Frontiers in Microbiology最新文献

Introduction: Persistent organic pollutants (POPs) and trace metals are increasingly recognized as critical drivers of ecological change in polar environments. However, their combined impact on sediment microbial communities remains largely unexplored.

Methods: We analyzed sediments from 12 high-latitude lakes and ponds, five from the Arctic (Svalbard) and seven from the Antarctic (South Shetland Islands/Deception Island), to examine contaminant profiles (polychlorinated biphenyls [PCBs] and trace metals) and prokaryotic community structure using 16S rRNA gene amplicon sequencing. Finally, we assessed the associations between the identified communities and detected pollutants, and compared these associations across lakes and sites.

Results: The results revealed distinct chemical signatures between poles: Arctic sediments were mainly contaminated by polycyclic aromatic hydrocarbons (∑PAHs, 18.5-685.7 ppb; phenanthrene was the most abundant), whereas Antarctic sediments showed relatively higher concentrations of chlorobenzenes (∑CBs, 1.9-3.6 ppb) and polychlorinated biphenyls (∑PCBs, 0.9-1.4 ppb), with 2-methylnaphthalene as the most abundant PAH. Manganese was the most abundant metal in both regions, reaching 760 ppm in the Arctic, while elevated arsenic and lead characterized specific Antarctic sites. Amplicon sequencing identified five dominant phyla (i.e., Actinobacteriota, Bacteroidota, Alpha- and Gammaproteobacteria, and Desulfobacterota) with significant compositional shifts between poles.

Discussion: Notably, the distinct contaminant signatures between regions appeared to be associated with shifts in microbial community composition, suggesting that both the type and intensity of POP and metal exposure may influence bacterial diversity and ecological functions in polar lake sediments. These findings provide a robust baseline for Arctic-Antarctic comparisons, positioning polar lakes as sensitive sentinels of contaminant-driven ecological change. They also underscore the urgent need for functional studies and long-term monitoring to evaluate ecosystem resilience under accelerating climate change.

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae severely limits treatment options, with increasing resistance even to first-line and last-line ceftriaxone (CRO), posing a major global public health threat. In this study, we systematically identified 53 significantly different mutations between ceftriaxone-resistant and susceptible strains in multiple proteins through bioinformatics analysis. Among these, 33 mutations were identified for the first time, notably including the PorB Q143K via structural analysis. Minimum spanning tree (MST) analysis based on these mutations marked improved sensitivity and specificity for identifying ceftriaxone-resistant strains compared to traditional sequence typing of PenA, PonA, PorB, and MtrR (68.4% vs. 53.2%; 77.3% vs. 57.5%, respectively). Furthermore, analysis of PenA sequences from global 8,325 strains (470 MLST types) revealed that mutation frequencies at key PenA sites are highly associated with MLST types, with 34 high-frequency MLST types (STs) identified. The proportions of these 34 STs were 88.38% in 611 decreased susceptibility to ceftriaxone (CRO-DS) strains and 33.09% in 8,325 background strains, respectively, revealing an extremely significant association between 34 high-frequency STs and CRO-DS (P < 0.0001). In conclusion, this work provides further insights into the molecular mechanisms of CRO resistance while offering significant value for monitoring and predicting emerging CRO-DS-associated MLST types.

Feline milk serves as a natural reservoir of host-adapted microorganisms that shape early-life gut microbiota and immune development. Our previous work identified Pediococcus acidilactici M22 from feline milk, which showed robust gastrointestinal tolerance, antioxidant capacity, and safety, providing the first evidence that feline milk-derived probiotics could be suitable for simulated pet milk formulations. However, P. acidilactici species possess limited genomic versatility and metabolic adaptability, warranting exploration of other lactic acid bacteria with broader functional repertoires. MNN exhibited superior acid and bile tolerance (99.83% survival at pH 2.5 and 88% at 0.3% bile) compared with M22 (59.93 and 84.38%, respectively), indicating enhanced gastrointestinal resilience. It demonstrated notable antioxidant capacity (DPPH 52.64%, ABTS 55.59%, superoxide 63.17%) and increased serum SOD and GSH while reducing MDA in mice, reflecting a stronger antioxidative defense than M22, whose effects were primarily systemic. Genome sequencing revealed a 3.29 Mb chromosome-1.23 Mb larger than M22-harboring 3,091 coding sequences enriched in stress response (groEL, dnaK, trxA), antioxidant (katA, gshA), and antimicrobial (plnE, plnF) genes, as well as expanded membrane transport and carbohydrate metabolism pathways. Unlike M22, MNN also preserved gut microbial homeostasis in vivo, maintaining α/β diversity and subtly enriching beneficial genera (Oscillibacter, Adlercreutzia) without dysbiosis. Functional prediction confirmed stable carbohydrate and amino acid metabolism, with no enrichment of resistance or virulence genes. Compared with P. acidilactici M22, L. plantarum MNN exhibits higher genomic plasticity, stronger antioxidative capacity, and distinct ecological compatibility, marking a functional transition from "safety-verified probiotic" to "host-adapted microbiota-stabilizing probiotic." Integrating genomic, functional, and ecological analyses, this study identifies MNN as a next-generation probiotic candidate for enhancing intestinal homeostasis and antioxidant defense in companion animals.

Over the past 25 years, antimicrobial resistance (AMR) has become a significant global health threat and a major cause of mortality. Foodborne diseases caused by drug-resistant bacteria capable of forming biofilms present serious health risks, necessitating innovative solutions for infectious disease management. Cellulose nanoparticles (CNPs), biocompatible and biodegradable, have found applications in targeted drug delivery, regenerative medicine, and tissue engineering. This study focuses on the synthesis and characterization of curcumin-loaded cellulose nanoparticles (CLCN) and their effects on quorum sensing (QS) and biofilm formation in both Gram-negative and Gram-positive foodborne bacteria (Escherichia coli, Pseudomonas aeruginosa, Serratia marcescens, Chromobacterium violaceum, and Listeria monocytogenes). FTIR confirmed molecular interactions between cellulose hydroxyl groups and curcumin. Thermal analysis (TGA/DSC) demonstrated enhanced structural stability with a gradual mass loss profile. Further, elemental composition analysis showed presence of carbon (50.6%) and oxygen (49.4%) in CLCN. CLCN exhibited MICs of 2 mg/mL against all test strains except in L. monocytogenes (8 mg/mL). At highest tested sub-MIC, violacein pigment was inhibited by over 58% in C. violaceum 12,472. CLCN disrupted pyocyanin, pyoverdin, LasB elastase, and rhamnolipid production by 53, 44, 39, and 47%, respectively. Exoprotease activity in test pathogens decreased by up to 58%. Biofilm production in all pathogens was significantly inhibited in the range of 48-68% at 0.5xMICs. Also, CLCN effectively removed preformed biofilms up to 46%. This study demonstrates that CLCN disrupt QS-regulated virulence traits and destabilizing biofilm architecture. By targeting virulence rather than growth, CLCN minimize the likelihood of resistance development and may serve as an adjunct or alternative to conventional antibiotic therapy. Thus, CLCN offer a biocompatible and sustainable antimicrobial strategy for food packaging systems, that limits surface-associated contamination and enhance food safety.

Saprolegniasis, predominantly caused by Saprolegnia spp., particularly Saprolegnia parasitica, has reemerged as a major threat in aquaculture, resulting in substantial economic losses of millions of dollars annually. Historically, malachite green was highly effective against this disease; however, its use was banned in aquaculture due to its carcinogenic nature. Consequently, there is an urgent need for novel and effective agents to mitigate economic losses. Several studies, including a subtractive-proteomics study from our laboratory, have identified multiple anti-saprolegnia compounds; however, their efficacy remains to be confirmed in vivo. Targeting mitochondrial energy production in Saprolegnia offers a potential strategy to combat this pathogen. Notably, cytochrome P450 is unique to Saprolegnia species and was previously shown to be inhibited by malachite green. In this study, we performed a virtual screening of FDA-approved drugs to identify compounds that target P450 and thereby disrupt energy production. To ensure robust ranking of potential inhibitors, we integrated multiple docking tools and applied consensus scoring. Based on ranking and water solubility, selected compounds were subjected to in vitro testing. Among these, chlorhexidine and diminazene exhibited strong anti-saprolegnia activity in liquid culture, with MIC₅₀ values of 10.93 and 417 μg/ml, respectively. Although chlorhexidine was less potent than malachite green, it demonstrated substantial inhibitory activity at low microgram per milliliter concentrations, highlighting its potential as a promising candidate for further development in aquaculture.

Introduction: Polycystic ovary syndrome (PCOS) is marked by disruptions in metabolic and reproductive endocrine functions. This study synthesizes systemic metabolic profiles, alterations in gut microbiota, and follicular fluid metabolism to elucidate the reproductive and endocrine metabolic changes associated with PCOS. Furthermore, it aims to elucidate the potential mechanisms through which acupuncture may exert therapeutic effects.

Methods: In this open-label randomized controlled trial conducted in China (November 2021-January 2023), 60 women with PCOS scheduled for In Vitro Fertilization (IVF) were randomized to receive acupuncture combined with IVF treatment or IVF treatment alone, with 30 healthy women serving as controls. Gut microbiota was sequenced and analyzed by 16S rRNA and metagenomics; follicular fluid metabolites were determined by untargeted metabolomics.

Results: Compared with healthy controls, PCOS exhibited gut microbiota dysbiosis and metabolic disorders. The specific gut microbiota in PCOS dominated by s_Lachnospiraceae, s_Blautia_sp. and g_Escherichia-Shigella, which correlated with body mass index (BMI), waist circumference, waist-to-hip ratio, and hormone levels. Acupuncture combined with IVF significantly regulated glucose and lipid metabolism, reduced g_Escherichia-Shigell abundance, and showed potential advantages in enhancing oocyte quality and embryonic developmental potential (p = 0.011). Analysis of the correlation between differential metabolites and oocyte and embryo quality demonstrated that methionine sulfoxide and boldione may be key metabolites to affect follicle quality.

Conclusion: PCOS is associated with systemic multi-pathway metabolic dysregulation and gut microbiota dysbiosis. It described the potential therapeutic benefits of acupuncture combined with IVF for PCOS, laying a foundation for further understanding the disease and the mechanisms of acupuncture for PCOS metabolic disorders, and providing directions for future research.

The emergence of drug-resistant bacterial infections has profoundly impacted global public health. Key pathogens include multidrug-resistant Pseudomonas aeruginosa (MDR-PA), MDR Acinetobacter baumannii, and methicillin-resistant Staphylococcus aureus. Among these pathogens, MDR-PA carries numerous virulence factors that induce extensive tissue destruction. Its inherent ability to form biofilms promotes chronic infection persistence and multidrug resistance, leading to mortality rates up to 40%. Currently, antibiotics remain the mainstay for the treatment of MDR-PA infections. Nevertheless, the escalating prevalence of drug resistance has rendered conventional antibiotic regimens increasingly recalcitrant. Consequently, the imperative for innovative antimicrobial therapeutic modalities to combat Pseudomonas aeruginosa has intensified in the realm of public health. In this context, phage therapy, with its precise bactericidal activity and high host biosafety, has emerged as a compelling alternative. This review provides a comprehensive synthesis of recent advancements in phage therapy targeting MDR-PA, covering clinical applications, current therapeutic approaches, and emerging technological platforms. It further dissects the resistance mechanisms encountered during treatment and puts forward novel counterstrategies to address antimicrobial resistance challenges-including optimized phage-antibiotic synergy, phage genome engineering, and dynamic adaptive therapeutic frameworks-aimed at advancing clinical translation.

Low primary productivity in Barents Sea surface waters and limited nutrient flux to the seafloor favor nitrification and nitrogen fixation in deep waters, resulting in a dearth of organic substrates in local sediments. The addition of labile hydrocarbons naturally occurring through seepage from subsurface reservoirs could promote microbial activity in organic-lean sediments, notably by denitrifying and sulfate-reducing microbes. Using gravity cores from an area with numerous hydrocarbon reservoirs, we document pore water geochemistry, dissolved gas concentrations, and total cell counts supplemented with taxonomic and functional marker gene analyses from metagenomes and metagenome-assembled genomes. We assess the contribution of the subsurface biosphere in producing geochemical gradients in oligotrophic sediments facing different exposure to minor seepage. In pristine seabed, i.e., not affected by hydrocarbon seepage, nitrate and ammonium profiles were consistent with denitrification down to 1 m below seafloor. By contrast, minor hydrocarbon seepage caused very different pore water profiles, which were indicative of more reducing geochemical conditions in the sediment and more advanced consumption of electron acceptors in pore water. Delivery of favorable organic substrates to anaerobic microbes through seepage was reflected in slightly higher cell densities, CH₄ and CO₂ concentrations, but appeared to have little impact on community diversity. This could be explained by metabolic versatility across functional guilds, with limited differentiation of sedimentary niches, favoring polyvalent fermenters at the expense of canonical denitrifiers and sulfate reducers. These versatile fermenters exhibited diverse predicted capabilities for nitrate and sulfate reduction combined with hydrocarbon degradation, (homo)acetogenesis, and nitrogen fixation. Our results further indicate that specific clades of homoacetogens (Lokiarchaeia, Bathyarchaeia, and Dehalococcoidia) could support cross-feeding interactions when fueled by simple hydrocarbons through seepage, particularly those associated with dissimilatory sulfur metabolism and fermentation of intermediate metabolites. In the absence of hydrocarbon-derived electron donors, the same clades appear capable of energy-conserving (homo)acetogenic fermentation on organic residues. Thus, we conclude that slow-growing (homo)acetogens that are ubiquitous in the marine subseafloor actively contribute to balancing biogeochemical cycles in oligotrophic sediments impacted by minor hydrocarbon seepage.

The European spruce bark beetle, Ips typographus, primarily colonizes Norway spruce and plays a pivotal ecological and economic role across Eurasia. Over decades, numerous studies have identified fungal species associated with I. typographus to comprehend their composition and relationships with the beetle and its tree host. The literature reveals a complex, diverse, and dynamic fungal community posing challenges in identifying consistent patterns. To enhance our understanding of the relationships in this tri-trophic system, a comprehensive overview of fungal associates is required. In this meta-analysis, we summarize the fungal species that have been found in association with I. typographus. Across 58 studies conducted over the last 80 years, 712 fungal species have been documented. Among these, 14 phytopathogenic species have been consistently recorded throughout the beetle's distribution range in Europe and Asia, therefore considered being part of its core mycobiome. A further 150 species were documented in only one part of the beetles' distribution range, and were classified as potential members of the core mycobiome. A significant proportion of the fungal assemblages were identified as passively associated species, constituting 77% of the total. We emphasize and engage in a critical discussion of the biases reflected in this data set, specifically those arising from the scientific methods employed and the sampled geographic areas. The majority of studies incorporated within this meta-analysis (n = 52) are based on conventional fungal culturing techniques with few recent publications (n = 6) incorporating modern molecular methods. At this point, the data suggest that the integration and complementary use of both methods may provide a more comprehensive representation of the mycobiome. Most studies have focused on Central and Northern Europe, with only six in Asia, leading to a significant data imbalance across the beetle's range. Hence, the data here provide a snapshot of current research, with expectations for further development with future studies. This identified diverse array of fungi within the beetle's mycobiome underscores the dynamic interactions between host trees, bark beetles, and their associated fungal community, highlighting their crucial roles in the beetle's ecological success and illustrating its deep integration into a complex fungal ecosystem.

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.