Frontiers in Microbiology最新文献

Objective: Based on whole-genome sequencing (WGS) technology, the species distribution, genetic correlations, virulence and drug resistance gene characteristics of the clinical isolates of Mycobacterium abscessus complex (MABC) in the tropical island of China (Hainan) were analyzed to provide a basis for clinical precise diagnosis and treatment.

Methods: A total of 113 MABC strains from the Second Affiliated Hospital of Hainan Medical University from 2014 to 2023 were collected. Whole-genome sequencing (WGS) was used for subspecies identification (Average Nucleotide Identity, ANI), genetic distance analysis (single nucleotide polymorphism, SNP), and pan-genome analysis. The distribution of virulence and antibiotic resistance genes was analyzed through the Virulence Factor Database (VFDB) and the Comprehensive Antibiotic Resistance Database (CARD). The drug susceptibility phenotypes were detected by the microbroth dilution method.

Results: Among the 113 MABC strains, M. abscessus subsp. abscessus (Mab) accounted for 65.5%, M. abscessus subsp. massiliense (Mma) accounted for 33.6%, and M. abscessus subsp. bolletii (Mbo) accounted for 0.9%. The strains showed high genetic diversity among them, but two pairs of Mab strains with high genetic similarity (differing by 5 and 8 SNPs respectively) were identified, suggesting the possibility of local common exposure. The pan-genome is open-ended and consists of 3,626 core genes and highly variable accessory/unique genes. The virulence genes show species-specific differences: the detection rate of the phenolic lipid synthesis gene papA5 in Mma is significantly higher than that in Mab (92.1% vs. 47.3%, p < 0.001), while the PDIM synthesis gene ppsE is significantly lower in Mma (0.0% vs. 98.6%, p < 0.001). The drug sensitivity test shows that the 14-day induction of resistance rate of Mma to clarithromycin is significantly lower than that of Mab (5.3% vs. 86.5%, p < 0.001). Resistance genes are widely carried, including rrs a1408g (99.1%), rrl a2059g (98.2%) mutations, and the efflux pump gene qacJ in Mma (97.4%).

Conclusion: In Hainan region, environmental exposure is the main source of MABC infection. Whole genome analysis suggests the potential risk of local common exposure. Mma has a better treatment prospect due to its low clindamycin resistance rate. The differentiation of virulence and resistance genes among subtypes provides a molecular basis for the precise prevention and control of MABC infection in tropical regions.

Flavoenzymes of the 4-phenol oxidoreductase family are versatile biocatalysts that catalyze the oxidation of a wide variety of phenol derivatives to alcohols, aldehydes, ketones or alkenes. The promiscuous FAD-dependent vanillyl alcohol oxidases from Penicillium simplicissimum (PsVAO) and Diplodia corticola (DcVAO) have been described to catalyze the oxidative deamination of p-hydroxybenzylamines, giving rise to valuable flavor compounds, but starting from p-alkyl substituted phenols, the ketones are usually not accessible as these oxidases preferably stop at chiral benzylic alcohols. Here we took a closer look into the fungal VAO family with the aim to identify new members that can perform this deamination reaction and also the overoxidation of benzylic alcohols to ketones at a sufficient rate for application. Phylogenetic and amino acid cluster analysis revealed one clade that differed significantly in the constitution of the active site, while maintaining residues essential for catalysis. From this clade, five candidates were chosen for investigation, which revealed that VAO from Paecilomyces variotii (PvVAO) showed promising activities with vanillylamine and 4-(1-amino)ethylphenol, especially above pH 9.0, while also offering the ability to perform the overoxidation of p-alkyl substituted phenols toward ketones. Hence, the identified PvVAO offers two reaction routes toward benzylic ketones.

Growing interest in the circular economy has promoted the use of agri-food wastes as fermentable and readily available substrates for microbial cultivation, offering a sustainable and cost-effective strategy for natural pigment production. In this study, cheese whey was utilized as a nutritional substrate for pigment synthesis by an isolated strain identified as Agrococcus sp. NP24 (PQ097720.1). The work further aimed to characterize the produced pigment and evaluate its bioactivity. The culture medium was optimized using a Box-Behnken design (BBD). The carotenoid profile of the extracted pigment was analyzed by HPLC-DAD and LC-MS. Pigment stability was assessed across a range of pH values and temperatures, and its antimicrobial, antioxidant, and anticancer activities were examined. The pigment was identified as zeaxanthin monoester (C14:0). The maximum pigment yield (0.0567 mg/mL extract) was achieved after 72 h at 20 °C using a medium containing 80% whey (v/v), 0.5% peptone (w/v), 0.97 g % casein (w/v), and supplemented with 0.5% (w/v) yeast extract and 0.5% (w/v) MgSO₄. The pigment remained fully stable up to 50 °C. Acidic conditions (pH 3-5) enhanced pigment absorbance compared to neutral and alkaline pHs. In contrast, exposure to daylight markedly reduced pigment stability, leaving only 26% residual activity after 1 h. The pigment exhibited potent antioxidant activity with an IC₅₀ of 6 μg/mL. It also showed cytotoxic and significant selectivity against the triple-negative breast cancer cell line MDA-MB-231 and the colorectal carcinoma cell line HCT-116, with IC₅₀ values of 3.3 mg/mL and 0.56 mg/mL, respectively, while no cytotoxicity was observed toward the HepG-2 hepatoblastoma cell line. The carotenoid did not display significant antimicrobial activity. In conclusion, the cost-effective production of NP24 carotenoids, combined with their favorable stability and bioactivity, supports their potential use as natural colorants in food applications.

Introduction: The incidence of hypertriglyceridemia pancreatitis (HTGP) has been rising annually with a poor prognosis, and its pathogenesis is complex. In recent years, the role of gut microbiota and short-chain fatty acids (SCFAs) has gradually attracted attention in HTGP. Therefore, the aim of this study was to investigate the characteristic alterations in gut microbiota and SCFAs and their potential clinical significance and molecular mechanisms in HTGP.

Materials and methods: This study collected feces and serum samples from 18 HTGP patients and 18 healthy volunteers. We compared baseline clinical characteristics, gut microbiota diversity (via 16S rRNA sequencing), and serum SCFA concentrations (using mass spectrometry and other techniques) between the two groups to identify characteristic alterations. Correlation analyses explored associations between microbiota, metabolites, and clinical parameters. Further animal models validated the in vivo functions and molecular mechanisms of SCFAs.

Results: HTGP patients exhibited higher body mass index (BMI), triglyceride (TG) levels, metabolic complication incidence and disease severity scores. In addition, the gut microbiota showed significantly reduced richness and diversity in HTGP. Serum metabolomics analysis revealed significantly higher concentrations of isovaleric acid, decanoic acid and octanoic acid in HTGP patients, demonstrating good diagnostic value. Correlation analysis indicated that differential gut microbiota and metabolites were closely associated with clinical parameters. Animal experiments confirmed that butyrate can alleviate HTGP disease severity by inhibiting NF- κ B/NLRP3 pathway activation.

Discussion: In summary, this study identified differential gut microbiota and SCFAs in HTGP patients compared to healthy volunteers, and confirmed that butyrate exerts a protective effect through NF-κB/NLRP3 pathway.

The clinical management of bladder cancer faces major challenges due to treatment resistance and recurrence, which require the development of new adjuvant strategies. The role of the gut microbiome in influencing bladder cancer progression and treatment response through the "gut-bladder axis" is gaining recognition. This understanding provides a theoretical rationale for exploring microbiota-targeting interventions, such as fecal microbiota transplantation (FMT). As a method capable of thoroughly reshaping the gut microbiota, FMT may have broad clinical potential. This review systematically explores the possible role of FMT in treating bladder cancer. It begins by summarizing the observational and causal evidence linking gut microbiota dysbiosis to bladder cancer, which forms the rationale for considering FMT as an intervention. Then, it discusses how FMT might improve therapeutic effectiveness, including regulation of microbial metabolites (such as short-chain fatty acids, tryptophan, and bile acids), repair of the intestinal barrier, induction of epigenetic reprogramming and modulation of the urinary microbiota. The review also considers potential scenarios for combining FMT with existing adjuvant therapies, including immunotherapy, chemotherapy, and radiotherapy. Finally, it objectively evaluates the key challenges in translating FMT into clinical practice, including effectiveness, safety, standardization, and regulatory or ethical issues, and outlines future directions. By synthesizing current evidence, this review highlights FMT as a potentially promising and innovative adjuvant strategy worthy of further investigation, which, if validated, could contribute to overcoming current therapeutic challenges in bladder cancer.

Introduction: Phosphate-solubilizing bacteria (PSB) that tolerate heavy metals may enhance phosphorus availability in contaminated soils and provide candidates for bio-based management.

Methods: PSB were isolated from farmland rhizosphere soil and screened on tricalcium phosphate medium. Soluble phosphorus (soluble P) was quantified in liquid culture using tricalcium phosphate, ferric phosphate, aluminum phosphate, and lecithin as insoluble phosphorus (insoluble P) sources. Pb/Cr tolerance was assessed by growth on metal-amended plates and minimum inhibitory concentration (MIC) assays, and six dominant isolates were identified by 16S rRNA gene sequencing.

Results: Eighteen PSB isolates were obtained. All strains solubilized tricalcium phosphate (2.82253.53 mg L^-1) and ferric phosphate (6.24206.48 mg L^-1); most also solubilized aluminum phosphate (13.0244.73 mg L^-1), and 13 isolates solubilized lecithin (2.8230.84 mg L^-1). The six strains able to grow at 6 mmol L^-1 Pb or Cr were identified as Bacillus sp. (HY-1, HY-6), Bacillus subtilis (HY-3, HY-16), Bacillus thuringiensis (HY-12), and Duganella sp. (HY-13). MICs were higher for Cr (1720 mmol L^-1) than for Pb (67 mmol L^-1), and increasing Pb or Cr suppressed both growth (OD₆₀₀) and phosphate solubilization. Single-factor optimization identified glucose as the most suitable carbon source and 0.3 g L^-1 NaCl as optimal; the best initial pH was 6 for five strains (pH 7 for HY-12), and temperature optima were strain-dependent (3040 °C).

Conclusion: These results define cultivation parameters for inoculum preparation and support further testing in soil and plant systems under environmentally relevant conditions.

Introduction: Agricultural mulches are commonly used for their benefits, however, the mechanisms by which they affect microbial communities to mediate soil properties that influence tomato growth remain unclear.

Methods: A three-year experiment was conducted comparing four treatments: plastic film mulching alone (SBF), straw mulching alone (SM), film-straw dual mulching (SBFSF), and no mulching (CK). Their effects on soil properties, microbial communities, and tomato growth were systematically evaluated.

Results: All mulching treatments significantly increased tomato yield, with SBF, SM, and SBFSF demonstrating improvement of 32.87%, 22.17%, and 50.17%, respectively. SBFSF exhibited the greatest dry matter weight (shoot plus root), root length, and root surface area 40 days post-transplanting, and it showed the strongest effect on soil moisture and thermoregulation. SM and SBFSF significantly increased soil organic carbon (SOC: +5.92%, +4.04%), total nitrogen (TN: +6.34%, +4.46%), available potassium (AK: +18.15%, +10.91%), and available phosphorus (AP: +2.60%, +2.15%). SBFSF significantly reduced the diversity of soil bacteria and fungi, howerer, it selectively increased the relative abundances of plant growth-promoting rhizobacteria and functional microorganisms involved in carbon-nitrogen cycling, such as the bacterial phylum Firmicutes(+125.18% to +193.55%), genera Lysobacter (+49.19% to +186.62%) and Bacillus (+168.56% to +273.00%), and fungal phyla Ascomycota (+7.99% to +8.19%) and Mortierellomycota (+11.05% to +98.71%), including the genus Trichocladium (+30.43% to +269.95%). In contrast, SM and SBF led to an increase in the abundance of pathogenic fungi (Fusarium, Cladosporium, Alternaria, and Cephaliophora), elucidating their inferior yield performance compared to SBFSF.

Discussion: Partial least squares path modeling (PLS-PM) analysis indicated that mulching practices directly and positively influenced the soil bacterial and fungal community composition and negatively affected soil fungal community diversity, which indirectly effecting tomato growth by modulating soil properties. These results provide a scientific foundation for improving mulching, and sustainable agricultural practices.

Brucellosis in water buffalo remains endemic in southern Italy, particularly in areas of the province of Caserta characterized by high animal density. This retrospective cohort study (2016-2021) assessed the effectiveness of stamping out (whole-herd depopulation) versus selective culling in counteracting brucellosis in water buffalo herds. Data from 222 outbreaks were analyzed using Cox regression, incorporating herd size, buffalo density, eradication method, and co-infection with Mycobacterium bovis. Stamping out reduced reinfection risk by 80% (HR = 0.2; p < 0.001), especially in municipalities exceeding 200 buffaloes/km². Co-infection with M. bovis was not statistically associated with reinfection. These results indicate that control strategies should prioritize stamping out, coupled with reinforced structural and operational biosecurity measures, even in high-density settings, to achieve disease-free status. Integrated surveillance and education, in line with One Health principles, are essential for sustainable eradication and protection of the buffalo dairy sector.

The soil microbiome drives soil nutrient cycling and is intrinsically linked to plant productivity in agriculture. Archaea are members of many soil microbiomes and play important roles in nutrient cycling, particularly in the carbon and nitrogen cycle. Many archaeal groups contribute to both carbon and nitrogen cycles, but their dual roles are often underappreciated. For instance, ammonia-oxidizing archaea couple ammonia oxidation to carbon fixation, contributing to carbon sequestration in soils. Methanogenic archaea use ATP produced through methanogenesis for nitrogen fixation. N-DAMO archaea directly couple carbon and nitrogen cycling through nitrate-dependent anaerobic methane oxidation, while haloarchaea contribute to carbon sequestration and denitrification. Here, we synthesize the latest research regarding the dual roles of archaea in carbon and nitrogen cycling in agricultural soils. We pay special attention to how nutrient input influences these roles. We show that the relevance of the processes is highly context dependent. In addition, we identify several research directions that will help harness the difference roles of archaea in carbon and nitrogen cycling to increase agricultural productivity and sustainability. Finally, we showcase that abundance and activity of archaea in the soil microbiome could be steered through nutrient input or microbiome engineering strategies.

Microbial management offers a sustainable pathway to enhance crop performance by optimizing plant-associated microbiomes. However, integrated strategies that concurrently target both the rhizosphere and phyllosphere to improve fruit tree productivity and quality remain underexplored. This study systematically evaluated the effects of combined soil and foliar microbial applications on the yield, fruit quality, and microbiome dynamics of 'Yuluxiang' pear. We compared conventional fertilization (CK) with two treatments: CK plus a soil-applied anti-replant disease agent (CF) and CK plus both the soil agent and a foliar growth-promoting inoculant (CFW). Microbial applications significantly increased the yield by up to 60.4% in CF treatment, and enhanced key fruit quality parameters, including soluble solids content (increased by 17.2% in CF and 16.7% in CFW) and fruit shape index. These agronomic improvements were closely associated with a targeted restructuring of bacterial communities in both the phyllosphere and rhizosphere. Specifically, beneficial phyla such as Actinomycetota were enriched in the phyllosphere under CFW treatment, while Bacillota increased in the rhizosphere under microbial amendments. Furthermore, co-occurrence network analysis revealed that microbial applications fostered more complex and cooperative microbial networks, with increased nodes and edges across both compartments. This work demonstrates that an integrated soil and foliar microbiome management strategy can mitigate replant disease constraints and elevate fruit quality, providing a practical approach for sustainable orchard production.