. c. cerana larvae was more susceptible to CSBV. The SOD activity of 7-day-old A. c. cerana larvae fed with 1×10⁴ CFU/kg B. subtilis significantly increased, while other doses of B. subtilis had no significant effect on the SOD activity in the larvae. All doses of B. subtilis significantly reduced the MDA content in bees. The relative expression levels of CSBV in the three treatment groups of 1×10⁴, 1×10⁶, and 1×10⁸ CFU/kg were significantly down-regulated. Moreover, the expression level of CSBV in the 1×10⁶ CFU/kg group was the lowest and significantly lower than that in the 1×10⁸ CFU/kg group. However, there were no significant differences in the expression levels of the four antimicrobial peptide genes among different treatment groups. [Conclusion] CSBV infection has a more significant impact on the gut microbiota diversity of A. c. cerana larvae. B. subtilis has a certain inhibitory effect on CSBV.

[Objective] To investigate the metabolite differences among different varieties and grades of flue-cured tobacco, as well as the impacts of nicotine-degrading bacteria on the quality of different grades of tobacco leaves. [Methods] This study employed untargeted metabolomics to identify and analyze metabolites in fermented tobacco leaves of ‘Yunyan 87’ and ‘Yunyan 97’, specifically B2F and C2F grades, while also examining the influences of nicotine-degrading bacteria on the quality of different grades of flue-cured tobacco leaves. [Results] There were significant metabolite differences between tobacco leaves of different varieties and grades. A total of 131 differential metabolites were identified between the samples of ‘Yunyan 87’ and ‘Yunyan 97’, while 138 differential metabolites were identified between B2F and C2F grades. These differential metabolites mainly included amino acids, flavonoids, alkaloids, and their derivatives. Analysis of KEGG metabolic pathways and enrichment levels for differential metabolites across different varieties and grades all indicated that flavonoid biosynthesis pathways were the most prominent. Furthermore, this study successfully isolated two bacterial strains, Pseudomonas sp. TR9 and Pseudomonas sp. TR14, from tobacco-cultivated soil, both capable of utilizing nicotine as the sole carbon and nitrogen source. Inoculation of the strain combination into different grades of tobacco leaves significantly reduced the content of nicotine, protein, and starch in lower-grade tobacco leaves. [Conclusion] This study reveals the mechanism by which varieties and grades affect the quality of tobacco leaves through the flavonoid biosynthesis pathways, and verifies the improvement effects of nicotine-degrading bacteria on low-grade tobacco leaves, providing theoretical support for the improvement of flue-cured tobacco quality and the optimization of fermentation processes.

[Objective] To provide a theoretical basis for developing microbiome-based ecological control strategies against citrus Huanglongbing (HLB), a devastating bacterial disease seriously threatening the global citrus industry. [Methods] Rhizosphere soil samples from both HLB-infected and healthy citrus trees in Yizhang County, Hunan Province, were investigated. Using 16S rRNA gene and ITS region amplicon sequencing, we systematically analyzed the impact mechanism of HLB on the rhizosphere micro-ecosystem. [Results] The results showed that HLB infection significantly reduced the organic matter (6.65 g/kg) and available phosphorus (7.25 mg/kg) content of the rhizosphere soil compared with that of the healthy plants, and triggered a significant decrease in the alpha diversity of bacterial communities and a significant increase in the alpha diversity of fungal communities (P<0.05). Beta diversity analysis showed that HLB significantly altered the structure of the microbial communities. Specifically, the relative abundance of pro-biotic bacteria such as Pseudomonadota and Gemmatimonadota decreased, while oligotrophic Acidobacteriota and Chloroflexota were significantly enriched. In fungal communities, the abundance of saprophytic fungi in the phyla Ascomycota and Basidiomycota increased by 5.32% and 7.38%, respectively, while the phylas Rozellomycota and Mortierellomycota decreased by 12.30% and 3.23%, respectively. HLB disrupted the rhizosphere microbial balance by inhibiting Rozellomycota, leading to excessive proliferation of saprophytic fungi and weakening the system’s disease resistance. Analysis at the order level further revealed that beneficial bacterial groups such as Burkholderiales and Hyphomicrobiales were significantly depleted, whereas stress-adaptive groups like Ktedonobacterales showed significant proliferation. PICRUSt2 analysis revealed that HLB disturbed the structure of the citrus rhizosphere bacterial community via metabolic pathways and genetic information processing. HLB also utilized saprophytic and ectomycorrhizal fungi to maintain soil health. [Conclusion] This study revealed that HLB affects soil microecological balance by remodeling the structure and function of citrus rhizosphere microorganisms, and the results may provide a theoretical basis for the development of ecological prevention and control strategies for HLB based on microbiome regulation.

[Objective] To investigate the biostimulatory effects of Bacillus velezensis XZT106 on the tuber crop sweet potato (Ipomoea batatas) and elucidate the potential mechanisms underlying its yield increase. [Methods] Sweet potato plants were treated by foliar spraying with B. velezensis fermentation broth, with the plants treated with inactivated B. velezensis fermentation broth as the control. We analyzed the chloroplast content, chloroplast ultrastructure, and antioxidant enzyme activity as well as the structure and metabolite composition of endophyte communities in different ecological niches of sweet potato plants to delve into the mechanisms by which B. velezensis fermentation broth increases the sweet potato yield. [Results] Foliar application of B. velezensis increased the sweet potato yield, enhanced the antioxidant enzyme activity in the roots, induced changes of chloroplast ultrastructure, and led to a more compact matrix structure with enlarged intracellular starch granules. In addition, foliar application of B. velezensis caused significant changes of endophyte community structures in various parts of sweet potato plants, significantly reducing the relative abundance of Fusarium and increasing the relative abundance of Pantoea. Moreover, the foliar application significantly altered the metabolome profiles of leaves and soil. Riboflavin metabolism, zeatin biosynthesis, and isoflavone biosynthesis, which regulate growth and enhance stress resistance, were significantly upregulated in leaves. The axon regeneration pathway promoting lateral root development and the glycerophospholipid metabolism pathway promoting cell proliferation were significantly upregulated in soil. [Conclusion] B. velezensis fermentation broth exerts a plant growth-promoting effect by enhancing antioxidant capacity, improving leaf cell ultrastructure, reshaping the endophyte community structure, and activating key growth-promoting and stress response metabolic pathways in sweet potato plants. These findings provide a new theoretical foundation for the application of B. velezensis-based microbial inoculants in enhancing the sweet potato yield.

[Objective] By examining intracellular and extracellular metabolite changes in ectomycorrhizal fungi (ECMF) under acidic aluminum stress, we identified key resistance-related metabolites and pathways, aiming to elucidate the aluminum tolerance mechanisms from the perspective of metabolic physiology and offer a theoretical basis for using ECMF in restoring aluminum-contaminated forests. [Methods] Pisolithus tinctorius was cultured in vitro in the acidic medium (pH 3.8) containing 0.0 mmol/L or 1.0 mmol/L Al³⁺. Untargeted metabolomics was employed to analyze changes in intracellular and extracellular metabolite levels. [Results] Compared with that under the 0.0 mmol/L Al³⁺ treatment, the colony diameter of P. tinctorius under 1.0 mmol/L Al³⁺ stress decreased significantly by 23.67%. In addition, the intracellular levels of nucleotides including uridylic acid, cytidine monophosphate, uridine, uridine diphosphate, cytidine, and guanosine were upregulated under 1.0 mmol/L Al³⁺ stress. Extracellular levels of organic acids such as shikimic acid, fumaric acid, heptanoic acid, and tartaric acid, along with carbohydrates including l-arabinose, trehalose, sucrose, and glucose, were also upregulated. Pyrimidine metabolism and citric acid cycle pathways were enriched intracellularly, while ABC transporters and phosphotransferase system pathways were enriched extracellularly. The potential biomarkers identified in the intracellular environment was citric acid, and those identified in the extracellular environment were trehalose and tartaric acid. [Conclusion] Acidic aluminum stress inhibits the growth of P. tinctorius. Intracellularly, P. tinctorius maintains cellular homeostasis and energy supply through enhanced nucleotide accumulation and activation of the citric acid cycle. Extracellularly, P. tinctorius promotes organic acid secretion and carbohydrate efflux to resist aluminum toxicity and associated oxidative damage.

[Objective] As soil acidification in southwestern China becomes increasingly severe, the labile phosphorus pool is transformed into a non-labile phosphorus pool, which reduces the availability of soil phosphorus, affecting crop yield and wasting phosphate fertilizer resources. In this study, we prepared a biochar-immobilized phosphorus-solubilizing bacterial agent with biochar as the carrier and a strain capable solubilizing both organic phosphorus and inorganic phosphorus as the immobilized strain and then optimized the preparation conditions. Furthermore, this bacterial agent was evaluated in terms of the stability and the solubilizing effects on insoluble phosphorus. [Methods] Selective media were used for the isolation of phosphorus-solubilizing bacteria from plant rhizosphere soil. The molybdenum-antimony colorimetric method was employed to quantify the ability of bacteria to solubilize phosphorus. The bacterial strain was identified through physiological and biochemical tests and molecular biological analysis. The immobilized bacterial agent was prepared by the adsorption method, and the preparation conditions were optimized by single factor experiments. The prepared agent was characterized by Fourier transform infrared spectrometry and scanning electron microscopy. Furthermore, the metabolic spectrum of organic acids and phosphatase activity were qualitatively and quantitatively tested by HPLC and the fluorescence method, respectively. [Results] The strain Klebsiella sp. was isolated for immobilization, and its abilities to solubilize lecithin and tricalcium phosphate were 236.5 mg/L and 200.3 mg/L, respectively. Genome analysis showed that the strain N107 carried 27 genes related to organic and inorganic phosphorus solubilization. The optimized preparation conditions were biochar addition of 30.0 mg/mL, N107 inoculation amount of 6.0%, immobilization temperature of 30.0 ℃, and immobilization time of 12.0 h. The bacterial agent prepared under the optimal conditions increased the phosphorus-solubilizing capacity for lecithin and tricalcium phosphate by 24.0% and 22.5%, respectively, compared with the free bacterial strain. The biochar-immobilized phosphorus-solubilizing bacterial agent contained more oxygen-containing functional groups, compared with the original biochar, its total specific surface area and external surface area increased by 61.9% and 165.1%, respectively. The mechanism of phosphorus solubilization by the immobilized bacterial agent was preliminarily analyzed. The results showed that the levels of tartaric acid, citric acid, and total acids changed significantly and the activities of acid and alkaline phosphatases in the culture medium were effectively improved, although the types of organic acids secreted by the agent had no obvious changes. The structural equation model showed that pH value was closely related to phosphatase activity and organic acid content, and the immobilized bacterial agent can promote the activation of insoluble phosphorus by increasing phosphatase activity and organic acid content. [Conclusion] The immobilized phosphorus-solubilizing bacterial agent prepared in this study provides a good bioremediation material for the activation of insoluble phosphorus. This study provides an innovative perspective for developing green remediation strategies based on microbiomes.

[Objective] To investigate the antifungal activity of Kobusin against Trichophyton interdigitale and its underlying mechanisms. [Methods] The minimal inhibitory concentration (MIC) of Kobusin was determined by the broth microdilution assay. The inhibitory effect of Kobusin on spore germination was observed microscopically, while that on hyphal radial growth was assessed on the agar plates containing Kobusin. Scanning electron microscopy (SEM) was employed to examine the morphological alterations in hyphae. Fluorescence microscopy and nucleic acid and protein leakage assays were employed to evaluated cell membrane integrity. Malvern Zetasizer was used to measure the changes in Zeta potential. A microplate reader was used to measure transmembrane potential, alkaline phosphatase (AKP) activity, malondialdehyde (MDA) content, reactive oxygen species (ROS) accumulation, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities, mitochondrial membrane potential (MMP), ATP levels, as well as succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) activities. [Results] Kobusin exhibited a MIC of 39 μg/mL against T. interdigitale, significantly inhibiting spore germination and hyphal growth. SEM revealed severe ultrastructural damage to hyphae. Fluorescence microscopy confirmed compromised membrane integrity, evidenced by increased nucleic acid and protein leakage and disrupted Zeta/transmembrane potentials. Meanwhile, Kobusin significantly increased the MDA content and ROS accumulation, inhibited the activities of AKP, SOD, CAT, and POD, markedly reduced MMP, decreased ATP synthesis, and weakened the activities of SDH and MDH. [Conclusion] Kobusin exerts antifungal effects by inhibiting spore germination and hyphal growth, disrupting cell membrane and cell wall integrity, interfering with membrane potential stability, inducing oxidative stress damage, and impairing mitochondrial energy metabolism.

Probiotic products have attracted increasing attention for their potential to modulate the microbiota. However, most commercial products are designed for oral administration, and their probiotic properties relevant to topical use in the reproductive tract remain insufficiently evaluated. [Objective] To assess the probiotic properties of lactic acid bacteria (LAB) derived from probiotic products, with a particular focus on their potential for topical application, thus providing scientific evidence for their use in vaginal health. [Methods] Seven common oral probiotic products (P1-P7) containing at least two different LAB species were selected from major e-commerce platforms via keyword screening, along with one clinical probiotic product (P8). LAB strains were isolated and identified from these products. We evaluated the acid tolerance, as well as the growth characteristics under different pH conditions, of the isolates by culturing them in the media of varying pH values. The antimicrobial activities of the isolates were determined via co-culture assays with pathogenic microorganisms, while hemolysis assays and genomic comparison were conducted to assess safety. [Results] The isolation rates of LAB strains from P1 to P8 were 50.0% (2/4), 0 (0/4), 66.7% (2/3), 12.5% (1/8), 33.3% (2/6), 40.0% (2/5), 0 (0/7), and 100.0% (1/1), respectively. Most strains grew well at pH 6.0-7.0, and some maintained growth at pH 4.0. Strains P4 and P8 exhibited superior acid tolerance to the others. The inhibitory effects of different strains against common vaginal pathogens varied significantly. Strains P1-2, P5-1, P6-1 and P6-2 demonstrated moderate to strong broad-spectrum inhibitory activity against all tested pathogens. Other isolated strains except P8 exhibited inhibitory activity against Gardnerellavaginalis, while strain P8 showed weak inhibitory activities against the tested pathogens. Strains P4, P5-2, P6-1, and P6-2 achieved inhibition rates exceeding 99.73% against Candidaalbicans across all three tested inoculum concentrations, and strain P5-1 reached an inhibition rate of over 94.64%. None of the strains exhibited β-hemolytic activity, and no antibiotic resistance or virulence genes were detected. [Conclusion] Several LAB isolates from commercial probiotic products exhibited notable inhibitory activities against pathogenic microorganisms and demonstrated good safety profiles. Topical administration may therefore offer greater practical value in promoting female reproductive tract health.

[Objective] To explore the influence of Acinetobacter pittii LSQ 3 on the biofilm formation of Bacillus velezensis LSQ 19 and analyze the genomic characteristics of strain LSQ 3. [Methods] The effect of the cell-free supernatant (CFS) of LSQ 3 on the biofilm formation of LSQ 19 was analyzed by crystal violet staining, cell surface property analysis, the phenol-sulfuric acid method, XTT reduction assay, and scanning electron microscopy (SEM). Whole-genome sequencing was employed to determine the taxonomic status of strain LSQ 3, and the biosynthetic gene clusters for secondary metabolites were predicted based on the whole-genome data. [Results] The CFS of strain LSQ 3 significantly inhibited the biofilm formation of strain LSQ 19, and the volume ratio of 10 µL bacterial suspension to 190 µL CFS was determined as the minimum inhibitory concentration (MIC). Compared with the control, the CFS of strain LSQ 3 at MIC significantly reduced the surface hydrophobicity, adhesion, extracellular polymeric substances (EPS) production rate, and biofilm metabolic activity, while significantly improving the self-aggregation ability of LSQ 19 cells. In the presence of the CFS at MIC, LSQ 19 failed to form a biofilm on the glass surface. Strain LSQ 3 was identified as A. pittii based on whole-genome sequencing data. Its genome size was 3 939 365 bp, with the G+C content of 38.82% and 3 601 DNA coding sequences. The genome contained multiple genes involved in biofilm formation and virulence factors. The antiSMASH analysis showed that the genome of strain LSQ 3 contained seven biosynthetic gene clusters for secondary metabolites. [Conclusion] The CFS of A. pittii LSQ 3 can inhibit the biofilm formation of B. velezensis LSQ 19. This study provides a theoretical basis and reference for the construction of synthetic bacterial communities from the perspective of biofilms.

As a widely conserved interspecies quorum sensing signaling molecule, autoinducer-2 (AI-2) is involved in regulating various crucial physiological processes such as bioluminescence, chemotaxis, and biofilm formation. However, the effects of AI-2 on Halomonas elongata and its underlying mechanisms remain unreported. [Objective] To reveal the receptor that regulates the chemotaxis and biofilm formation of H. elongata in response to AI-2. [Methods] The quantitative capillary assay was employed to examine the chemotactic response of H. elongata to AI-2. We conducted protein domain identification, sequence alignment, and molecular docking of methyl-accepting chemotaxis proteins to identify the key amino acid sites in Tar1, the potential AI-2 receptor. The ligand-binding domain (LBD) of Tar1 and single-point mutants were expressed and purified, and the binding between Tar1-LBD and AI-2 was measured by the Vibrio harveyi MM32 bioluminescence assay. tar1 was deleted by homologous recombination, and the effects of AI-2 on the chemotaxis and biofilm formation of H. elongata were evaluated by quantitative capillary and biofilm formation assays. [Results] The quantitative capillary assay revealed that H. elongata exhibited chemotaxis to AI-2. Four methyl-accepting chemotaxis proteins were identified in H. elongata. Protein domain identification, sequence alignment, molecular docking, and V. harveyi MM32 bioluminescence assay demonstrated that Tar1-LBD bound to AI-2. The tar1-deleted mutant of H. elongata was successfully constructed by homologous recombination. The deletion of tar1 impaired the chemotaxis of H. elongata to AI-2, whereas the complementation of this gene restored the chemotaxis to level comparable to that in the wild-type. Furthermore, biofilm formation assay revealed that AI-2 enhanced the biofilm formation in H. elongatavia Tar1. [Conclusion] H. elongata exhibits chemotaxis to AI-2, and this signal molecule binds to the LBD of Tar1, thereby modulating chemotaxis and biofilm formation.

[Objective] The human intestinal tract is rich in microbial resources, which play a significant role in the host’s digestion, absorption, growth, development, etc. Currently, culturomics is widely used in the isolation of beneficial intestinal microorganisms. However, different culture media have preferences, and a single medium is difficult to comprehensively isolate the culturable microorganisms in the intestinal tract. [Methods] We used six reported culture media [brain heart infusion (BHI), Wilkins_Chalgren anaerobe broth (WCBM), (Man-Rogosa-Sharpe) MRS, reinforced clostridial medium (RCM), mucin medium (MM) and modified mucin medium (MMM)] to isolate the microorganisms in the feces of 58 volunteers, with the aim of clarifying the diversity of culturable microorganisms in the intestinal tract and obtaining potential beneficial bacterial strains in the intestinal tract. [Results] A total of 1 052 bacterial strains were isolated from 58 samples, and they were identified as 101 species belonging to 39 genera of 5 phyla. The BHI medium isolated the most bacterial species (50, 49.50%), while the MMM medium isolated the fewest bacterial species (24, 23.76%). Except the MM medium, each of other media could isolate unique genera, and BHI and MMM isolated the most unique genera (5 each). Among the isolated strains, 466 strains were reported to have probiotic effects, including Bacteroides fragilis, Lactiplantibacillus plantarum, Pediococcus acidilactici, and Bifidobacterium bifidum. BHI and MRS media could isolate more beneficial microbial species (10/16, 62.50%). [Conclusion] We explored the diversity of beneficial bacteria in the human intestinal tract from the perspective of pure culture by using multiple culture media, providing rich strain resources for the development of intestinal beneficial microorganisms.

[Objective] The type VI secretion system (T6SS) is a novel virulence factor of Edwardsiella tarda. E. tarda virulence protein P (EvpP) is an effector of the T6SS. To date, the functional mechanisms of EvpP are still poorly understood. This study aimed to comprehensively investigate the biological functions of EvpP and elucidate the roles of T6SS in the pathogenicity of E. tarda. [Methods] We constructed the evpP-deleted mutant (ΔevpP) and complemented strain (ΔevpP-C) to study the effects of evpP deletion on the biological characteristics of E. tarda and infection in macrophages. [Results] No significant differences were observed in the growth curves or physiological and biochemical properties among the wild-type (WT), ΔevpP, and ΔevpP-C. However, compared with WT, ΔevpP exhibited significantly reduced motility, biofilm formation, adhesion rate to RAW264.7 macrophages, intracellular proliferation capacity, and ability to induce host cell autophagy, while triggering increased secretion of tumor necrosis factor-α (TNF-α) by macrophages. The complementation of evpP-C did not fully restore the intracellular proliferation capability, but completely rescued the other phenotypic defects. [Conclusion] EvpP does not affect the growth or physiological and biochemical properties of E. tarda. However, it could enhance the bacterial motility, biofilm formation, adhesion to macrophages, intracellular proliferation, and autophagy, while suppressing TNF-α secretion in E. tarda-infected macrophages. These findings confirm that EvpP plays a critical role in the pathogenicity of E. tarda.

As a subterranean, soil-dwelling insect, Odontotermes formosanus is susceptible to infection by diverse soil-borne pathogenic fungi. Its symbiotic actinobacteria produce bioactive compounds to combat these pathogens, thereby maintaining a stable symbiotic system of O. formosanus with Termitomyces spp. [Objective] To screen and characterize antifungal metabolites from symbiotic actinobacteria of O. formosanus and to elucidate their defensive role in the termite-fungus symbiotic system. [Methods] Actinobacteria were isolated from O. formosanus-associated samples via diverse culture media. Antifungal strains were screened via dual-culture confrontation assays. The active strain OFGS46 was selected for whole-genome sequencing. Biosynthetic gene clusters (BGCs) were predicted by antiSMASH, and secondary metabolites were analyzed by HPLC-MS. [Results] Twenty-three actinobacteria strains were isolated. Strain OFGS46 exhibited inhibition rates of (62.05±0.98)% against Xylaria sp. and (79.99±0.58)% against Talaromyces sp. Whole-genome sequencing on the Illumina NovaSeq platform yielded approximately 1 Gb of high-quality data. De novo assembly generated a draft genome of 8 470 479 bp. CheckM evaluation demonstrated high assembly quality with 99.91% completeness and 4.63% contamination. HPLC-MS results revealed that strain OFGS46 was capable of producing multiple bioactive secondary metabolites, including enduracidin A, WS9326A, kitacinnamycin A, WAP-8294A2, skyllamycin A, cahuitamycin A, pentamycin, scabichelin, coprisamide C, and frankobactin A1. [Conclusion] This study systematically reveals that the symbiotic actinobacterium OFGS46 from O. formosanus suppresses nest pathogens through the production of diverse antimicrobial compounds. These findings not only elucidate, from a perspective of chemical ecology, the role of symbiotic bacteria in host immune defenses through suppressing multiple pathogenic fungi, but also provide a scientific basis for developing novel antimicrobial resources derived from the termite symbiotic system.

[Objective] Citric acid is the main metabolite of Aspergillus niger at pH≤5.0, while l-malic acid becomes the main metabolite at pH 6.0. In this study, we employed transcriptomics to analyze the differences in the expression of key genes in metabolic pathways, aiming to explore the biosynthesis mechanisms of the two organic acids. [Methods] The cells at 48 h and 72 h of the fermentation processes for citric acid and l-malic acid production were selected for transcriptomics analysis. [Results] The transcriptome data of 72 h and 48 h were compared. GO enrichment analysis showed that the upregulated genes related to the synthesis of citric acid were concentrated in carbohydrate metabolism, while those related to the synthesis of l-malic acid were concentrated in ion transport process. The acid protease genes ANI_1_62014 (aspergillin II) and ANI_1_654124 (aspartic protease pepA) showed extremely high transcription levels during citric acid synthesis, while the key genes ANI_1_2494074 [3-oxoacyl-(acyl carrier protein) synthase] and ANI_1_2488074 (biosynthetic fatty acid synthase subunit β) essential for fatty acid chain synthesis showed extremely high transcription levels in the l-malic acid synthesis pathway. The transcription level of zinc cluster transcription factor [Zn(II)₂Cys₆ transcription factor] was higher in the synthesis process of l-malic acid. HacA, AP-1, and AtfA in the bZIP family showed higher transcriptional levels in response to environmental low pH stress during citric acid synthesis. Compared with l-malic acid synthesis, citric acid synthesis was accompanied by upregulated transcription levels of ANI_1_66114 (hexokinase), ANI_1_2950014 (citrate synthase), and ANI_1_478154 (citrate transporter) and a downregulated transcription level of ANI_1_3136024 (isocitrate dehydrogenase). Efficient glycolysis, citric acid synthesis, and citric acid transport capacity and low isocitrate dehydrogenase level were the key factors for citric acid production. In the process of l-malic acid synthesis, cytoplasmic ANI_1_440184 (pyruvate carboxylase), cytoplasmic ANI_1_12134 (malate dehydrogenase), ANI_1_914104 (isocitrate lyase), and ANI_1_2040144 (malate transporter) showed upregulated transcriptional levels. The cytoplasmic rTCA pathway and glyoxylic acid carboxylation pathway were thereby determined to be the main pathways for l-malic acid synthesis. [Conclusion] This study inferred the key differential metabolic pathways for the production of citric acid and l-malic acid by analyzing integrated transcriptomic data, and screened significant differentially expressed core genes, transcription factors, and potential transporters. These results provide important clues and a theoretical basis for elucidating the regulatory mechanisms of citric acid and l-malic acid synthesis.

The lined seahorse (Hippocampus erectus) is a major cultured seahorse species with significant economic value in China. Bacterial diseases frequently occur in intensive aquaculture environments, among which skin ulceration is one of the most detrimental diseases affecting H. erectus farming. Skin ulceration is mainly caused by Vibrio spp., while the pathogen complexity and diversity remain unclear. [Objective] This study identified dominant bacterial strains from ulcerative lesions of H. erectus in Zhangzhou, Fujian and characterized their pathogenicity, antibiotic resistance profiles, and virulence traits, aiming to provide a scientific basis for disease prevention and control. [Methods] Bacteria were isolated from ulcerated and internal tissue samples of diseased seahorses. Species identification was performed via morphological observation, physiological-biochemical tests, 16S rRNA gene phylogenetic analysis, and reinfection of seahorses. The isolates were cultured for the measurement of hemolytic activity, caseinase production, and salinity tolerance. Ten virulence genes were detected by PCR. The susceptibility of the isolates to 30 antibiotics was tested via the disk diffusion method. Artificial infection was performed with zebrafish as a model to determine the median lethal dose (LD₅₀). [Results] Fifteen dominant strains were isolated from various tissue samples of diseased seahorses. Among them, three strains (HCE003, HCE070, and HCE098) exhibited β-hemolysis and high overall antibiotic resistance rates (50.0%-56.7%). HCE003 carried vvh, pPHDD1, and hlyAch, while both HCE070 and HCE098 carried hlyA, trh, hlyAch, and vhh. HCE003, HCE070, and HCE098 were preliminarily identified as highly pathogenic strains and were further characterized as Citrobacter freundii, Shewanella algae, and Vibrio rotiferianus, respectively. The three strains were capable of growing normally at the salinity of 15‰. Artificial challenge tests demonstrated that they could induce skin ulceration in H. erectus upon reinfection. The median lethal doses of HCE003, HCE070, and HCE098 in zebrafish were 1.71×10⁵ CFU/mL, 3.68×10⁵ CFU/mL, and 2.51×10⁶ CFU/mL, respectively. [Conclusion] This study is the first to report the isolation of multidrug-resistant and highly virulent C. freundii and S. algae from H. erectus with skin ulceration, indicating that non-Vibrio pathogens can also contribute to skin ulceration in seahorses. These findings provide scientific support for the development of targeted disease management strategies and therapeutic agents in seahorse aquaculture.

[Objective] To investigate the regulatory effect of the cAMP receptor protein (CRP), a transcription factor in Acinetobacter baumannii, on the cas3 gene. [Methods] CRP was expressed and purified via a prokaryotic expression system. EMSA was employed to examine CRP binding to the cas3 promoter. qPCR was conducted to evaluate the regulatory effect of CRP on cas3 expression. To further confirm the regulatory function of CRP, we constructed a mutant strain Δcrp. The impact of crp deletion on A. baumannii virulence was then analyzed via the biofilm formation assay, adhesion and invasion assays with A549 cells, a Galleria mellonella model, and a murine model of bacterial infection. [Results] EMSA demonstrated that CRP specifically bound to the cas3 promoter. The qPCR results showed that cas3 transcription was downregulated (P<0.001) in Δcrp. Compared with the wild-type strain, Δcrp exhibited no significant difference in growth capacity but enhanced biofilm formation (P<0.001) as well as strengthened adhesion (P=0.003<0.050) and invasion (P<0.001) in A549 cells. Furthermore, Δcrp demonstrated a markedly increased lethality rate in G. mellonella within 72 h. Furthermore, the murine infection experiment revealed that Δcrp possessed higher colonization capacity in the lungs than the wild-type strain (P<0.001). [Conclusion] CRP acts as a transcriptional activator that directly binds to the cas3 promoter to activate its transcription, thereby attenuating the virulence and pathogenicity of A. baumannii.

[Objective] To evaluate the edible safety of Penicillium polonicum CK2023-1, a key strain responsible for flavor formation of traditional bacon in Chengkou, thus providing a scientific basis for developing microbial starter for bacon fermentation. [Methods] The genomic DNA sequence of P. polonicum CK2023-1 was determined via third-generation sequencing combined with second-generation sequencing and annotated via GO, KEGG, and antiSMASH databases. The spore suspension (1×10⁹ spores/kg) of CK2023-1was applied to cured meat surfaces, followed by 26 d local smoking in Chengkou. Non-volatile metabolites were analyzed via LC-MS/MS. Acute oral toxicity (7 d) and subacute oral toxicity (28 d) tests in mice were conducted to assess pathogenicity. [Results] The genome of CK2023-1 was 33.27 Mb, with the N₅₀ of 5 236 196 bp and the G+C content of 52.91%, containing 10 901 predicted coding genes (49.02% of the genome). Eighty-three biosynthetic gene clusters (BGCs) for secondary metabolites were identified, including known mycotoxin (verrucosidin) BGC. Compared with that in the toxigenic strain P. polonicum X6, the BGC in CK2023-1 exhibited an inversion. No mycotoxins were detected in fermented bacon, and neither acute nor subacute toxicity tests caused morbidity or mortality in mice. [Conclusion] P. polonicum CK2023-1 has a well-defined genomic structure, produces no mycotoxins, and is non-pathogenic, meeting the safety criteria for food-grade microbial strains.

[Objective] To develop a low-cost and highly sensitive endotoxin detection reagent and detection method with recombinant horseshoe crab factor C enzymogen (rFC). [Methods] The Bac-to-Bac baculovirus expression system was used to express rFC in Sf9 cells and the activity of rFC was measured by the end-point fluorescence assay with endotoxin. The conditions of protein expression were optimized, and ion exchange was used for crude enzyme separation. An endotoxin detection method with rFC based on end-point fluorescence assay was established after the reaction conditions were optimized. Furthermore, the established method was compared with the conventional limulus amebocyte lysate (LAL). [Results] The expression level of rFC was 110.42 mg/L, increasing by 4.75 times. The linear range of endotoxin detection was 0.005-1.000 EU/mL in 1 h, with a good linearity and the limit of detection being 0.005 EU/mL. The applicability rate of this method for actual samples was 92.45%. The consistency of the detection results was 83.67%, and 89.80% of the samples had consistent detection limits with LAL. [Conclusion] This study achieves the efficient expression of rFC and establishes an endotoxin detection method with higher sensitivity than LAL, which has great potential for application.

[Objective] To establish a method of semi-thin section preparation and scanning electron microscopy (SEM) observation with a simple operation, a short cycle, and a low technical threshold, which can be used as a rapid pre-screening strategy for the complex process of transmission electron microscopy (TEM) ultra-thin sections, in response to the requirements of rapid identification and dynamic observation of typical subcellular structures (such as cell wall, cytoplasm, spore, and vacuole) of microbial samples in the process of fermentation production. [Methods] Bacillus subtilis, Escherichia coli, and Pichia pastoris, taken as the research objects, were embedded in Embed 812 epoxy resin to prepare semi-thin sections with different thicknesses (200, 500, and 1 000 nm) and resin embedding blocks (> 1 000 nm) with samples. After platinum coating by ion sputtering, the subcellular structure was observed by SEM. Ultra-thin sections (70 nm) of the above microbial samples were also prepared, stained with lead and uranium, and imaged by TEM. The imaging effect and operation efficiency of the above two methods were compared. [Results] The 200 nm semi-thin section can clearly and completely display various kinds of microbial subcellular structures under a scanning electron microscope. The image quality was significantly better than that of 500 and 1 000 nm sections and resin block samples. Its resolution was close to the TEM observation level, and it can save about 6.5 h. [Conclusion] The method of SEM combined with 200 nm semi-thin sections was successfully applied to the high-resolution imaging of microbial subcellular structure for the first time, which can clearly identify the typical ultrastructural morphology, and has the advantages of a simple operation, a short cycle, a low cost, and high safety. It has strong versatility and promotion value, and provides a new and effective solution for the biological electron microscopy technology system.

To systematically analyze the current status and research trends and identify the key research hotspots in the field of gut microbiota and metabolic syndrome (MetS) from 2005 to 2024, thus providing references for future research and intervention strategies. Relevant literature on gut microbiota and MetS was retrieved and screened from the Web of Science Core Collection. Bibliometric tools such as VOSviewer, CiteSpace, and the R package bibliometrix were used to analyze the publication trends, countries and institutions, research themes, and emerging hotspots. A total of 4 210 relevant publications were included. The annual number of publications showed an increasing trend, which was particular rapid after 2010. China and the United States led in publication output, and major research findings were published in journals such as Nutrients, Gut, and Nature. Research hotspots primarily covered the fields of nutrition and diet, biochemistry and molecular biology, and microbiology. Keyword evolution analysis revealed a shift from early descriptive studies on gut microbiota composition to mechanism investigations focusing on dysbiosis-related pathways such as energy metabolism, inflammatory responses, and gut-organ axes. Co-occurrence analysis further indicated that key microbial metabolites (e.g., short-chain fatty acids and bile acids) and microbiota-targeted interventions (e.g., probiotics and fecal microbiota transplantation) had become focal points in recent studies. This bibliometric study comprehensively summarizes the research landscape of gut microbiota and MetS and highlights emerging trends and directions. Given the limitations of conventional therapies in terms of targeting specificity, patient adherence, and long-term safety, microbiota-based interventions offer a promising breakthrough for the prevention and treatment of MetS, providing valuable theoretical support for future precision medicine.