Microorganisms最新文献

The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.

Porcine epidemic diarrhea virus (PEDV) is a major cause of fatal diarrhea in piglets. The continuous emergence of new variants, driven by recombination and mutation, poses a persistent global threat to the swine industry, resulting in significant economic losses. Therefore, ongoing surveillance of PEDV evolution is critical. In this study, we isolated a novel PEDV strain, designated PEDV/FJLY202201, from experimental intestinal samples collected from a diarrheal piglet in Fujian, China, and sequenced its complete genome. Complete genome analysis, phylogenetic analysis, and recombination analysis were conducted. Results showed that PEDV/FJLY202201 was a recombinant strain derived from two recombination events between G2a and G2b strains, with three breakpoints located in the ORF1b, Domain 0 (D0) and S2 subunit, respectively. Notably, multiple mutations were identified in the S2 subunit, a finding that has been rarely reported before. Furthermore, following challenge with the PEDV/FJLY202201 strain, 3-day-old piglets exhibited severe diarrhea, sustained a 30.35% weight loss, and reached 100% mortality, collectively demonstrating its high virulence. These data reveal the complex evolution of PEDV/FJLY202201 and provide a foundation for a better understanding of the genetic evolution and molecular pathogenesis of PEDV.

Bovine Parainfluenza Virus Type 3 (BPIV3) is a critical pathogen in the Bovine Respiratory Disease Complex (BRDC), leading to significant economic losses in the cattle industry. However, the metabolic reprogramming induced by BPIV3 in cattle remains poorly understood. This study aimed to investigate the impact of BPIV3 infection on the serum metabolome of Simmental cattle using untargeted metabolomics and ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS). The results revealed significant alterations in the lipidome, including the upregulation of phosphatidylcholine (PC) and phosphatidylglycerol (PG), and the downregulation of phosphatidylinositol (PI). Sphingolipid metabolism also showed considerable changes, with increased levels of Trihexosylceramide and D-erythro-Sphingosine C-17. Furthermore, metabolic pathway analysis identified enriched pathways related to lipid metabolism, amino acid metabolism, and energy sensing. These findings suggest that BPIV3 infection induces substantial shifts in lipid metabolism, which may facilitate viral replication and immune evasion. Our results provide a deeper understanding of the metabolic changes in BPIV3-infected cattle and propose potential targets for therapeutic intervention.

Candida spp. are important opportunistic human fungal pathogens. This study aimed to identify and characterize Candida spp. obtained from patients admitted to an Intensive Care Unit (ICU), focusing on virulence attributes and susceptibility to antifungal agents. A total of 131 isolates from oral and tracheobronchial secretions of adult ICU patients were evaluated. Phenotypic identification was performed using chromogenic culture media for Candida, followed by MALDI-TOF mass spectrometry, with representative isolates confirmed by ITS sequencing. Antifungal susceptibility to fluconazole, ketoconazole, and amphotericin B was determined only by the agar disk diffusion method, and virulence was assessed through esterase, DNase, protease, and hemolytic activity assays. C. albicans was the prevalent species, followed by C. tropicalis, C. krusei, C. glabrata, C. parapsilosis, C. dubliniensis, C. lusitaniae, and C. guilliermondii. Antifungal resistance rates reached 51.1% for fluconazole, 42.7% for ketoconazole, and 19.1% for amphotericin B, as determined by disk diffusion method. Overall, 64.9% of the isolates exhibited esterase activity, 18.3% DNase, 45.8% protease, and 67.2% exhibited hemolytic activity. Oral isolates were more frequent than tracheal isolates and demonstrated a higher prevalence of antifungal resistance and virulence traits. These findings underscore the epidemiological importance of characterizing Candida species in hospitals to better understand the yeast profile and to support adequate clinical management.

Despite increasing interest in probiotics as antibiotic alternatives in swine production, few studies have directly compared the functional efficacy of different commercial probiotic formulations under controlled conditions. We conducted an in vitro study using porcine intestinal epithelial (IPEC-J2) and macrophage-like (3D4/21) cell models to compare the efficacy of three commercial probiotic consortia (C1: three strains of Bacillus velezensis; C2: B. licheniformis + B. subtilis; C3: Clostridium butyricum). Treatments were evaluated for their ability to inhibit pathogenic Escherichia coli, Clostridium perfringens, and Salmonella spp., enhance epithelial barrier integrity, and modulate immune responses. Experimental endpoints included pathogen inhibition assays, adhesion to IPEC-J2 cells, transepithelial electrical resistance (TEER), tight junction protein expression, and cytokine profiling via RT-qPCR and proteomics. Data were analyzed using the Kruskal-Wallis test with false discovery rate (FDR) control at 5%. C1 cell-free supernatant (CFS) strongly inhibited pathogen growth (84.8 ± 5.3% inhibition of ETEC F4⁺F18^- vs. medium control; p < 0.05), whereas C2 had no effect, and C3 inhibited only one isolate. The coculture of IPEC-J2 cells with C1 CFS increased the expression of TJ proteins ZO-1, MUC13, and MUC20 (+12.9-46.6% vs. control; p < 0.001) and anti-inflammatory TGF-β; reduced pro-inflammatory IL-6 in LPS-stimulated 3D4/21 cells. In comparison, C2 and C3 showed minimal impact on epithelial barrier integrity and immune modulation, as indicated by negligible changes in TEER values, tight junction protein expression (ZO-1, MUC13, MUC20), and cytokine profiles relative to the control. In conclusion, C1 demonstrated greater in vitro efficacy than C2 (B. licheniformis + B. subtilis) and C3 (Clostridium butyricum), including pathogen inhibition assays, epithelial adhesion, TEER measurements, and cytokine modulation, suggesting its potential as a leading candidate for functional probiotic applications.

Astaxanthin, derived from Haematococcus pluvialis, is a potent antioxidant with significant therapeutic potential. However, its large-scale commercialization is hindered by the "thick-wall challenge", a phenomenon where the stress conditions required for astaxanthin accumulation also trigger the formation of resistant secondary cell walls. This challenge complicates extraction and reduces bioaccessibility, thereby increasing production costs. Recent advancements have focused on uncoupling astaxanthin biosynthesis from cell wall reinforcement, utilizing metabolic engineering and strain selection to reduce wall formation while maintaining high yields. Furthermore, green extraction techniques, such as electrotechnologies and ionic liquids, are being explored to improve efficiency and environmental sustainability. This review synthesizes these innovations, including biorefinery systems that maximize biomass valorization, and discusses emerging clinical applications. We highlight the challenges in bridging the gap between laboratory successes and clinical translation, and suggest future directions for resolving the thick-wall challenge, advancing astaxanthin production, and expanding its therapeutic uses in nutraceuticals and pharmaceuticals.

Sustaining agricultural productivity and soil health under intensive cultivation requires a comprehensive understanding of fertilization effects, particularly on deeper soil layers, which has received limited attention compared to surface soils. This study investigated how different fertilization regimes (inorganic, organic, and combined organic-inorganic fertilizers) influence soil physicochemical properties, microbial diversity, community structure, and functional gene abundances at three soil depths (0-20 cm, 20-40 cm, and 40-60 cm) in a 40-year fertilization experiment. Organic fertilization significantly improved topsoil fertility indicators such as soil organic matter (56.6-109.2%), total nitrogen (66.7-122.0%), total phosphorus (198.6-413.2%), and available phosphorus (984.8-1622.1%) and potassium (35.3-438.1%). Compared with the unfertilized control and nitrogen-only treatment, rice yield increased by 97.1-130.5% under NPK and sole organic fertilization, and further increased by 184.1-255.9% under combined organic-inorganic fertilization. However, fertilization effects diminished with soil depth due to limited nutrient mobility. Microbial diversity significantly decreased with depth and was minimally influenced by fertilization treatments. Microbial community structure varied notably among fertilization treatments at the surface layer, mainly driven by soil nutrients, whereas soil depth had a dominant effect on microbial community structure and compositions. Co-occurrence networks showed the highest complexity in surface soil microbial communities, which declined with soil depth, reflecting potential synergistic and mutualistic relationships in topsoil and the adaptation of microbial communities to nutrient-limited conditions in subsoil. Microbial functional gene analyses highlighted clear depth-dependent distributions, with surface layers enriched in decomposition-related genes, while deeper layers favored anaerobic processes. Overall, long-term fertilization exerted strong depth-dependent effects on soil fertility, microbial community structure, and functional potential in paddy soils.

The human skin microbiome has gained considerable attention as a resource for the development of innovative probiotics for cosmetic purposes or promoting skin health. However, the evaluation of new probiotic strains to ensure their "generally recognized as safe" (GRAS) status remains challenging. Here, we have subjected the annotated draft genome sequences of four human skin-derived bacterial strains, namely Bacillus subtilis MBF10-19J, Micrococcus luteus MBF05-19J, Staphylococcus hominis MBF12-19J, and Staphylococcus warneri MBF02-19J, to bioinformatic analyses to detect the genes associated with important probiotic traits, as well as undesirable characteristics such as antibiotic resistance, virulence factors, and toxic metabolites. Each bacterium harbors at least one type of adhesin-encoding gene, while only S. hominis MBF12-19J and S. warneri MBF02-19J contain the putative genes encoding enzymes for metabolism improvement. In vitro assays, including antibiotic susceptibility and antimicrobial activity testing, revealed strain-specific safety characteristics that complement the genomic findings. With regard to antibiotic resistance determinants, S. hominis MBF12-19J showed the most favorable profile, S. warneri MBF02-19J and M. luteus MBF05-19J appeared suitable when used with appropriate caution, and B. subtilis MBF10-19J exhibited amoxicillin resistance, i.e., warrants careful evaluation. Further in vivo validation is needed to determine whether these strains do indeed comply with GRAS evaluation frameworks.

Previous studies have demonstrated that Bacillus velezensis HN-Q-8 shows significant inhibitory effects against various plant pathogenic fungi causing potato diseases, primarily attributed to the production of fengycin. However, the low yield of fengycin in wild-type strains limits its practical application, and the influence of its biosynthesis pathway on volatile organic compound production remains unclear. In this study, to enhance fengycin production in Bacillus velezensis HN-Q-8, we applied metabolic engineering by targeting competitive pathways. Specifically, a double mutant (ΔsrfAAΔbaeBE) was constructed by knocking out the surfactin synthase gene srfAA and the bacillaene synthesis gene baeBE. The fengycin yield of the ΔsrfAAΔbaeBE mutant in the basal (sodium glutamate) fermentation medium reached 98.83 mg/L, representing a 2.39-fold increase over the wild-type strain. Subsequent medium optimization by supplementing peptone further boosted production to 155.61 mg/L, which was 3.77-fold higher than the wild-type level. The lipopeptide extract from the double mutant strain ΔsrfAAΔbaeBE demonstrated potentiated antifungal activity against four major potato fungal pathogens: Alternaria solani (early blight), Rhizoctonia solani (black scurf), Fusarium oxysporum (wilt), and Botrytis cinerea (gray mold). The active volatile compounds released by ΔsrfAAΔbaeBE, such as benzaldehyde and 2,5-dimethylpyrazine were significantly increased. The knockout of srfAA and baeBE also distinctly altered the physiology of the strain: the double mutant exhibited enhanced biofilm formation, an accelerated early growth rate followed by early decline, and a severely reduced sporulation capacity. These results confirmed the feasibility of molecularly modifying Bacillus velezensis HN-Q-8 to improve fengycin production and antifungal activity for further agricultural application.

The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet-microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet-microbiome associations in 79 prostate-cancer survivors (ages 62-81) enrolled in a randomized exercise intervention trial, 59.5% of whom still have active metastatic disease. Dietary intake was assessed using the Diet History Questionnaire (201 variables) and analyzed using three validated dietary pattern scores: Mediterranean Diet Adherence Score (MEDAS), Healthy Eating Index-2015 (HEI-2015), and the Mediterranean-Dash Intervention for Neurodegenerative Delay (MIND) diet score. Gut microbiome composition was characterized via 16S rRNA sequencing. Dimensionality reduction strategies, including theory-driven diet scores and data-driven machine learning (Random Forest, and Least Absolute Shrinkage and Selection Operator (LASSO)), were used. Statistical analyses included beta regression for alpha diversity, Permutational Multivariate Analysis of Variance (PERMANOVA) for beta diversity (both Bray-Curtis and Sørensen metrics), and Microbiome Multivariable Associations with Linear Models (MaAsLin2) with negative binomial regression for taxa-level associations. All models tested interactions with exercise intervention, APOLIPOPROTEIN E (APOE) genotype, and testosterone levels. There was an interaction between MEDAS and exercise type on gut alpha diversity (Shannon: p = 0.0022), with stronger diet-diversity associations in strength training and Tai Chi groups than flexibility controls. All three diet-quality scores predicted beta diversity (HEI p = 0.002; MIND p = 0.025; MEDAS p = 0.034) but not Bray-Curtis (abundance-weighted) distance, suggesting diet shapes community membership rather than relative abundances. Taxa-level analysis revealed 129 genera with diet associations or diet × host factor interactions. Among 297 dietary variables tested for cognitive outcomes, only caffeine significantly predicted Montreal Cognitive Assessment (MoCA) scores after False Discovery Rate (FDR) correction (p = 0.0009, q = 0.014) through direct pathways beneficial to cognitive performance without notable gut microbiome modulation. In cancer survivors, dietary recommendations should be tailored to exercise habits, genetic background, and hormonal status.