Frontiers in Microbiology最新文献

Introduction: Blueberries are considered a superfood because of their rich content of vitamins, antioxidants, and fiber, supporting multiple health benefits. Plants host complex microbiomes that play crucial roles in resistance to pathogens, productivity, and stress tolerance. Despite its importance, a comprehensive characterization of the microbiota across all major compartments of cultivated blueberry (Vaccinium corymbosum) is still lacking.

Methods: Using high-throughput sequencing of marker genes, we provide the first integrative survey of fungal and bacterial communities associated with three distinct plant compartments: rhizosphere, leaf surface, and fruit surface, as well as the bulk soil, across 100 samples, generating datasets of over 4,000 unique fungal and 38,000 unique bacterial amplicon sequence variants (ASVs).

Results: We found clear compartment differentiation, with pronounced shifts in richness, diversity, and taxonomic composition between belowground and aboveground compartments. Alpha diversity peaked in bulk soils and declined progressively toward aboveground tissues. We further detected minimal overlap across compartments, with only 9 fungal and 12 bacterial ASVs shared across all compartments. These findings challenge the soil-origin hypothesis for aboveground microbiota.

Conclusion: Blueberry plants harbor highly compartmentalized microbial communities shaped by selective environmental and physiological filtering. Our findings provide a baseline for future development of targeted, compartment-specific bioinoculants aimed at enhancing beneficial microorganisms for blueberry cultivation.

Introduction: Short-chain fatty acids (SCFAs), particularly propionate, play crucial roles in host metabolism, immunity, and gut barrier function. However, the direct physiological effects of propionate on healthy organisms remain unclear. This study investigated the impact of sodium propionate (SP) supplementation on intestinal barrier function, gut microbiota, and hematological parameters in healthy C57BL/6 mice.

Methods: Mice were orally administered 200 mg/kg SP for 21 days.

Results: Results showed no significant changes in body weight, intestinal histopathology, or blood parameters. The immunohistochemical results showed decreased IL-6 expression, while IL-10 and occludin expression were increased. Gut microbiota analysis revealed decreased α-diversity in the SP group, along with shifts in microbial composition, including increased Akkermansia and Bacteroides. No significant differences in colonic SCFA concentrations were observed.

Conclusion: These findings suggest that propionate modulates gut microbiota and hematological parameters in healthy mice, providing insights into its physiological roles under normal conditions.

Antimicrobial resistance (AMR) in livestock is a major contributor to the global AMR crisis, yet little is known about its dynamics in high-altitude pastoral systems. We performed deep metagenomic sequencing of 100 fecal samples from Tibetan Awang sheep reared under grazing (aw_fm) and captive (aw_qs) conditions. Microbiome profiling revealed striking community shifts: grazing sheep were enriched in Bacteroidetes and Firmicutes, whereas captive sheep showed expansion of Proteobacteria, particularly Acinetobacter, suggesting dysbiosis. The resistome comprised 302 unique ARGs, dominated by rpoB2 (43.3%), Bifidobacterium_adolescentis_rpoB (11.2%), and ugd (10.2%). Grazing sheep carried ARGs mainly against rifamycins and peptide antibiotics, reflecting natural selective pressures, while captive sheep exhibited significantly broader resistance, including tetracyclines, macrolides, and fluoroquinolones (p < 0.05). Enrichment of efflux pump genes (MexK, adeJ) in captive sheep highlighted a shift toward multidrug resistance. These findings demonstrate that rearing practices profoundly restructure the gut resistome, underscoring the need for targeted antibiotic stewardship in high-altitude livestock systems.

Bacterial wilt caused by Ralstonia solanacearum is a major constraint to global peanut production, leading to serious yield and economic losses, particularly in tropical and subtropical regions. The disease reduces plant vigor, pod development, and overall productivity, posing a significant threat to food security and farmer income. Conventional control methods, including crop rotation, resistant varieties, soil amendments and chemicals, remain inconsistent and often provide limited long-term effectiveness. This inconsistency is due to the pathogen's broad host range, prolonged soil survival, and high genetic adaptability, which enable rapid spread and persistence. These challenges indicate the need for sustainable alternatives that are effective and environmentally sound. Nanoparticle-based antimicrobial delivery systems have emerged as a promising strategy because of their precision targeting, improved stability, enhanced bioavailability, and controlled release of active agents. Key nanomaterial design parameters, including composition, size, surface functionalization, and carrier efficiency, critically influence antimicrobial activity against R. solanacearum. These characteristics affect interactions with bacterial cells and plant tissues. Major mechanisms of pathogen suppression involve membrane disruption, metabolic interference, oxidative stress generation, and induction of plant systemic resistance. Environmental aspects, such as nanoparticle fate, bioaccumulation, persistence in soil, and ecotoxicological risks, must also be considered to ensure ecological safety and sustainability. Integrating nanotechnology with plant breeding and biocontrol strategies can promote resilient and eco-friendly peanut production. Nanoparticle-enabled disease management offers a transformative approach for mitigating bacterial wilt while strengthening sustainable crop protection systems worldwide. Policy support and responsible innovation will accelerate the safe adoption of these technologies in the field.

Daqu, the core fermentation starter for Chinese Baijiu, harbors intricate and functionally important fungal communities. To comprehensively characterize its biodiversity, we employed an integrated approach combining third-generation amplicon sequencing with culturomics to systematically investigate the fungal communities in low-, medium-, and high-temperature Daqu. Our analysis identified 109 amplicon sequence variants and 135 cultivable isolates, encompassing both cultivable and non-cultivable fungal taxa. Third-generation sequencing revealed greater fungal species richness, whereas culturomics effectively isolated dominant functional fungi, including Saccharomycopsis fibuligera and Lichtheimia ramosa. Moreover, the fungal communities in Daqu exhibited distinct temperature-dependent patterns, with the thermophilic fungus Thermoascus crustaceus being the predominant species in high-temperature Daqu. This integrative approach provides complementary insights into the fungal ecology of Daqu and establishes a foundation for the development fungal resources with potential industrial applications.

Background: The rice-eel system, a cultivation method integrating aquatic animals with rice, offers ecological and agronomic advantages, yet its long-term effects of substituting chemical fertilizers with straw or organic fertilizers on soil properties remain unclear.

Aims: This study aimed to quantify the effects of organic waste substitutions within the rice-eel system on soil physicochemical properties and microbial communities.

Methods: A 2016-established field experiment on sandy loam soil under rice-fallow rotation, and soil samples (0-20 cm and 20-40 cm depths) were taken in March 2025. The study included five treatments: conventional fertilization (100%) without eel (RT), conventional fertilization (100%) + eel (IRT), 70% chemical fertilization + eel (I70), 70% chemical fertilization + 30% straw + eel (IS), and 70% chemical fertilization + 30% organic fertilizer + eel (IO).

Results: The system improved soil macroaggregate stability, with the strongest effects under IS and IO. Compared with RT, IS and IO significantly increased soil organic matter (SOM) by 16.04% on average, at 0-20 cm, and increased SOM and available phosphorus (AP) by 18.60 and 33.70%, respectively, at 20-40 cm. IS and IO significantly increased bacterial and fungal gene copies by an average of 64.95% (0-20 cm) and 76.20% (20-40 cm). The rice-eel system improved microbial diversity, reshaped community composition, and increased taxa such as Chloroflexi, Acidobacteriota, Pleosporales and Chytridiomycota which contribute to organic matter decomposition and aggregate formation. The relative abundance of microorganisms associated with aerobic respiration (cytochrome c pathway) increased, while functional pathways related to biosynthesis and degradation/utilization/assimilation were also strengthened.

Conclusion: The rice-eel system-particularly IO-significantly improved fertility, aggregate stability, and microbial function. These findings indicate that the rice-eel system reduces reliance on chemical fertilizers while sustaining productivity, offering a practical strategy for ecological agriculture.

Staphylococcus aureus uridine monophosphate kinase (saUMPK) functions as a hexameric enzyme that catalyzes the reversible reaction: Mg²⁺ ⋅ ATP + UMP ↔ Mg²⁺ ⋅ ADP + UDP. As a key enzyme in pyrimidine metabolism with no detectable homologs in eukaryotes, saUMPK represents an attractive antibacterial target. In this study, we determined crystal structures of saUMPK in complex with various nucleotides, including UMP (3.26 Å), UDP (2.75 Å), GTP (2.88 Å), UTP (2.30 Å), ATP/GTP (2.88 Å), and ATP/UMP (2.57 Å), and performed complementary biochemical assays. Structurally, our analyses revealed several key findings: (1) We captured a previously unobserved apo-like conformation of saUMPK; (2) We identified key residues involved in UMP recognition and revealed the substrate-binding plasticity at the ATP donor site; (3) We uncovered that the allosteric site accommodates different nucleotides through a conserved network of basic residues (R101, R119, R122, K126, and R128). Notably, both the type and number of bound nucleotides cooperatively regulate the final conformational state of the saUMPK hexamer. GTP molecules fully occupy the allosteric sites, stabilizing the open conformation and preserving the global threefold symmetry. In contrast, UTP, ATP, or UDP only partially occupy the allosteric sites, resulting in a loss of this symmetry, while ATP or UDP binding further induces a U-shaped closed conformation of the hexamer. Site-directed mutagenesis identified key residues critical for enzymatic activity. These insights provide a foundation for designing broad-spectrum inhibitors targeting UMP kinase from Staphylococcus aureus and related Gram-positive bacteria.

This mini review article focuses on pharmacomicrobiomics, or the study of how the composition and activity of microorganisms in the body, in particular in the gut, impact drug pharmacokinetics and pharmacodynamics. This evolving field has profound implications for personalized medicine in the management of chronic inflammatory diseases. Particularly in dermatology, patient response to an expanding collection of biologic and small molecule inhibitor therapies coming out on the market remains unpredictable. The decision to start which therapy depends on physician preference, rather than based on what is expected to be the treatment response of each individual. This therapeutic uncertainty leads to sequential treatment failures, increased patient morbidity, and substantial healthcare expenditure. This mini-review synthesizes the evidence surrounding the gut microbiome as a predictive biomarker for therapeutic response in inflammatory skin diseases. We will examine the past use of pharmacomicrobiomics in oncology, where gut microbial signatures were found to predict response to immunotherapy in melanoma. We then analyze the present, focusing on the robust translational models from inflammatory bowel disease (IBD) and rheumatoid arthritis (RA), and the established gut dysbiosis in dermatologic conditions such as psoriasis and hidradenitis suppurativa (HS). Finally, we consider the future, discussing the potential for microbiome-based diagnostics to guide therapy selection for chronic inflammatory skin diseases.

Introduction: The global spread of the plasmid-mediated colistin resistance gene mcr-1 poses a serious threat to public health. This study aimed to conduct a preliminary characterization of the epidemiology and genomic features of Enterobacteriaceae carrying the mcr-1 gene in a hospital setting in Hainan, China.

Methods: A total of 2,700 Enterobacteriaceae strains, including 2,200 fecal samples and 500 respiratory, blood, and urine isolates, were collected from Haikou People's Hospital between October 2020 to September 2024. Specifically, the mcr-1 gene was screened by PCR. Antimicrobial susceptibility testing was performed with the VITEK 2 system. Four mcr-1 positive strains underwent whole-genome sequencing using Illumina and Nanopore platforms, which were combined with CARD, multilocus sequence typing (MLST), and plasmid analysis to elucidate resistance mechanisms.

Results: The positivity rate for mcr-1 was 0.15% (4/2,700). All positive isolates were identified as Escherichia coli, with two strains originating from urine and two from fecal samples. Antimicrobial susceptibility testing showed that the urine isolates (C29 and C180) were extensively drug resistant (XDR). The fecal strain S321.4 was multidrug resistant (MDR), while S118.1 was sensitive. Patients with XDR/MDR strains had recent antibiotic exposure and invasive procedures. Whole-genome analysis revealed that MLST types of the strains were diverse (ST410, ST167, ST11165, ST1266), and mcr-1 was located on plasmids of IncI2 or IncX4 types. The IncI2 plasmid carried a complete conjugative operon. Plasmid C180_5 harbored bla _CTX-M-199 through IS150, forming a multidrug resistance plasmid. Strain C29 exhibited a reduced colistin minimum inhibitory concentration (MIC) of 0.5 μg/mL due to disruption of mcr-1 by IS3, which likely impairs gene function. However, this requires further functional validation.

Conclusion: This preliminary study indicates a low prevalence of mcr-1 in our setting. However, the genomic identification of conjugative plasmids, including one carrying both mcr-1 and an extended-spectrum β-lactamase gene, highlights a tangible risk for horizontal co-transfer of resistance. The association of these isolates with healthcare exposures underscores the need for ongoing surveillance to monitor plasmid evolution in hospital ecosystems.