Frontiers in Microbiology最新文献

Objective: This study systematically evaluates the current situation, knowledge structure and development trend of bacteriophage-mediated intestinal microbiota regulation research from 2005 to 2024 through literature measurement analysis.

Method: Retrieve relevant research from the Web of Science core collection, Scopus and PubMed databases. After screening according to inclusion criteria, CiteSpace, VOSviewer, and R-bibliometrix were employed for bibliometric and visualization analysis. This systematically mapped publication trends, collaboration networks among countries/institutions/authors, core journals, and research hotspots.

Results: Thousands of relevant studies were included. From 2005 to 2024, the number of papers published in microbiology journals showed a step-by-step increase, reaching a peak of 355 articles in 2022. The United States and China are the main contributors. University College Cork in Ireland and San Diego State University in the United States have become core research institutions, and Colin Hill is listed as the most influential author. The Frontiers in Microbiology has published the largest number of papers, and Microbiome and Nature Communications have become platforms for the publication of high-impact research results. The research focus has shifted from the description of early bacteriophage-bacterial binary interaction to exploring the ternary relationship of "bacteriophage-microbiota-host health." In recent years, short-chain fatty acids, microbiota disorders and clinical intervention have become the core research directions. This study included 16 clinical trials on phage-mediated gut microbiota regulation, 14 of which were based on moderate to high-quality clinical evidence, indicating that research design in this field has advanced from the initial observational stage to the intervention verification stage.

Conclusion: This research systematically sorts out the research progress of 20 years in the field of bacteriophage-mediated intestinal microbiota regulation through the method of literature metrology. The research clearly outlines the evolutionary trajectory of this field from basic description to mechanism exploration to clinical transformation. Future research should focus on the following directions: clarifying the molecular mechanism of the interaction of core diseases, establishing a standardized research framework, and carrying out large-scale multi-center clinical trials to promote the transformation of this field from basic research to clinical application.

Objective: To investigate the distribution and antimicrobial resistance profiles of pathogens causing bloodstream infections (BSIs) in a maternal and child health hospital, providing evidence for rational clinical therapy.

Methods: A retrospective analysis was conducted on 395 bacterial isolates recovered from positive blood cultures of inpatients at Longgang District Maternity & Child Healthcare Hospital of Shenzhen City between January 1, 2021 and October 31, 2025. Duplicate isolates from the same patient were excluded.

Results: Among all isolates, Gram-positive bacteria accounted for 60.5% and Gram-negative bacteria for 39.5%. Coagulase-negative staphylococci (40.3%) were the most frequently detected, although many were likely contaminants. The major clinically relevant pathogens were Escherichia coli (28.6%), Streptococcus agalactiae (3.3%), Klebsiella pneumoniae subsp. pneumoniae (2.8%), and Staphylococcus aureus (2.3%). Escherichia coli showed a 44.3% Extended-Spectrum β-Lactamase (ESBL)-positive rate and elevated resistance to third-generation cephalosporins, with one carbapenem-resistant Enterobacteriaceae (CRE) isolate identified. Klebsiella pneumoniae exhibited overall low resistance levels. Among Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA) accounted for 22.2%, all susceptible to vancomycin, linezolid, and tigecycline. Streptococcus agalactiae retained excellent β-lactam and glycopeptide susceptibility, whereas Streptococcus pneumoniae exhibited pronounced macrolide resistance.

Conclusion: Escherichia coli and Staphylococcus aureus were the leading pathogens. The high ESBL rate in Escherichia coli and the detection of a CRE isolate indicate emerging β-lactam resistance risks. Although MRSA was detected, complete susceptibility to glycopeptides was preserved, highlighting the importance of ongoing monitoring.

Cyanophages represent important models for understanding virus-host interactions, yet high-resolution structural, functional, and dynamical studies remain relatively few due to challenges with preparing enough sample of sufficient quality for cryo-electron microscopy (cryo-EM) and multi-omics studies. Here we developed an integrated methodology for scaling production of the model cyanophage P-SSP7 from laboratory maintenance volumes (5-100 mL) to production scales (up to 40 L) while dramatically improving the quality of phage preparation for structural applications. Our systematic approach integrates host cultivation using adaptation to local seawater to reduce production costs, optimized infection protocols to maximize infectious titer yields, and multi-stage purification workflows specifically designed for cryo-EM quality requirements. The final methodology consistently produces infectious phage titers exceeding 3 × 10¹² units/mL with recoverable yields of 10¹³ total infectious units and >95% purity validated by cryo-EM at each optimization step. Most significantly, this approach achieves a 60-fold reduction in cryo-EM data collection time between the initial and final optimization steps by increasing usable particles per field of view for single particle analysis. Overall, our final preparations demonstrate robust phage stability, retaining 68% infectivity after 3 months and 23% after 6 months at 4 °C. This workflow moves cyanophage culturing and downstream structural studies from specialized, resource-intensive endeavors toward routine research capability and establishes an adaptable framework for scaling production that can be applied to other host-virus systems.

Introduction: This study investigated the synergistic effects of combining ferulic acid esterase (FAE)-producing lactobacillus with homofermentative and heterofermentative lactic acid bacteria (LAB) on the fermentation quality, nutrient composition, and aerobic stability of corn stover silage.

Methods: In this study, five LAB strains were isolated and identified from various silages. Among them, strain AR1 was identified as Lactiplantibacillus pentosus and exhibited high FAE activity. The homofermentative strains R10, JF1, and JF2 were identified as Lactiplantibacillus plantarum, Pediococcus acidilactici, and Pediococcus pentosaceus, respectively. The heterofermentative strain R3 was Leuconostoc mesenteroides subsp. mesenteroides. A total of 11 treatment groups were designed in triplicate, including a control group (CK), a commercial inoculant group (JCK), and nine LAB treatments at three concentrations (1 × 10⁶, 1 × 10⁷, 1 × 10⁸ CFU/g FW). The groups were AR1-only (R), a homofermentative-heterofermentative combination (LPL), and a homofermentative-heterofermentative combination with AR1 (LPLR).

Results: The results showed that the co-fermentation of homofermentative and heterofermentative strains improved silage fermentation quality. The addition of AR1 to the combination of homofermentative and heterofermentative LAB further enhanced lactic acid and acetic acid production, decreased neutral and acid detergent fiber contents, and improved aerobic stability. Principal component analysis and membership function analysis identified the LPLR group (an equal mixture of AR1, R10, JF2, and R3 at 1 × 10⁷ CFU/g fresh weight) as the optimal formula, achieving the highest comprehensive score of 0.696. Discussion: This study provides a theoretical basis for the development of silage additives.

Objectives: Carbapenem-resistant Klebsiella pneumoniae (CRKP) and Klebsiella oxytoca (CRKO) strains threaten neonatal health. This study investigates concurrent outbreaks in a Chinese neonatal intensive care unit (NICU).

Methods: We characterized 13 clinical isolates (10 CRKP [TJ01-TJ10] and 3 CRKO [TJ11-TJ13]) recovered from preterm infants between September 2013 and January 2014. The whole genome sequencing of strains (CRKP TJ03 and CRKO TJ11) was performed using MiSeq and MinION platforms, while the plasmids pNDM-TJ03 and pNDM-TJ11 were derived from the above-mentioned strains. Antimicrobial susceptibility testing, plasmid conjugal transfer, and other experiments were conducted.

Results: PFGE revealed clonal dissemination of CRKP ST30 and CRKO ST2 strains. This represents both the first documented neonatal outbreak caused by CRKP ST30 globally and the first report of CRKO ST2 in China, demonstrating novel transmission patterns of these high-risk clones in neonatal settings. All isolates carried bla _{NDM - 1}, bla _{OXA - 1}, bla _{DHA - 1}, qnrB4, and aac(6')-Ib-cr genes. Plasmid analysis identified both as IncH-type, showing high homology with pNDM-MAR. Their structure included contained a conserved IncH backbone region and separate accessory modules that contained five insertion sequences, transposon Tn6344, and a multidrug-resistant (MDR) region. The MDR region contained four mobile elements (ΔTn125, ΔInRBDHA, ΔTn1548, and ΔTn5393c) carrying a complement of 10 resistance genes. Conjugation experiments confirmed successful transfer of both plasmids to Escherichia coli J53Azi^R.

Conclusions: This study demonstrates that there may have been intra-strain and inter-species spread of a bla _{NDM - 1}-harboring IncH plasmid in the NICU. Our findings provide new insights into horizontal transfer of resistance genes mediated by IncH-type plasmids.

The MarR family of transcription factors in Mycobacterium tuberculosis plays a critical role in bacterial adaptation to host stresses, yet the function of many members remains unknown. Here, we characterize the novel MarR regulator Rv0737 and its homolog Ms_1492 in M. smegmatis. Overexpression of Rv0737 severely impaired bacterial growth, cell division, and biofilm formation, while increasing susceptibility to oxidative stress and the cell wall-targeting drug isoniazid. Conversely, deletion of ms_1492 altered cell envelope permeability and lipid composition, enhanced ATP synthesis, and conferred mild tolerance to H₂O₂ and isoniazid. Lipid profiling and transcriptomic analysis revealed significant dysregulation of lipid metabolism genes. Crucially, electrophoretic mobility shift assays demonstrated that both Rv0737 and Ms_1492 directly bind to the promoter region of the sigL-rslA operon, which encodes an alternative sigma factor and its anti-sigma factor. Our findings establish a direct regulatory pathway wherein Rv0737/Ms_1492 modulates bacterial growth, cell envelope integrity, and stress response by targeting the sigL-rslA operon, identifying this system as a potential therapeutic target for combating drug-resistant tuberculosis.

Utilizing beneficial plant growth-promoting rhizobacteria (PGPR) offers an effective approach for achieving sustainable crop production. However, research on the application and mechanisms of PGPR seed coating in potato (Solanum tuberosum L.) remains limited. Therefore, we conducted a two-year field experiment involving five seed-coating treatments: untreated (CK), chemical coating (CB), Bacillus velezensis coating (SM), and two composite formulations, CM1 (Bacillus subtilis + Paenibacillus mucilaginosus) and CM2 (Bacillus subtilis + Bacillus licheniformis). The results showed that PGPR markedly improved soil NO₃^--N and available P contents by stimulating carbon (C), nitrogen (N), and phosphorus (P) cycling enzymes. During potato flowering stages, soil NO₃^--N and available P increased by 16.29 and 17.29%, respectively. PGPR also increased plant height and stem diameter by 10.89 and 34.46% relative to CB, and elevated SPAD values and net photosynthetic rate (P_n ) at flowering by 20.22 and 32.22%, respectively. At maturity, potato aboveground, root, and tuber dry matter under PGPR increasing by 31.27, 44.21, and 41.88% compared with CB. Enhanced root biomass and nutrient acquisition promoted nutrient redistribution in potato, increasing N and P translocation to tubers by 17.13 and 50.48%, respectively. CM2 exhibited the highest tuber N and P accumulation, increasing by 66.74 and 55.25%, and achieved a 38.9% higher yield compared with the other treatments. Overall, PGPR enhanced soil nutrient availability, plant photosynthetic performance, nutrient acquisition, and nutrient translocation, thereby supporting greater biomass accumulation and promoting sustainable potato production. The PGPR seed coating represents an effective and scalable strategy for achieving resource-efficient and sustainable potato production.

Introduction: Shigella spp. are waterborne pathogens responsible for global diarrheal disease outbreaks via contaminated groundwater, drinking water, and recreational water systems. Their extremely low infectious dose necessitates the development of highly sensitive detection methods capable of distinguishing viable pathogens.

Methods: In this study, we developed and optimized a viability-discriminative droplet digital PCR (ddPCR) assay incorporating propidium monoazide (PMAxx) treatment and duplex amplification targeting both chromosomal and virulence plasmid genes. Key reaction parameters-including annealing temperature, primer and probe concentrations, and PMAxx treatment conditions-were systematically optimized. Singleplex and duplex assays were compared to verify amplification consistency. Additionally, three DNA concentration methods (direct centrifugation, PEG precipitation, and a commercial kit) were evaluated for their suitability in field applications using fecal-spiked water samples.

Results: The optimized PMAxx-ddPCR assay enabled simultaneous detection of viable S. flexneri and S. sonnei with excellent specificity. Duplex amplification showed amplification efficiencies comparable to those of singleplex assays across all targets. The method achieved a detection limit of ≤10 CFU/reaction in fecal-spiked water, and PMAxx treatment effectively suppressed signals from dead cells. Comparative evaluation of concentration methods identified effective protocols suitable for field deployment.

Conclusion: This PMAxx-ddPCR approach enables the simultaneous quantification of viable, virulent Shigella in water samples, offering a robust tool for advancing water safety monitoring and public health protection.

Introduction: Sugar beet is a crucial sugar crop, and its yield and quality are vulnerable to the adverse effects of continuous cropping. Plant growth-promoting rhizobacteria function as biological control agents and exhibit high potential for crop growth promotion.

Methods: In this study, soil subjected to continuous sugar beet cropping was selected as the experimental substrate to evaluate the effects of Sphingobium abikonense strain W2, Sphingomonas panni strain W9, Sphingomonas sp. strain W13, and their mixed bacterial suspension on sugar beet seedling growth and soil properties using pot experiments. High-throughput sequencing was used to characterize changes in the rhizosphere soil microbial community structure.

Results: The results indicated that Sphingomonads inoculation significantly improved the agronomic performance of sugar beet seedlings, as evidenced by increased plant height, stem diameter, aboveground and root fresh weight, and enhanced nitrogen and phosphorus uptake. In addition, inoculation increased soil pH, available potassium content, and sucrase activity. Microbial community analysis revealed that all inoculation treatments markedly altered the diversity and composition of the rhizosphere microbiome. Compared with the continuous cropping control, the inoculated soils exhibited a significantly higher abundance of Pseudomonadota, exceeding that observed under crop rotation. Moreover, beneficial genera (e.g., Pseudomonas, Cupriavidus, Massilia, and Novosphingobium) were enriched. Functional prediction demonstrated a significant enhancement of key metabolic processes, including ureolysis and xylanolysis.

Conclusion: Overall, Sphingomonad inoculation effectively regulated the structure and function of the rhizosphere microbial community, improved soil enzyme activity and nutrient availability, and promoted sugar beet seedling growth. This study provides a theoretical foundation and potential biocontrol strategy for mitigating continuous cropping obstacles in sugar beet cultivation.

Hydrocarbon contamination, particularly with polycyclic aromatic hydrocarbons (PAHs), poses a significant environmental challenge due to its persistence and carcinogenic effects on ecosystems and human health globally. This review explores how ML algorithms can enhance the efficiency of bio-augmentation and phytoremediation through predictive modeling, real-time optimization of microbial consortia, and plant species selection. Traditional bioremediation methods, such as bioaugmentation and phytoremediation, are characterized by slow degradation rates and sub-optimal performance in complex, multi-contaminant environmental milieus. The use of machine learning (ML) models with multi-omics data presents an advanced predictive approach to optimizing bioremediation processes by providing a systematic understanding of microbial and plant-mediated hydrocarbon degradation strategies and processes. ML models can predict which microbial strains or plant species will effectively degrade hydrocarbons under specific environmental conditions by utilizing supervised learning methods such as support vector machines and neural networks. Additionally, the combination of multi-omics data with ML facilitates the identification of critical genes, enzymes, and metabolic pathways involved in the degradation of hydrocarbons, and offers insights into the molecular mechanisms which drive the bioremediation process. The translation of laboratory-based ML models into large-scale, real-world bioremediation strategy is hindered by the complex, dynamic nature of our contaminated environments. This review paper showcases these hinderances and provides a direction for future research, including the development of field-deployable technologies, adaptive ML models, and real-time environmental monitoring strategies. The integration of ML with multi-omics holds substantial promise for enhanced efficiency, adaptability, and scalability of bioremediation strategies which ultimately mitigates carcinogenic risks often associated with hydrocarbon-polluted lithosphere.