Frontiers in Microbiology最新文献

The present study provides first time the comprehensive molecular and phenotypic characterization of antimicrobial-resistant, biofilm-forming, and virulent Salmonella spp. isolated from apparently healthy ducks and their environments in West Bengal, India. A total of 462 samples from Indigenous, Khaki Campbell, and Pekin ducks yielded 436 isolates, of which 42.2% were ESBL producers carrying bla _TEM (36.5%), bla _CTX-M (20.6%), bla _SHV (17.7%), and bla _AmpC (32.6%). Sequence analysis revealed multiple clinically relevant alleles, including bla _TEM -164, bla _CTX-M -15, and bla _SHV -45, underscoring their potential public health significance. The isolates were also screened for biofilm genes (csgA, sdiA, rpoS, rcsA), and the virulence gene invA. Biofilm-associated genes were widely distributed (csgA: 54.59%, sdiA: 52.52%, rpoS: 80.28%, rcsA: 63.76%), while 141 (32.34%) of isolates possessed the invA virulence marker. Of 26 selected strains, high multi-drug resistance was detected, mainly against tetracycline and cefixime. Phylogenetic analysis of ESBL gene sequences showed clustering across avian, animal, and clinical (human) Salmonella isolates, indicating potential interspecies transmission and evolutionary divergence. Notably, strong positive correlations were observed among biofilm formation, multidrug resistance, and virulence (τ = 0.656, ρ = 0.765, p < 0.001). Western blotting further identified two unique polypeptide markers (69 and 35 kDa) with diagnostic potential for detecting resistant, virulent, and biofilm-forming Salmonella. In short, these findings highlight, for the first time, duck as silent reservoirs of high-risk Salmonella strains, and propose novel protein markers to facilitate early detection at the human-animal-environment interface.

Background: We aim to construct a machine learning (ML) model to predict stroke risk in patients with hypertension.

Methods: In all, 68 variables, including demographic information, medical history and medication use, lifestyle, anthropometry laboratory tests, electrocardiography, and echocardiography, were selected for baseline analysis. Of these, 10 optimal variables were selected by Recursive feature elimination (RFE) and then the model was trained and tested using eXtreme Gradient Boosting (XGBoost). A 10- fold cycle of cross-validation was used during the process. Next, XGBoost was used to develop a prediction model. Four traditional Cox regression models including the China-PAR Score and the Framingham Stroke Risk Score model were established and compared with the ML model. Finally, the results of the performance assessment of the models were compared using C-statistics for discrimination and Brier score for calibration.

Results: In all, we included 5,197 hypertensive participants (mean age = 57.16 ± 10.20 years) from the Northeast China Rural Cardiovascular Health Study (NCRCHS). Of these, end point events occurred in 294 patients (5.7%, 185 males and 109 females) during a mean follow-up period of 4.26 ± 1.03 years. Using RFE, 10 variables were selected to construct the XGBoost model. The ML model demonstrated better discrimination than the best performing Cox regression model [C-statistic 0.967 (95% CI, 0.956, 0.978) vs. 0.781 (95% CI, 0.772, 0.785), respectively] with an acceptable calibration (Brier score = 0.053).

Conclusion: Using the ML method, we constructed a high-precision prognostic model to predict stroke risk in patients with hypertension. This model exhibited a better classification effect and better performance compared with the traditional risk scales. The model could be used in clinical practice to achieve early prevention and intervention of stroke.

Introduction: Xylanases are key catalysts for valorizing lignocellulosic biomass, yet many available enzymes lack sufficient thermal stability and exhibit suboptimal activity on complex substrates. To address these limitations, we combined enrichment culturing with metagenomic analysis to discover and characterize two novel GH10 family xylanases, Tc15-Xyn6 and Tc15-Xyn10, from the Qiaoquan geothermal area in Tengchong, Yunnan Province.

Methods: Following molecular cloning, heterologous expression, and purification by Ni²⁺-chelating affinity chromatography, both enzymes were comprehensively profiled.

Results: Tc15-Xyn6 displayed optimal activity at 65 °C and pH 6.6 with a half-life of 2 h at 65 °C, while Tc15-Xyn10 exhibited optimal activity at 60 °C and pH 6.0 with a half-life of 1 h at 60 °C. Both enzymes showed broad pH stability at low temperature: after incubation at 4 °C for 12-24 h across pH 4.0-10.0, Tc15-Xyn6 and Tc15-Xyn10 retained more than 60 and 40% of their initial activity, respectively. Both efficiently hydrolyzed xylan in alkali-treated wheat straw, rice straw, and corn stover, as well as xylan from hot water-treated wheat bran, but yielded distinct product profiles: Tc15-Xyn6 primarily produced xylobiose and xylotetraose, whereas Tc15-Xyn10 generated xylotriose as the main product. The resulting xylooligosaccharides significantly promoted the growth of Lactococcus lactis. Kinetic analyses showed K _m and V _max values of 4.675 mg/mL and 125 μmol/min/mg for Tc15-Xyn6, and 9.36 mg/mL and 59.52 μmol/min/mg for Tc15-Xyn10.

Discussion: Collectively, Tc15-Xyn6 and Tc15-Xyn10 combine thermophilicity, thermostability, near-neutral pH preference, and strong performance on complex lignocellulosic substrates, supporting their application in feed processing and targeted production of prebiotic xylooligosaccharides from biomass.

The decline in soil microecological balance and fertility caused by continuous cropping obstacles and excessive application of chemical fertilizers has become a critical bottleneck restricting the sustainable development of the peanut industry. However, intercropping can enhance resource utilization efficiency, and microbial fertilizers can improve soil properties and increase nutrient usability. Therefore, we evaluated the effects of six fertilization treatments [no fertilization (CK), 100% chemical fertilizer (T1), microbial fertilizer (T2), 100%chemical fertilizer+microbial fertilizer (T3), 80% chemical fertilizer+microbial fertilizer (T4) and 60% chemical fertilizer+microbial fertilizer (T5)] on chemical properties and microbial communities of the rhizosphere soil of intercropped peanuts. The results showed that compared with T1, the combined application of chemical and microbial fertilizers significantly increased soil organic matter content and alleviated soil acidification. Microbial analysis indicated that the T4 treatment had the highest Shannon diversity, which was significantly higher than T1, demonstrating its effectiveness in reversing the suppressive effect of chemical fertilizer alone on microbial diversity. Principal coordinate analysis and redundancy analysis further confirmed that fertilization significantly altered microbial community structure, with a clear separation between the combined application and chemical-fertilizer-alone treatments, forming a distinct microbial community. Specifically, the T4 treatment significantly increased the abundance of rhizobia. Under T4 treatment, the abundance of assimilatory nitrate reductase genes (such as nasB and NR) decreased, while that of narB, and nirA increased; simultaneously, the abundance of dissimilatory nitrate reductase and denitrification-specific genes significantly increased. Mantel test analysis revealed significant positive correlations between soil total nitrogen, available nitrogen content, microbial communities, and crop yield. In summary, the combined application of chemical and microbial fertilizers optimizes the soil microenvironment by synergistically enhancing soil fertility (increasing organic matter, regulating pH) and reshaping microbial community structure (increasing diversity, enriching beneficial bacteria). These findings can provide theoretical basis for the optimization of fertilization strategy in peanut intercropping system.

Introduction: Probiotic-fortified yogurt has gained substantial consumer preference owing to its well-documented health benefits. However, stability of probiotic yogurt necessitates a comprehensive understanding of microbial dynamics throughout fermentation and storage.

Methods: This study employed an integrated approach combining fermentation kinetics, post-acidification profiling, and untargeted metabolomics to explore the complex interactions between three Bifidobacterium strains (B. animalis 23426, B. bifidum 91, and B. longum BB68S) and starter cultures (HYY) during symbiotic fermentation.

Results: The results demonstrate that Bifidobacterium supplementation notably enhanced the biomass of S. thermophilus (8.13-8.54 lg CFU/mL) after 2 h by upregulating galactose catabolism and riboflavin biosynthesis, thereby reducing fermentation time by 0.5 to 2 h. In contrast, competitive exclusion effects caused a decrease in L. bulgaricus biomass by 0.2 to 0.8 log CFU/mL. Over 21-day of refrigerated storage, the acid accumulation in Bifidobacterium-enriched yogurts was significantly lower (Δ 3.08-7.49 °T) than in HYY yogurt (Δ 9.42 °T), primarily by downregulation key metabolic pathways involving glycerophospholipid metabolism, branched-chain and aromatic amino acid metabolism, and cofactor biosynthesis, leading to reduced post-acidification.

Discussion: Therefore, Bifidobacterium accelerates fermentation by promoting S. thermophilus biomass while mitigating post-acidification by inhibiting L. bulgaricus. The results provide a scientific basis for developing next-generation probiotic yogurts with controlled acidification profiles and improved shelf-life characteristics.

Salmonella enterica is a leading cause of bacterial infection in humans and animals. Newport is among the most prevalent serotypes linked to fresh produce-associated salmonellosis outbreaks in the United States and among the top serotypes that cause foodborne outbreaks overall. In this study, comparative pathogenomic analyses and phenotypic assays were performed to uncover genetic and phenotypic traits contributing to pathogenicity and epidemiological prevalence of Newport. The 10 clinical strains were placed in four sequence types (ST5, ST31, ST45, and ST118) using classical MLST method and 10 SNP clusters using NCBI Pathogen Detection pipeline. Of the 10 SNP clusters, several persistent genotypes were identified, including PDS000127718 and PDS000029636, and each contained more than 4,000 matched strains and had been detected over a long period of time (> 20 years). In contrast, some SNP clusters appeared to represent transient genotypes, such as PDS000002512 that contained less than 10 matched strains and had been detected within a short period of time (< 5 years). The core virulence determinants in Newport included SPI-1 and SPI-2 encoded T3SS, SPI-4 and SPI-9 encoded T1SS, SPI-6 encoded T6SS, and many fimbriae and nonfimbrial adhesins. Among the seven SPIs detected, SPI-6 exhibited the greatest sequence divergence, including a large deletion that abolished both T6SS and Saf fimbriae simultaneously. Of the 11 fimbriae examined, Peg and Ste fimbriae genes were detected only in the lineage II strains while Stc fimbriae genes were detected only in the lineage III strains. Vast strain variation was revealed in expression of curli fimbriae, biofilm formation, and adherence to cantaloupe rind. Expression of curli fimbriae appeared to be strain-specific and was not associated with ST or lineage. Under the condition tested, curli enhanced biofilm formation significantly but tempered adherence of Newport to cantaloupe rind, implying a role of other adhesins in the initial interaction between Newport cells and the surface of cantaloupe rind. More accessory genes were identified in strains with a persistent genotype than in strains with a transient genotype, suggesting a role of accessory genes in dissemination of S. enterica Newport.

A pronounced nutrient gradient spans from the eutrophic Pearl River Estuary (PRE) to the oligotrophic Northern South China Sea (NSCS), yet its influence on microbial community distribution and cross-domain interactions remains poorly understood. Here, we combined rRNA amplicon sequencing, cross-domain network analysis, and null model approaches to characterize and compare the community structure, assembly processes, and interactions of archaeal, bacterial, and eukaryotic communities in particle-attached (PA) and free-living (FL) fractions along the PRE-NSCS gradient. In the PRE, microbial community assembly was predominantly governed by stochastic processes, resulting in pronounced differences in potential connectivity predicted by null models. Notably, ammonia-oxidizing archaea associated with particles likely functioned as key connectors linking nitrification modules with heterotrophic clusters. In contrast, in the NSCS, cross-domain network analysis revealed that eukaryotes play a central role in maintaining inter-domain connectivity, while FL heterotrophic bacteria formed tightly coupled core networks with their autotrophic partners. Consistent with these patterns, validated topological structures indicated that PRE communities are dominated by stochastic processes (dispersal limitation and drift), whereas NSCS FL communities are primarily shaped by homogeneous selection. Collectively, these results demonstrate that geography and particle partitioning jointly regulate microbial community assembly and network connectivity, thereby influencing distinct microbial remineralization pathways associated with particulate versus dissolved organic matter, and providing new insights into carbon-nitrogen coupling in dynamic coastal ecosystems.

Introduction: Arbuscular mycorrhizal fungi (AMF) and plant rhizosphere microbes reportedly enhance plant tolerance to abiotic stresses and promote plant growth in contaminated soils. Soil salinization represents a severe environmental problem. Although the influence of AMF in the phytoremediation of saline-alkali soils has been fully demonstrated, the underlying interactive mechanisms between AMF and rhizosphere microbes are still unclear.

Methods: A greenhouse pot experiment was conducted to explore the effects of AMF (Claroideoglomus etunicatum) on tall fescue growth promotion and the rhizosphere microbial community in saline-alkali soils. We aimed to investigate the mechanism of AMF affecting plant growth under saline-alkali stress conditions via interactions with rhizosphere microbes.

Results: We found that AMF significantly increased plant shoot, root, and total biomass in saline-alkali stress soil. AMF significantly increased the diversity of bacterial and fungal communities and altered their composition. For bacteria, the AMF inoculation treatment (M+) showed higher relative abundance of Proteobacteria, Actinobacteriota, and Firmicutes and lower relative abundance of Acidobacteriota and Chloroflexi compared to the no-AMF application treatment (M-). For fungi, the M+ treatment showed lower relative abundance of Ascomycota and higher relative abundance of Mortierellomycota compared to the M- treatment. Furthermore, structural equation modeling (SEM) revealed that AMF promoted plant growth under saline-alkali stress conditions mainly by regulating the diversity of bacterial communities in the rhizosphere soil.

Discussion: This study provides a theoretical basis for improving plant adaptation to saline-alkali stress through soil microbial management practices.

Pancreatic cancer (PC) is a lethal malignancy with limited early detection strategies and poor therapeutic response. Emerging evidence implicates the gut microbiota in carcinogenesis, yet whether microbial alterations are causal or secondary remains uncertain. In this study, we integrated cross-sectional 16S rDNA sequencing, two-sample Mendelian randomization (MR), and mediation analysis to investigate the causal role of gut microbiota in PC risk. We profiled fecal microbiota in a Beijing-based cohort of 26 newly diagnosed PC patients and 9 healthy controls, revealing significant dysbiosis characterized by reduced microbial diversity, depletion of butyrate-producing genera (e.g., Faecalibacterium), and enrichment of pro-inflammatory taxa such as Olsenella. Using European GWAS summary data, MR analysis identified 17 gut microbial taxa causally associated with PC risk, including Olsenella and Pauljensenia sp000411415. Notably, higher abundance of Pauljensenia sp000411415 was associated with increased PC risk, an effect partially mediated by reduced circulating levels of octanoylcarnitine (C8) and glutarylcarnitine (C5-DC)-metabolites independently linked to lower PC risk. Population-matched MR in East Asian cohorts validated several causal associations, enhancing ancestral relevance. Our findings support a causal role for specific gut microbes in pancreatic carcinogenesis and highlight a Pauljensenia-acylcarnitine axis whereby microbial suppression of protective metabolites may contribute to disease development. This integrative approach bridges microbial dysbiosis with functional mechanisms, offering novel insights for microbiome-informed strategies in PC prevention and early detection.

Introduction: The search for sustainable agricultural strategies has highlighted the importance of plant-microbe interactions within soil ecosystems. In particular, extracellular metabolites produced by soil bacteria represent a promising, yet underexplored, source of bioactive compounds capable of modulating plant germination and early development.

Methods: This study evaluated the biostimulant potential of extracellular metabolites present in bacterial cell-free supernatants on the germination and early growth of Hibiscus sabdariffa and Prosopis juliflora under controlled laboratory conditions. Two native bacterial strains isolated from soils of Nuevo León, Mexico, were identified as Lysinibacillus xylanilyticus and Bacillus cereus using MALDI-TOF mass spectrometry. Supernatants obtained after cultivation in Luria-Bertani (LB) medium were applied directly to seeds, and germination and growth parameters were recorded. Phytochemical screening of the supernatants was also performed.

Results: The L. xylanilyticus supernatant significantly enhanced seed germination (96.66 ± 5.77%; p < 0.0001) and promoted early growth in both plant species, increasing shoot length, leaf width, and fresh biomass. In contrast, the B. cereus supernatant inhibited H. sabdariffa germination (30 ± 10%; p = 0.0146) and showed limited effects on P. juliflora. Notably, a 50:50 mixture of both supernatants completely inhibited H. sabdariffa germination while significantly stimulating P. juliflora germination (90 ± 10%; p = 0.0130). Phytochemical analysis revealed low concentrations of carbohydrates and coumarins, suggesting that the observed effects were likely mediated by other, unidentified bioactive metabolites.

Discussion: These findings demonstrate that extracellular metabolites produced by soil-derived bacteria exert species-specific and measurable biological effects on seed germination and early plant growth. The contrasting responses observed between plant species and supernatant combinations underscore the complexity of plant-microbe chemical interactions. Overall, this study highlights the potential of bacterial extracellular metabolites as microbiome-based tools for sustainable agriculture and ecological restoration.