Citrus reticulata cv. Gonggan in Deqing is a national geographical indication product of China, and its quality formation is intricately linked to microbial ecology. In-depth exploration of the microbial resources associated with Gonggan is of great significance for enhancing the quality and increasing the yield of this fruit. [Objective] To isolate and culture bacteria from the rhizosphere soil and phyllosphere surface of Gonggan in Deqing and systematically evaluate their plant growth-promoting functions, thus providing applicable bacterial resources for the eco-friendly cultivation of Gonggan in Deqing. [Methods] Samples of rhizosphere soil and leaves of Gonggan in Deqing were collected. Bacteria within the samples were isolated via the dilution plating method. Bacterial strains were identified based on the homology of their 16S rRNA gene sequences. The functional media for phosphate solubilization, potassium release, nitrogen fixation, and siderophore production were used to evaluate the plant growth-promoting ability of bacterial strains, and the strains with strong plant growth-promoting functions were screened out. Ultimately, pot experiments were conducted to validate the plant growth-promoting functions of the selected strains. [Results] A total of 240 bacterial isolates were obtained, including 96 strains from the rhizosphere soil and 144 strains from the phyllosphere. These strains belonged to 51 genera, 29 families of 4 phyla, where Pseudomonadota was the dominant phylum and Bacillaceae was the dominant family. Functional characterization revealed that 230 (95.83%) strains exhibited at least one plant growth-promoting function, while 123 strains (51.25%) possessed three or more such functions. Given the extended growth cycle of Gonggan in Deqing, we utilized tomato as a model plant to evaluate the plant growth-promoting functions of eight bacterial strains possessing at least two functions through pot experiments. The results demonstrated that the tested strains significantly increased both plant height and fresh weight of tomato plants. [Conclusion] The rhizosphere soil and phyllosphere of Gonggan in Deqing harbor abundant functional microbial resources. This study successfully screened multiple strains of plant growth-promoting bacteria, and pot experiments demonstrated their significant ability to promote tomato growth. These findings provide a solid theoretical foundation for exploiting microbial resources of Gonggan in Deqing and advancing eco-friendly cultivation practices.

Siderophores are low-molecular-weight, high-affinity iron-chelating molecules produced by bacteria in response to iron deficiency. Pseudomonas secrete siderophores to efficiently chelate insoluble Fe³⁺ in the environment, which is a crucial mechanism for their adaptation to iron-limited conditions. This article systematically reviews the types, structural characteristics, biosynthetic pathways (the non-ribosomal peptide synthetase,NRPS), and regulatory mechanisms of siderophores in Pseudomonas. Several regulatory factors at multiple levels were vitally elucidated, including Fur protein, σ factors, quorum sensing, and two-component system. Moreover, siderophores not only promote iron absorption in plants and bioremediation to remove pollutants but also are virulence factors in pathogen infection and factors in microbial spoilage. The siderophore-iron complex can be specifically recognized and actively taken up by bacteria, which is known as the “Trojan horse” mechanism, enabling covalently conjugated antibiotics to enter the cell and thus significantly boosting antibiotic efficacy. Future research should delve into the molecular regulatory networks and microbial interaction mechanisms to promote the application and development of siderophores in agriculture, medicine, and environmental protection.

Monascus, as a genus of edible fungi used in fermentation, are widely used in various industries such as wine making, food colorants, and pharmaceuticals due to their abundant secondary metabolites. McrA, a global regulator discovered in Aspergillus nidulans, has the function of regulating the growth and secondary metabolism of filamentous fungi. We had identified and cloned mcrA in Monascus purpureus in the previous study. [Objective] On the basis of transcriptome analysis, we mined the differentially expressed genes (DEGs) of ΔmcrA and trpC:mcrA strains to explore the function of mcrA. [Methods] The knockout strain ΔmcrA and overexpression strain trpC:mcrA of M. purpureus were constructed by homologous recombination. The colonies and microscopic morphology on different media were observed. The yields of Monascus pigments and citrinin were determined. The metabolic pathways involving DEGs were analyzed by transcriptome sequencing. [Results] The yields of Monascus pigments and citrinin of ΔmcrA decreased. Transcriptome sequencing results showed that the ΔmcrA strain up-regulated 111 genes and down-regulated 47 genes. The metabolic pathways involving the DEGs of ΔmcrA were mainly glycolysis, pyruvate metabolism, fatty acid synthesis, tyrosine metabolism and so on. The trpC:mcrA strain up-regulated 1 199 genes and down-regulated 867 genes. The main metabolic pathways involving the DEGs of trpC:mcrA were tryptophan metabolism, sucrose and starch metabolism, arginine and proline metabolism, fatty acid degradation, etc. [Conclusion] McrA is a global transcriptional regulator, and the knockout and overexpression of its gene will affect carbohydrate, lipid, and amino acid-related metabolic pathways, thus affecting the production of secondary metabolites.

The global prevalence of obesity and its associated metabolic disorders keeps rising, presenting a major challenge to public health. The gut microbiota plays a pivotal role in obesity onset and development, and its dysbiosis and dysfunction are closely associated with obesity and its complications. This review synthesizes the pathological mechanisms underlying the heredity, neuroendocrine, chronic inflammation, and the gut microbiota-metabolism axis of obesity. Then, we explore the positive and negative regulatory effects of opportunistic pathogens (e.g., Desulfovibrio spp., Megamonas spp.) and putative beneficial bacteria (e.g., Lactobacillus spp., Akkermansia muciniphila) on obesity. Furthermore, we summarize the mechanisms by which these signature gut microbes drive the development of obesity-related conditions, including type 2 diabetes mellitus, metabolic dysfunction-associated steatotic liver disease, cardiovascular diseases, and hypertension. We firstly propose a gut microbiota trajectory hypothesis to delineate the interrelationships between these representative gut microbial signatures and the onset and progression of obesity and its complications. Finally, the review discusses future research directions and the potential for developing early diagnostic technologies based on these microbial signatures. Collectively, this work aims to provide novel strategies for the early diagnosis and precision intervention of obesity and related metabolic disorders, thereby advancing the development of personalized therapeutics.

[Objective] To investigate the biocontrol potential of Penicillium sinense GS218, a new endophytic fungus, and to analyze the antifungal mechanism, so as to provide elite strain resources and lay a theoretical foundation for the biocontrol of Colletotrichum gloeosporioides in pepper. [Methods] Plate assays were employed to determine the hydrolase activity and siderophore production capacity of GS218. The inhibitory effects of GS218 on different phytopathogenic fungi were evaluated by the plate confrontation method. Whole genome sequencing was performed to obtain insights into the genetic information and physiological functions of the strain. The metabolome of strain GS218 co-cultured with C. gloeosporioides was analyzed to explore the potential active substances for the inhibitory effects. The medicated plate method was employed to validate the inhibitory activities of differential metabolites. [Results] Strain GS218 had hydrolase activity, produced siderophores, and exhibited strong inhibitory effects on five pathogenic fungi (with the inhibition rate of 72.76% on C. gloeosporioides in pepper). The sterile fermentation filtrate of strain GS218 demonstrated a good control effect on pepper anthracnose. The genome size of strain GS218 was 27.77 Mb, which has abundant metabolic pathways, and its genome contained 30 synthetic gene clusters for secondary metabolites. The metabolomics analysis showed that strain GS218 contained rich antimicrobial substances in organic acids and derivatives, phenylpropanoids and polyketides, and lipids and lipid-like molecules (including terpenoids). Compounds such as 7-ethoxycoumarin and pyruvic acid showed inhibitory effects against C. gloeosporioides in pepper. [Conclusion] The new strain, P. sinense GS218, has significant inhibitory effects on C. gloeosporioides and promising application prospects in the green development of agriculture. Whole genome sequencing and metabolomics analysis provide a theoretical basis for deciphering the biocontrol mechanism of strain GS218.

Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by abdominal pain, abdominal distension, and abnormal bowel movements. Its pathogenesis involves multiple factors such as imbalance of gut microbiota, immune activation, and dysfunction of the gut-brain axis. Although conventional therapies can alleviate symptoms temporarily, the limitations such as drug side effects and insufficient efficacy persistence have made microbial-targeted therapy a research hotspot. Probiotics are live microorganisms and have been proven to be beneficial to human health. Studies have shown that probiotics inhibit pathogen adhesion through competitive colonization, regulate immune responses, and repair the intestinal barrier function through metabolic products, thereby improving intestinal motility and osmotic balance. This review discusses the specific effects and potential pathways of probiotics on constipation, diarrhea, abdominal pain and distension, and mental symptoms in IBS patients. However, the clinical application of probiotics still faces challenges, including strain heterogeneity, host individual differences, and the lack of standardized treatment plans. In the future, it is necessary to combine multi-omics technologies to screen biomarkers, develop individualized intervention strategies, and optimize efficacy through dynamic monitoring, which are expected to provide more precise microbial-targeted therapy for the treatment of IBS.

[Objective] To explore the structural differences and associated environmental factors of bacterial communities in the water and sediment of river ecosystems during winter. [Methods] Fourteen sampling sites were established for Diannong River in winter. We employed high-throughput 16S rRNA gene sequencing to systematically analyze the bacterial community composition and diversity, constructed co-occurrence networks, and evaluated the roles of random processes in community assembly. Furthermore, we performed correlation analysis with environmental factors. [Results] The bacterial communities in the sediment had higher alpha diversity indexes than those in the water (P<0.001) and more stable community structures. The beta diversity decomposition showed that the community differences between water and sediment were mainly related to species turnover. Random processes dominated community assembly in both habitats. The co-occurrence network of bacteria in the sediment was more complex with stronger cooperation. Key species were primarily involved in carbon and sulfur cycles, and rare taxa played an important role in network stability. The bacterial communities in water were mainly influenced by environmental factors such as dissolved oxygen, chlorophyll a, and water temperature, while those in the sediment were influenced by pH, organic matter, and nitrogen factors. [Conclusion] This study systematically reveals the differences in the structure, co-occurrence network, and related environmental factors of bacterial communities in the water and sediment of Diannong River during winter, providing scientific evidence for a deeper understanding of the ecological adaptability of river bacterial communities in the freezing period and the different patterns of bacterial communities between water and sediment.

[Objective] This study examined the characteristics of the microbial communities and their associations with chemical components in aged tobacco leaves from different production areas in Yunnan Province, aiming to provide a theoretical foundation for the targeted exploitation of tobacco microbial resources and quality improvement of tobacco. [Methods] A systematic approach integrating metagenomic sequencing, GC/LC-MS, and Spearman’s correlation analysis was employed to investigate the microbial communities, chemical components, and their correlations of aged tobacco leaf samples collected from Dali, Wenshan, Honghe, Luoping, Pu’er, Zhaotong, and Lincang. [Results] The dominant bacterial phylum was Pseudomonadota in aged tobacco leaf samples. The dominant bacterial genera varied among different production areas. Specifically, Salinivibrio was identified as the core genus in the samples from Wenshan, while Methylobacterium and Sphingomonas exhibited significant enrichment in the samples from Luoping. For fungal communities, Ascomycota and Mucoromycota were the predominant phyla, and dominant fungal genera showed negligible variations. Alpha diversity analysis revealed the highest microbial richness and diversity in the samples from Lincang and the lowest in the samples from Wenshan. KEGG analysis revealed that metabolic pathways exhibited high relative abundance across samples from all regions, whereas environmental information processing pathways were more abundant in the samples from Wenshan. CAZy analysis showed that genes annotated as glycoside hydrolases (GHs) and glycosyl transferases (GTs) were the most prevalent, with both generally exhibiting lower abundance in the samples from Wenshan. Chemical profiling revealed that reducing sugar, total sugar and other conventional components were more concentrated in the samples from Dali, whereas total sugar-to-nicotine ratio and potassium-to-chloride ratio were elevated in the samples from Pu’er. Additionally, neutral aroma compounds, including benzyl alcohol, had significantly higher levels in the samples from Wenshan, while polyphenols such as anthocyanins exhibited markedly higher concentrations in the samples from Luoping. Correlation analysis further disclosed that Microbacterium had a significantly positive correlation with total nitrogen, while Aureobasidium showed a significantly negative correlation with total nitrogen. Leucosporidium exhibited significantly positive correlations with potassium ions and potassium-to-chloride ratio. Salinivibrio had significantly positive correlations with multiple neutral aroma components. In contrast, Methylobacterium and Friedmanniomyces showed significantly negative correlations with the majority of neutral aroma components. Additionally, Methylobacterium, Sphingomonas, Friedmanniomyces, and Metschnikowia had significantly positive correlations with multiple polyphenols. [Conclusion] Microbial communities and chemical components of aged tobacco leaves exhibited marked differences across different production areas in Yunnan. Notably, dominant genera are strongly correlated with aroma compounds, which lays a theoretical basis for targeted screening of functional microbes and the development of biotechnologies to improve tobacco quality.

[Objective] We explored the nuclear translocation dynamics and pathways of the structural protein VP1 of Junonia coenia densovirus (JcDV) in the epidermal cell line HaEpi derived from the larvae of Helicoverpa armigera, aiming to provide theoretical support for clarifying the assembly and proliferation processes of JcDV. [Methods] The wild-type and mutant plasmids of VP1 protein fused with green fluorescent protein (GFP) were constructed and transfected into HaEpi cells. Subsequently, the subcellular localization dynamics of the VP1 protein were analyzed, and the nuclear localization signal (NLS) and key amino acid residues of the protein were identified. The importin genes expressed by HaEpi cells were cloned. Subsequently, the plasmids of importins fused with DsRed2 were constructed to analyze their subcellular localization. The co-localization and co-immunoprecipitation (Co-IP) assays were employed to analyze the interactions between VP1 protein and importins. [Results] The VP1 protein was located in the cytoplasm at 6 h post transfection, and then gradually translocated to the nucleus until 48 h. The NLS of VP1 protein was located at 325-EGTKRKADTPVEEGPSKKGAH-345, among which K328, R329, K341 were the key amino acid residues affecting the nuclear localization. The importins Haimpα1, Haimpα4, and Haimpα7 were located in the nucleus, while Haimpβ1 was mainly located around the nuclear membrane. The co-localization and Co-IP results indicated that the VP1 protein interacted with Haimpα1, Haimpα4, and Haimpβ1 but not with Haimpα7. [Conclusion] The structural protein VP1 of JcDV can be translocated into the nucleus through the dual pathways of importin α/β and importin β.

[Objective] Birds, with unique life history characteristics, are ideal models for studying gut microorganisms. The niche overlap between wild birds and poultry increased the risk of interactive transmission of pathogens. This study focused on the community characteristics of gut fungi and pathogens in wild birds (crested myna, tundra swan, and common coot) and sympatric poultry (domestic duck and domestic chicken) in Chaohu Lake. [Methods] High-throughput sequencing (Illumina MiSeq) was employed to analyze the fungal communities in guts of wild birds and sympatric poultry in Chaohu Lake of China, and the characteristics of gut pathogens of each species were particularly studied. [Results] The gut fungal diversity of domestic duck and common coot was significantly higher than that of domestic chicken, crested myna, and tundra swan. There were significant differences in gut fungal community composition among different species. Due to grain-based diets, the guts of poultry were significantly enriched with the fungal taxa related to grain degradation, such as Ascomycota, Mortierellomycota, and Kazachstania. Tundra swan is herbivorous waterfowl. The genus Cladosporium, efficient plant-degrading fungi, dominated in the gut of tundra swan. The gut of tundra swan maintained higher relative abundance of plant saprotroph. The fungal community assembly in guts of wild birds was dominated by deterministic processes, which indicated that wild birds had a stronger gut filtering capacity. In addition, wild birds had lower diversity and relative abundance of pathogens. [Conclusion] The characteristics of gut fungal communities in wild birds and domestic poultry showed significant host specificity. Due to grain-based diets, the guts of poultry were significantly enriched with fungal groups related to grain degradation. The guts of wild birds had a stronger filtering capacity, which reduced the diversity and relative abundance of pathogens.