Frontiers in Microbiology最新文献

Background: Antimicrobial resistance (AMR) is a global challenge affecting both healthcare and agricultural fields, as emphasized by the World Health Organization (WHO). Industrial poultry production plays a crucial role in the development and dissemination of AMR. A comprehensive understanding of the molecular mechanisms underlying AMR is imperative for developing effective control strategies.

Materials and methods: This study aimed to identify factors influencing AMR in Escherichia coli from large-scale commercial broiler farms. Samples, including 371 anal swabs, 95 fecal swabs, and 122 feed-trough swabs, were collected from Cobb broilers at the four production stages (1, 15, 26, and 38 days of age) on typical farms in Shandong Province. From these specimens, 508 E. coli strains were isolated and characterized. Antimicrobial susceptibility was assessed using the Kirby-Bauer disk diffusion method against 15 commonly used antibiotics, and results were interpreted according to CLSI guidelines.

Results: The resistance rates of the isolated strains varied between 24.41% and 95.47%. A total of 96.45% of the strains exhibited multidrug resistance, and 29 strains were resistant to all 15 antibiotics. The highest resistance was observed against penicillin (amoxicillin and ampicillin), followed by florfenicol, chloramphenicol, tetracycline, cefotaxime, and cefazolin. The lowest resistance was noted for ofloxacin and gentamicin. Drug resistance was most substantial at 15 days of age compared with that at 1, 26, and 38 days of age.

Discussion: An analysis of the relationship between drug resistance and drug use showed that doxycycline significantly increased the resistance rate (68.40%, p < 0.05). Additionally, the drug resistance of bacteria isolated from fecal swabs was higher than that of bacteria from anal and feed-trough swabs. The results indicate that sample type, drug type, and age all influence E. coli drug resistance in poultry, with drug type having the greatest impact.

Allergic rhinitis (AR) is a prevalent immune-mediated upper respiratory disorder that manifests as an itchy nose, nasal congestion, a runny nose, and other symptoms. Emerging research suggests that AR, beyond its IgE-mediated hypersensitivity, indirectly influences the immune system by altering the equilibrium of the lung and intestinal microbiota. Therefore, future research should systematically characterize the mechanistic involvement of the respiratory and intestinal microbiomes in AR development, which may reveal innovative therapeutic targets. This review highlights the mechanisms by which the lung and intestinal microbiota contribute to the pathogenesis of AR and discusses potential therapeutic strategies.

Introduction: Mycobacterium leprae remains uncultivable in axenic media, a constraint that continues to hamper leprosy research. As research animals, such as mice or armadillos, are the only reproducible method of sustained laboratory growth, this is restricted to a few specialized laboratories. The development of axenic media would increase access to this field.

Methods: We performed a descriptive bibliographic review (May 2025) across PubMed, Embase, and the Cochrane Library using both controlled vocabulary and free terms related to M. leprae cultivation. After de-duplication and screening, 78 studies met the inclusion criteria.

Results: Historically, claims of in vitro growth on egg-based or synthetic media have proven irreproducible or were subsequently attributed to non-leprae mycobacteria. Temperature and gas composition emerge as critical parameters: convergent evidence indicates thermosensitivity with optimal performance at 30-33 °C and deterioration at 37 °C; limited growth has been reported under microaerophilic atmospheres (~2.5% O₂ with added CO₂), yet durable subculture remains unachieved. Cell-based systems-such as macrophages or Schwann cells, which are traditional targets in vivo of M. leprae-can preserve viability for weeks and occasionally increase bacterial counts, but continuous, exponential replication has not been demonstrated. Mechanistic insights from genomics, transcriptomics, and metabolomics suggest that while M. leprae presents extensive gene decay, many core biosynthetic pathways persist. Lipid droplets (LD), immunomodulators (e.g., IL-10, PGE₂, and IGF-I), and L-arginine/nitric oxide pathways appear to shape the intracellular fate of the bacterium. An alternative unifying hypothesis posits that failure in vitro reflects structural fragility rather than a single auxotrophy, with host-derived factors (e.g., LDs and iron delivery) transiently compensating in vivo.

Discussion: To date, no reproducible, cell-free culture system exists. This review aims to provide a starting point for future research into this objective. Achieving a reproducible in vitro culture of Hansen's bacilli would represent a major advance in the field of leprology and would significantly accelerate translational research in this disease.

Introduction: Top-down microbial enrichment is a reliable approach for understanding and designing microbiomes for crude oil remediation. Environmental variables serve as valuable determinants for selecting desired microbiomes with superior performance. However, the linkages between selection methods and the structure and function of desired microbiomes remain unclear.

Methods: This study integrated substrate concentration gradients and cultivation patterns to investigate how selection pressures shape top-down enriched crude oil-degrading consortia. The resulting communities were analyzed using 16S rRNA gene sequencing, metagenomics, and co-occurrence network analysis. Key bacterial strains were isolated to validate their individual degradation capabilities.

Results: The top-down process led to a significant reduction in phylogenetic diversity but a notable increase in the potential for xenobiotic degradation and metabolic. The final consortia, GT4, achieved a 55.72% degradation rate of crude oil at an initial concentration of 5 g/L within 7 days. Metagenomic analysis identified Microbacterium as dominant genus harboring key enzymes for the degradation of alkanes and aromatic compounds. Co-occurrence network analysis revealed Mesorhizobium as a keystone genus, showing positive associations with multiple diazotrophic bacteria and hydrocarbon degrading bacteria. Nine bacterial strains were isolated from the consortium. Among them, Microbacterium sp. WS3 and Cellulosimicrobium sp. WS9 exhibited high degradation efficiencies (57.85 and 58.60%, respectively). To the best of our knowledge, this study provides the first experimental evidence for crude oil degradation by Paracandidimonas and Caulobacter, with degradation rates of 51.19 and 40.90%, respectively.

Discussion: These findings highlight the effectiveness of top-down enrichment strategy in generating functionally streamlined consortia and uncover novel oil-degrading microbes with potential for bioremediation applications.

Purpose: With the evolution of dietary habits, obesity has emerged as a significant global health issue. Numerous studies have demonstrated a close association between obesity and gut microbiota; however, the specific contribution of gut microbiota to varying degrees of obesity remains inadequately understood. Consequently, this study aims to characterize the gut microbiota of individuals across different obesity severity levels.

Methods: We conducted a comprehensive characterization of the gut microbiome in Chinese obese patients and a healthy control group through the application of 16S rRNA gene sequencing, supplemented by metagenomic sequencing. The study cohort was stratified into five distinct categories based on body mass index (BMI): healthy, overweight, and obesity grades I, II, and III.

Results: In obese populations, the gut microbiome structure shifted significantly, with beneficial genera like Faecalibacterium, Roseburia, and Ruminococcus decreasing, and potentially harmful genera such as Blautia, Collinsella, and Streptococcus increasing. These changes impacted host metabolic pathways, including ribosome synthesis, RNA polymerase activity, and DNA repair. Clinical analyses also revealed strong links between specific genera and metabolic markers like lipid metabolism and insulin resistance.

Conclusion: Populations with different obesity traits show unique changes in gut flora. The level of dysbiosis, or imbalance in intestinal microbiota, rises with obesity. These microbial changes are linked to host metabolism, indicating that targeting harmful bacteria and supplementing with beneficial ones from normal-weight populations could effectively reduce obesity.

Coastal hypoxia, intensified by global warming and eutrophication, profoundly affects marine nitrogen cycling. However, its impact on diazotrophic communities in large river estuaries remains poorly understood. During an unprecedented hypoxia event (minimum dissolved oxygen at 2.70 μmol L^-1) in August 2016 in the Changjiang Estuary, we sampled across a dissolved oxygen (DO) gradient spanning hypoxic and non-hypoxic waters. Using nifH gene amplicon sequencing, metagenomic binning, and multivariate statistical analyses, we found that higher diazotrophic biodiversity was observed in hypoxia zone, with non-cyanobacterial diazotrophs dominating the communities. The phylum Thermodesulfobacteriota (with relative abundance of 58.93% totally) exhibited significant hypoxia-specific enrichment. LEfSe analysis identified Thermodesulfobacteriota as potential hypoxia biomarkers, while network analysis revealed their keystone role, representing 68.6% of highly connected nodes. Environmental drivers, including low DO concentrations (7.50-61.88 μmol L^-1 in hypoxic vs. 66.56-255.63 μmol L^-1 in non-hypoxic zones), elevated salinity (30.67-34.50), increased dissolved reactive phosphorus (0.39-1.26 μmol L^-1), and nitrate depletion (0.30-22.50 μmol L^-1), collectively created favorable conditions for the development of the observed diazotrophic community under hypoxia. Metagenomic analysis revealed a hypoxia-driven increase in nifH gene abundance, with nifH-carrying metagenome-assembled genomes affiliated with Thermodesulfobacteriota showing approximately a 4.7-fold higher relative abundance in hypoxic zone compared to non-hypoxic zone. Reconstruction of metabolic pathways from metagenome-assembled genomes (MAGs) further suggested their potential involvement in both nitrogen fixation and carbon-sulfur cycling. Amplicon and metagenomic datasets consistently demonstrated Thermodesulfobacteriota's predominant in hypoxia. These findings redefine estuarine nitrogen flux models by highlighting hypoxia-driven taxonomic and functional shifts in diazotrophic communities, and provide a foundation for assessing the potential microbial resilience and ecosystem risks in expanding coastal hypoxic zones. Our study underscores the genomic potential of Thermodesulfobacteriota as key players in the nitrogen cycle under hypoxia, a hypothesis that warrants future validation through direct activity measurements.

Viral infection profoundly reprograms host glucose metabolism to support replication. This review proposes a "Sprint vs. Marathon" framework to explain how viral life cycles shape distinct metabolic hijacking styles. Acute RNA viruses employ a rapid, high-intensity "Sprint" strategy, aggressively activating glycolysis through pathways such as PI3K/Akt and HIF-1α. In contrast, chronic and latent viruses adopt a sustained "Marathon" strategy, subtly modulating glycolytic enzymes, glucose transporters, and survival pathways including NF-κB and mTOR. Understanding these divergent metabolic programs provides new insight into viral pathogenesis and highlights opportunities for developing host-directed antiviral therapies.

Introduction: Potentilla anserina Linnaeus (P. anserina) is a traditional Chinese herbal medicine with ethnic characteristics that grows in the Qinghai-Tibetan Plateau. It has the potential to be used as a novel feed for ruminants. However, the large area of saline-alkaline soils makes it difficult to rationally use Portulaca oleracea as a feed.

Methods: In this study, the effects of volatile metabolites, non-volatile, bacteria and fungi in stems and leaves of P. anserina under three different treatments (fresh grass, hay and silage) in high-salt were investigated using metabolomics and microbiological methods.

Results: Silage under salt stress also improved crude protein and crude fat content compared to hay and fresh treatments. A total of 996 volatile and 928 non-volatile metabolites were identified. Among them, the main volatile substance of silage was 1-Nonen-3-one, while the non-volatile substance was 3-O-Methylgalangin. SC-I-84, Methyloversatilis, and Pseudomonas was specific to P. anserina forage, while Podosphaera is greatly reduced in high-salts. The Pseudomonas bacteria produced specifically improved the drought resistance and salt tolerance of P. anserina.

Discussion: These findings provide essential insights for valorizing P. anserina as a sustainable feed resource, supporting its potential application in animal production within saline-alkaline environments.

This study aimed to isolate a potent cellulase-producing bacterium from tobacco leaves to enhance the utilization value of tobacco stem waste.A strain designated YCXW-01 was isolated using sodium carboxymethyl cellulose as the sole carbon source. It was identified via morphology, physiology, and 16S rRNA sequencing. Growth kinetics, extracellular enzyme activities (cellulase, protease, amylase, xylanase), and whole-genome sequencing were performed. The practical efficacy of its crude enzymes was tested on tobacco stems.The isolate was identified as Bacillus subtilis. It exhibited a high cellulase activity of 10.97 U/mL, alongside substantial protease (23.11 U/mL), amylase (28.96 U/mL), and xylanase (23.68 U/mL) production. Genomic analysis revealed genes encoding key glycoside hydrolases (GH1, GH5, GH11, GH43). Treatment of tobacco stems with the crude enzyme extract reduced cellulose content by 35.3%. B. subtilis YCXW-01 demonstrates significant potential for tobacco waste biorefining due to its high, multi-enzyme activity and relevant genetic repertoire. The genomic data provide a foundation for elucidating its cellulolytic mechanism and guiding future applications.

Bacterial soft rot is a destructive disease that hinders the production of Amorphophallus konjac. In this study, a bacterial strain (GZY0) antagonistic to Pectobacterium aroidearum was isolated from the rhizospheric soil of A. konjac using the solid agar plate confrontation test. Through 16S rRNA sequencing, gyrA gene sequencing, and ANI analysis, this GZY0 strain was identified as Bacillus velezensis. The cell suspension and cell-free supernatant of GZY0 produced bacteriostatic inhibition zones with diameters of 15.63 and 16.70 mm, respectively, against P. aroidearum. Both in vitro antagonist assays and greenhouse pot experiments demonstrated that GZY0 is effective at controlling soft rot in A. konjac. During in vitro antagonistic tests in A. konjac tissues, mixed inoculation with the cell suspension or cell-free supernatant of GZY0 provided control efficacy of 47.56% and 45.79%, respectively, compared with the inoculation of a P. aroidearum bacterial suspension alone. Greenhouse pot experiments further validated its disease-preventing potential, the disease index of the GZY0 + P. aroidearum-coinoculated group was 45.81% lower than that of the P. aroidearum-inoculatedgroup. Additional functional studies revealed that strain GZY0 exhibits excellent plant growth-promoting properties and capable of producing phosphorus-solubilizing zones on both inorganic and organic phosphorus media, with diameters of 11.68 mm and 7.50 mm, respectively. On CAS iron-supplemented medium, GZY0 produces an orange-yellow halo with a diameter of 11.33 mm and an A/Ar ratio of 1.19. Furthermore, GZY0 turns Salkowski reagent red, with an IAA yield of 17.77 mg/L. Furthermore, GZY0 exhibited antagonistic effects against Botryosphaeria dothidea, Fusarium oxysporum, F. solani, F. oxysporum f. sp. panax, and Colletotrichum gloeosporioides. Whole-genome sequencing demonstrated that the genome length of GZY0 was 4053804 bp and included 3,934 coding genes. In order to elucidate the biocontrol mechanisms of strain GZY0, genes related to nitrogen fixation, phosphorus solubilization, and IAA and siderophore production were identified, and 12 antagonism-related secondary metabolite synthesis gene clusters and induced systemic resistance-related genes were predicted. A total of 5,169 pan-genes were detected in the comparative genome, all possessing open pan-genes and closed core genes. Additionally, 3,240 homologous genes were shared among the six Bacillus spp. strains, with GZY0 harboring 171 unique homologous genes. In summary, our findings demonstrated that GZY0 exhibits plant growth promotion capabilities and serves as a potential biocontrol agent for soft rot in A. konjac. Hence, this strain warrants further development and application.