Frontiers in Microbiology最新文献

Introduction: This study conducted a systematic investigation of Bacillus velezensis YNK-FB0059 from genome to phenotype, aiming to comprehensively elucidate its genetic basis and functional traits through whole-genome sequencing and multi-dimensional in vitro validation experiments, thereby revealing its great potential as a multifunctional agricultural microorganism.

Methods: Whole-genome sequencing combined with multi-platform bioinformatics analysis was employed to systematically mine secondary metabolite biosynthesis gene clusters, plant growth-promoting genes, and environmental adaptability genes of YNK-FB0059. The complete genome sequence of B. velezensis YNK-FB0059 has been deposited in the GenBank database under the accession number CP140613.1. Targeted experiments were designed and conducted, including plate confrontation assays against pathogenic microorganisms, spore germination and mycelial growth inhibition tests, assessments of phosphorus and potassium solubilization and nitrogen fixation capabilities, detection of siderophore and IAA secretion, biofilm formation analysis, and seed germination and pot-based growth promotion experiments.

Results: Genomic analysis revealed that YNK-FB0059 has a chromosome size of 4.02 Mb, containing 14 secondary metabolite biosynthesis gene clusters encoding various antimicrobial substances such as surfactin, fengycin, bacilysin, and macrolactin H. Complete plant immunity activation gene systems (e.g., flagellin, chemotaxis proteins) and multiple growth-promoting pathways (e.g., nitrogen and sulfur metabolism, tryptophan synthesis) were also identified. In vitro experiments demonstrated that YNK-FB0059 exhibited broad-spectrum antifungal activity against eight important plant pathogenic fungi (inhibition rate: 77.8-88.6%). Its fermentation broth significantly inhibited pathogen spore germination, with a 24-h inhibition rate of 68.35%, and caused mycelial deformation and breakage. Additionally, YNK-FB0059 showed efficient phosphorus and potassium solubilization, nitrogen fixation, siderophore production, and IAA secretion (42.55 μg·mL^-1 after 48 h). Biofilm formation reached 148 mg, and it significantly promoted seed germination and seedling growth in crops such as tomato and rapeseed.

Discussion: Phylogenetic analysis combined with ANI/dDDH values confirmed its identity as B. velezensis. B. velezensis YNK-FB0059 exhibits excellent integrated traits of biocontrol, growth promotion, and rhizosphere colonization. Its rich secondary metabolite blueprint and complete genetic foundation for plant interaction make it an ideal candidate for developing efficient biopesticides and biofertilizers, holding significant application value in sustainable agricultural development.

Introduction: The gut micro biota is reportedly closely related to human health, and its composition and diversity are determined by a variety of factors, including age, diet, and probiotic intake. Although many studies on the gut micro biota have been conducted, most have focused on Western populations or have been limited by small sample sizes, making it difficult to understand micro biota differences across populations and lifestyles. In this study, we analyzed a large Korean cohort of 3,450 individuals, focusing on gut micro biome differences according to age and host-related markers, as well as the impact of probiotic supplementation.

Methods: Fecal samples from 3,450 Koreans were analyzed using 16S rRNA gene sequencing (V3-V4 region). Bioinformatics and taxonomic analyses were performed to compare microbial composition and diversity according to age and probiotic intake.

Results: The data revealed a significant increase in microbial diversity with age and distinct shifts in taxonomic composition between younger and older participants. In addition, probiotic intake did not alter overall community diversity but increased the detection of probiotics, suggesting that they serve as moderators rather than direct drivers of diversity.

Conclusion: These findings emphasize the importance of population-specific micro biome research and suggest that diverse host-related and lifestyle factors jointly contribute to shaping gut microbial ecology in Koreans. Probiotic supplementation primarily increased the detection of specific lactic acid bacteria and bifidobacterial species without substantially altering overall alpha diversity, consistent with a modulatory role on targeted taxa rather than broad community restructuring. Together, these results provide a useful framework for future studies linking probiotic-responsive microbial features to human health outcomes and for developing precision nutrition and probiotic strategies in Korean and similar populations.

As the "second genome" of the human body, the intestinal microbiota plays a key role in preventing the onset and progression of obesity, metabolic disorders, and inflammatory diseases by modulating immune function, maintaining metabolic homeostasis, and reinforcing mucosal barrier integrity. This review systematically investigates the biological and physiological mechanisms underlying the interaction between exercise and the gut microbiota in disease prevention. Existing evidence suggests that exercise, as a non-pharmacological intervention, can prevent and manage obesity, diabetes, and neurodegenerative diseases by reshaping the composition and function of the gut microbiota, suppressing oxidative stress, reducing inflammatory markers, and maintaining intestinal mucosal barrier homeostasis. Current evidence has begun to elucidate the molecular mechanisms by which the gut microbiota mediates disease prevention and progression under varying exercise intensities, modalities, and durations. However, the structural and functional changes of the gut microbiota induced by different exercise doses remain insufficiently characterized, limiting the ability to establish clear exercise-dose relationships for disease prevention. This article systematically reviews the fundamental characteristics of the gut microbiota and the physiological mechanisms underlying exercise intervention in disease prevention through the microbiota, with a focus on exploring the interaction network among the microbiota, exercise, and disease states. Although exercise-induced regulation of the gut microbiota and its metabolites, including short-chain fatty acids (SCFAs), tryptophan metabolites, and bile acids, has demonstrated adaptive and regulatory advantages in disease prevention, the specific effects of exercise-driven changes in the microbiota on various diseases still require extensive experimental validation. In the future, greater attention should be given to the differential effects of varying exercise doses on individual gut microbiota profiles, as well as the long-term impact of exercise-modulated gut microbiota on disease outcomes. On this basis, novel therapeutic strategies should be proposed to promote the enrichment of exercise-responsive microbial populations and harness the protective potential of the gut microbiota for disease prevention.

Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.

Diseases caused by bacteria have become the world's largest threat, and the treatment of bacterial infections urgently needs to be addressed. However, the abuse of antibiotics leads to superbugs, making bacterial infections more difficult to resolve. Therefore, there is an urgent need to develop new antibacterial agents. In this study, three antibacterial agents were synthesized. In vitro antibacterial experiments demonstrated that the antibacterial agent quaternized polyethyleneimine (QPEI) possessed favorable antibacterial activity and exhibited good antibacterial performance against a diverse array of bacteria and fungus, such as Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. QPEI-C6 has an inhibitory concentration of 8 μg/mL against Staphylococcus aureus, 128 μg/mL against Escherichia coli, 16 μg/mL against Candida albicans, and 32 μg/mL against Pseudomonas aeruginosa. Furthermore, through antibacterial and cell biocompatibility experiments, it was shown that QPEI-C6 had good biocompatibility and excellent antibacterial performance within the concentration range of 8-128 μg/mL. The antibacterial agent QPEI-C6 combined with the natural polyphenol tannic acid (TA) was subsequently employed to modify the surface of polypropylene (PP) material, leading to outstanding bactericidal, anti-inflammatory, and antioxidant efficacies. The hemolysis rate of the final material group was 3.4%, and the in vitro cell survival rate was as high as 110%. The antibacterial rate against S. aureus reaches 99%. On the surface of the modified material, excessive reactive oxygen species (ROS) could be effectively eliminated, and the generation of oxidative stress was significantly mitigated. Anti-inflammatory experiments indicated that the coating substantially reduced the expression levels of TNF-α and IL-6 while promoting the release of IL-10. In this work, the cationic antibacterial agent QPEI was successfully synthesized, and the PP material was surface modified. A suite of materials with excellent antibacterial, antioxidant, and biocompatibility properties, which have positive and significant implications in the biomedical field, are presented in this work.

Influenza A virus (IAV) is a zoonotic pathogen with a broad host range, posing an ongoing threat to global public health. As the core subunit of the IAV polymerase, polymerase basic protein 1 (PB1) is essential for viral replication and transcription, and its mutations are key drivers of viral evolution. This review evaluates the impact of PB1 mutations on IAV evolution, with a focus on polymerase activity, host adaptation, transmissibility, and virulence. Additionally, it discusses the implications of these mutations for vaccine development. The review aims to provide insights that can inform influenza surveillance, identify novel antiviral targets, and guide vaccine design.

Vibrio parahaemolyticus may enter the viable but non-culturable (VBNC) state under specific stress conditions such as low temperature and acidic environments. In this study, we simulated gastric fluid digestion of V. parahaemolyticus followed by transfer into intestinal fluids, and monitored changes in culturable cell counts, ATP levels, and morphological changes. The objective was to investigate the effects of pH and treatment duration of simulated gastrointestinal fluids on the induction and resuscitation of the VBNC state. Results showed that after 120 min of digestion in gastric fluid at pH 2.5 with added glucose, the lowest number of bacteria were induced into the VBNC state (1.98 × 10⁶ CFU/mL). In contrast, the highest VBNC induction occurred after 60 min of digestion in gastric fluid at pH 4.5 without glucose (1.26 × 10⁷ CFU/mL). When V. parahaemolyticus was treated with gastric fluid at pH 4.5 with glucose, followed by 120 min digestion in intestinal fluid, the highest number of viable cells were resuscitated (1.68 × 10⁷ CFU/mL). Moreover, prolonged exposure to intestinal fluid resulted in a greater number of resuscitated cells, accompanied by higher ATP levels compared with post-gastric fluid digestion. Microscopic observations revealed that most cells regained curved morphology, with elongated particle size and shape more similar to those of viable cells. These findings demonstrate that acidic gastric fluid environments can induce V. parahaemolyticus into the VBNC state, and that subsequent exposure to intestinal fluid promotes extensive resuscitation. Resuscitated cells released into the environment may pose potential risks to both ecological systems and human health. This study provides important evidence to inform prevention and control strategies for V. parahaemolyticus.

Land use conversion from flooded paddy fields to upland vegetable systems is becoming increasingly widespread, yet its ecological consequences for soil N₂O emissions remain poorly understood. Here, we integrated the potential denitrification-derived N₂O flux measurements, microbial community profiling, and network analyses to elucidate how paddy-to-vegetable land conversion reshapes soil microbial interactions and regulates N₂O emission dynamics in the Yangtze River Delta region of China. Results showed that N₂O emissions increased significantly following the conversion, with fluxes reaching approximately 0.43 and 0.0083 nmol N g^-1 h^-1 in soils under vegetable cultivation for 4 and 7 years, respectively. In contrast to the trend in N₂O emissions, bacterial diversity decreased significantly following the conversion, whereas fungal diversity showed no significant change. Co-occurrence network analysis demonstrated a divergent response of bacterial and fungal communities to land use conversion. In vegetable soils, bacterial networks exhibited enhanced connectivity, with average degrees 1.23 and 1.17 times higher than those in paddy soils after 4 and 7 years of conversion, respectively. Conversely, fungal networks showed markedly reduced connectivity, with average degrees declining by 54.67 and 36.70%, respectively. The number of edges, positive connection edges, negative connection edges, the number of vertices, and average degree in the bacterial network were all significantly positively correlated with N₂O emission rates, whereas fungal network connectivity showed opposite trends. Random forest modeling further identified bacterial network features were the most influential determinant of N₂O emissions, outperforming traditional soil environmental variables. Altogether, our findings demonstrate that paddy-to-vegetable land conversion alters the architecture, stability, and modularity of soil microbial networks, which may play a pivotal role in enhanced N₂O emissions. This study emphasizes the necessity of considering microbial network dynamics in greenhouse gas mitigation strategies.