Frontiers in Microbiology最新文献

Background: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.

Methods: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.

Results: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.

Conclusion: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.

Objective: Serratia marcescens (S. marcescens) is an opportunistic pathogen increasingly associated with nosocomial infections in immunocompromised pediatric patients. This study aimed to investigate the epidemiological and molecular epidemiological characteristics of S. marcescens-positive blood cultures and to provide evidence for targeted infection prevention strategies.

Methods: Eleven cases of S. marcescens-positive blood cultures were identified across eight pediatric wards of a tertiary hospital in China in October 2024. Clinical and microbiological assessments were conducted to distinguish true infections from contamination. Antimicrobial susceptibility testing was performed, and whole-genome sequencing (WGS) was used to characterize resistance, virulence, and plasmid replicons. Core genome single-nucleotide polymorphism (SNP)-based phylogenies, Bayesian temporal inference, and transmission tree reconstruction were used to explore genetic relatedness, transmission dynamics, and cryptic cases.

Results: Two cases were diagnosed as hospital-acquired sepsis, while nine were classified as contamination. The isolates exhibited intrinsic resistance to first- and second-generation cephalosporins but remained susceptible to carbapenems. Seven resistance genes-including aac(6')-Ic, oqxB, and tet(41)-and four virulence genes, including cheY and fliM, were identified. Nine isolates carried IncFII-type plasmids. Core genome SNP analysis revealed minimal genetic divergence, with the most recent common ancestor traceable to late 2023, suggesting approximately 10 months of silent transmission. Transmission tree inference further indicated the presence of undetected cryptic cases. Following the implementation of bundled interventions-including sink replacements and disinfectant use, reinforcement of hand hygiene, and environmental decontamination-no new cases occurred during 1 month of follow-up.

Conclusion: This study identified a highly clonal S. marcescens cluster with evidence of prolonged, unnoticed circulation and cross-ward transmission in the pediatric units. These findings underscore the hidden persistence of this pathogen in the hospital environment and the need for strengthened infection control measures.

Introduction: Soil salinization is a major constraint to agricultural productivity on Hainan Island, China, as it reduces soil fertility and disrupts microbial community structure. Nano-modified biochar has emerged as a promising strategy to improve soil quality and microbial resilience under saline conditions. This study evaluated the effects of iron- and zinc-modified nano-biochar on soil physicochemical properties and microbial communities in saline and non-saline paddy soils.

Methods: A pot experiment was conducted using four treatments: control (CK), pristine biochar (BC), iron-modified biochar (FeBC), and zinc-modified biochar (ZnBC). Soil physicochemical properties, enzyme activities, microbial biomass, and bacterial and fungal community composition were analyzed using standard chemical assays and high-throughput sequencing techniques.

Results: Application of nano-modified biochar significantly increased soil organic matter, soil organic carbon, and the availability of macronutrients (N, P, and K). FeBC and ZnBC enhanced microbial biomass carbon and nitrogen as well as urease and β-glycosidase activities in saline soil. Nano-biochar treatments altered microbial community composition, increasing the abundance of salt-tolerant bacterial phyla such as Proteobacteria, Chloroflexi, and Bacteroidota under saline conditions, while modifying fungal community structure, including increased relative abundance of Chytridiomycota under FeBC treatment.

Objective: The aim is to address the limitations of clinical surveillance-specifically, its high cost and underreporting of asymptomatic infections and untreated individuals-by implementing municipal wastewater surveillance. This study characterizes the epidemiological dynamics of Norovirus (NoV) and Rotavirus A (RVA) in Yantai City and evaluates the effectiveness of Wastewater-Based Epidemiology (WBE) for early outbreak warning.

Methods: From 2023 to 2024, weekly wastewater samples (1-2 samples per site) were collected from 10 municipal wastewater treatment plants (WWTPs) across five urban districts and three counties in Yantai City. Following concentration via polyethylene glycol (PEG) precipitation, viral nucleic acids of NoV GI/GII and RVA were examined using multiplex reverse transcription quantitative PCR (RT-qPCR), with quantification based on standard curves. Cross-correlation analysis was applied to assess time-lag relationships between viral concentrations in wastewater and clinical case peaks, and to evaluate the statistical significance (α = 0.05) of the early warning time window.

Results: Wastewater surveillance (no. samples: 1,391) identified NoV GII as the dominant virus with an overall detection rate of 85.84%. However, from 2023 to 2024, its annual detection rate declined significantly from 92.27% to 73.81% (P < 0.001). During the same period, NoV GI also declined annually from 83.55% to 69.07% (P < 0.001), whereas RVA detection increased substantially by 145.7% annually, rising from 26.6% to 65.36% (P < 0.001). NoV peaked in winter-spring seasons (GI: 76.61% in winter, 89.20% in spring; GII: 87.13% in winter, 91.31% in spring), whereas RVA peaked in spring (42.72%) and summer (55.79%). Seasonal fluctuation intensity followed this order: RVA (χ² = 69.07) > NoV GI (χ² = 49.28) > NoV GII (χ² = 21.44). Cross-correlation analysis indicated that NoV GII concentration in wastewater peaked 1 month ahead of clinical cases, showing significant positive correlations with both reported cases (r = 0.60, P = 0.002) and clinical positivity rates (r = 0.53, P = 0.009) at a one-month lag. A one-month lag for NoV GI and a two-month lag for RVA relative to clinical cases were observed but were not statistically significant (P > 0.05).

Conclusion: Systematic wastewater surveillance effectively captured population-level epidemiological dynamics of NoV and RVA. Notably, NoV GII provided a significant one-month early warning signal (P < 0.01), establishing its value as a leading indicator for diarrheal virus prevention and control in Yantai City.

Bacterial persistence contributes to antibiotic failure and recurrent infectious disease, yet the metabolic cues that promote persister formation remain poorly understood. Here we investigated Escherichia coli persistence after nutrient downshifts from glucose to various carbons. Compared to shifts to gluconeogenic carbons (pyruvate, malate, succinate, and fumarate), the glucose-to-fatty acid shift induced exceptionally high persister levels, with cells tolerating ampicillin (56%), carbenicillin (22%), and gentamicin (1%) after 24-h treatment. With an RNA-based biosensor and HPLC quantification, we detected up to 4-fold higher guanosine tetra- and penta-phosphate [(p)ppGpp] during the prolonged carbon starvation period post glucose-to-fatty acid shift, whereas (p)ppGpp levels remained low after glucose-to-gluconeogenic carbon shifts due to the shorter lag phase. Shortening the lag phase by pre-exposing cells to fatty acid substantially reduced persistence after the glucose-to-fatty acid shift. Overexpression of acyl-ACP synthase, which acylates free acyl carrier protein and thereby suppresses SpoT-dependent (p)ppGpp synthesis, lowered (p)ppGpp levels and reduced persistence. Furthermore, overexpression of PlsB, a growth-essential enzyme in phospholipid biosynthesis that is inhibited by (p)ppGpp, also reduced persistence. In addition, ¹³C isotope tracing and metabolomic analysis revealed that persisters remain metabolically adaptive, rerouting measurable carbon flux into gluconeogenesis and the pentose phosphate pathway for biomass synthesis. The metabolic remodeling could assist cells to balance redox homeostasis and mitigate oxidative stress. These findings establish the role of (p)ppGpp in nutrient shift persister formation and highlights critical pathways that may be targeted to reduce persistence and improve treatment outcomes against recurrent infections.

Trichoderma harzianum is a well-known biocontrol agent with growing interest as a multifunctional bioinoculant due to its diverse metabolic capabilities. Despite its promising potential, the transition from laboratory-scale cultivation to industrial-scale production still presents challenges, particularly in optimizing biomass and spore yield at low cost. This study focused on testing a new medium for spore/mycelium production of T. harzianum integrating traditional growth media with gazpacho, a tomato-based by-product of Andalusian food as cheap substrate. We also assessed its multifunctional activity, including the tolerance to salt stress, solubilization of rock phosphate and the antagonistic activity against three major tomato pathogens (Botrytis cinerea, Fusarium oxysporum, and Pyrenochaeta lycopersici) through dual culture assays. The results showed that media supplemented with 3 and 6% (v/v) gazpacho significantly increased T. harzianum biomass and sporulation in solid and submerged state fermentations, while 10% reduced spore formation in liquid submerged fermentation. Interestingly, biomass and sporulation were further improved in media containing 3-6% (v/v) gazpacho combined with 100 mM NaCl. Trichoderma harzianum was able to grow and sporulate in solid media with up to 100 mM NaCl. Moreover, the strain showed phosphate solubilization activity on gazpacho-containing media in submerged fermentation, and effectively inhibited over 70% of pathogenic mycelial growth, with B. cinerea showing the highest inhibition (78.40%). Overall, these results highlight the improvement in biomass and spore production of T. harzianum grown in traditional growth media supplemented with 6% gazpacho, as well as its multifunctional activities under these fermentation conditions, thus representing a promising approach towards the production of cheap bioinoculants and supporting the circular economy in microbial technology. Furthermore, salt tolerance further encourage T. harzianum as a robust candidate for bioformulations in challenging agro-environment.

In view of the excessive grease content in kitchen wastewater and the limited oil removal efficiency of conventional treatment systems, this study isolated a highly efficient oil-degrading bacterium (strain Y1) from soil beneath a kitchen waste pipeline and investigated its degradation performance. Through morphological observation, biochemical tests, and 16S rRNA gene sequencing, strain Y1 was identified as Klebsiella pneumoniae. The growth characteristics and oil degradation performance revealed the optimal degradation conditions to be 35 °C, pH 7.0, and 180 r/min. Under these conditions, the oil degradation rate reached 48.7%. In a simulated treatment of actual kitchen oil-rich wastewater, strain Y1 achieved the chemical oxygen demand (COD) removal rate of 62% in 48 h (reaching 62.8% at 66 h) and an oil degradation rate of 60.7% in 96 h (slightly increasing to 60.9% at 108 h). These results highlight the potential of strain Y1 for practical application in the bioremediation of oily wastewater. This study provides a new microbial resource and technical reference for the biological treatment of kitchen grease wastewater.

Introduction: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking.

Methods: In this study, metagenomic, metaproteomic, and non-targeted GC-MS analyses of Zaopei, along with HS-SPME-GC-MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation.

Results: The Wuliangye-specific variety Dajiugu, with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis, Enterobacter, and Klebsiella. Functional genera such as Saccharopolyspora, Pediococcus, and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu.

Discussion: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.

Adjunct starter cultures are of interest in pasteurized cheese production as they provide additional flavor, ensure reproducible quality, and enable faster ripening. In the current study, two adjunct culture strains were selected, namely Lacticaseibacillus paracasei LP46, selected out of 49 isolates from mature Gouda cheese, and Tetragenococcus halophilus TH63, selected out of 244 isolates from a Gouda cheese brine. To date, the use of a Tetragenococcus strain in cheese production has not been reported. Both strains were applied in pilot-scale Gouda cheese productions, and the cheeses were investigated up to 32 weeks of ripening by a multiphasic approach encompassing culture-dependent and culture-independent microbiological analysis, meta-metabolomics, and organoleptic evaluations. In the case of the Lacc. paracasei strain, three batches with each time a different primary starter culture mixture were produced to investigate the effect of the primary starter culture mixture on the adjunct starter culture. The adjunct starter culture strains were able to become abundant in the cheeses. Furthermore, both adjunct starter culture strains seemed to repress the Leuconostoc strains from the primary starter culture mixtures. The Lacc. paracasei adjunct starter culture was associated with higher concentrations of acetoin and cadaverine, despite showing no biogenic amine production during the screening process. The T. halophilus adjunct starter culture increased the total amino acid concentration by 55% and also resulted in higher concentrations of acetoin and 2,3-butanedione. However, the organoleptic evaluation could not indicate a significant difference between the negative controls and the cheeses with adjunct starter cultures. Nevertheless, this first application of a Tetragenococcus strain in Gouda cheese showed that T. halophilus seems a promising cheese adjunct starter culture.

Introduction: Elizabethkingia anophelis (E. anophelis) has emerged as a multidrug-resistant pathogen with limited therapeutic options. This study aimed to characterize antimicrobial resistance mechanisms and virulence determinants in six clinical isolates from Shanghai, China, to inform evidence-based treatment strategies.

Methods: Six strains were isolated from hospitalized patients (five community-acquired, one healthcare-associated) between September-November 2023. Antimicrobial susceptibility testing followed CLSI M100 guidelines. Whole-genome sequencing employed hybrid Illumina/PacBio approaches. Phylogenetic relationships were determined through 16S rRNA gene sequence analysis using the Neighbor-Joining method. Antimicrobial resistance genes and virulence factors were annotated using the Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factor Database (VFDB), with relative gene abundance quantified via a TPM-like (transcripts per million-like) method.

Results: All isolates exhibited resistance to β-lactams, fluoroquinolones, carbapenems, and aminoglycosides, but retained minocycline susceptibility (MIC ≤1 μg/mL). Phylogenetic analysis revealed two distinct clusters: Cluster I (EA1, EA3, EA6) aligning with East/Southeast Asian isolates, and Cluster II (EA2, EA4, EA5) showing diverse geographic affinities. Five core resistance mechanisms were identified: antibiotic efflux, antibiotic target alteration, antibiotic inactivation, antibiotic target replacement, and reduced permeability to antibiotics. Virulence determinants included bacterial movement, exotoxin production, biofilm formation, immune regulation, and effector delivery systems. Strain EA5 exhibited unique signatures, including absence of cesH, unique sigE expression, elevated AAC(6')-Iad/aadS and reduced qacL/OmpA.

Conclusion: This study reveals phylogenetically divergent E. anophelis lineages in Shanghai with extensive multidrug resistance but preserved minocycline susceptibility. Findings support minocycline-based therapy, enhanced diagnostics, and regional surveillance networks for strain monitoring.