Frontiers in Microbiology最新文献

Soil fauna play a critical role in the restoration of abandoned mining areas, uniquely contributing to soil formation, development, and the rehabilitation of degraded soils. This role is intricately linked with miwcrobial activity. Previous research has mainly concentrated on the direct effects of soil fauna on the physicochemical properties of soils in abandoned sites, often overlooking their indirect impacts on soil ecological functions via changes in soil microbial communities. This study undertakes a microcosm experiment by introducing soil fauna into the soil from coal mining abandoned lands to explore shifts in microbial communities. Results demonstrate that collembolan treatments significantly reduce fungi abundance, whereas earthworm treatments notably decrease the Shannon and Chao1 index for both bacterial and fungi communities. Soil fauna treatments modify the structure and composition of microbial communities, with more distinct differences in fungi community structures. Additionally, various soil fauna treatments markedly change microbial interactions; earthworm treatments impact microbial communities more than collembolan treatments, and combined treatments (EC) are more effective in enhancing microbial community stability compared to individual treatments (C, E). Network analysis has identified key microbial taxa that are positively correlated with soil fauna abundance, suggesting that future management strategies could manipulate key microbial taxa through soil fauna to enhance the restoration of soil ecological functions. These findings offer a detailed understanding of the dynamics of microbial communities under biotic interactions, essential for the ecological restoration of soils in abandoned mining areas.

[This corrects the article DOI: 10.3389/fmicb.2025.1735605.].

Introduction: Modules containing antibiotic resistance genes (ARGs) flanked by Xer site-specific recombination sites have been identified in Acinetobacter plasmids and are considered mobile genetic elements (MGEs) that facilitate horizontal gene transfer via the XerCD site-specific recombination (XerCD SSR) system. Although additional dif-like sites have been identified on the Acinetobacter chromosome beyond the main locus, it remains unclear whether these sites are associated with chromosomal dif modules.

Methods: MacConkey agar plates supplemented with meropenem were used to isolate the resistant strain. Whole-genome sequencing (WGS) was performed on the Oxford Nanopore platform, and the bacterial species was identified using Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH). Antimicrobial susceptibility testing was performed against 18 antibiotics. Identification of dif and pdif sites was performed using BLAST tools.

Results: This study identified numerous Xer modules containing resistance genes, IS elements, and other functional genes within the chromosome and plasmid of strain M10 (Acinetobacter sp.) isolated from a farmer at a cattle farm in Guangxi, China. Genome analysis and antimicrobial susceptibility testing confirm the association between these modules carrying resistance genes and resistant phenotypes. Chromosomal dif sites and associated dif modules in the strain were highly similar (sequence identity >99%) to plasmid-carried pdif sites and associated pdif modules in the public database. These suggest that additional chromosomal dif-like sites facilitate dif module formation, and that gene flow occurs between the chromosomes and plasmids of Acinetobacter. Furthermore, most Xer sites clustered to form a linear multi-module array, termed chromosomal dif module island and plasmid-borne pdif module island. Similar configurations were frequently observed in public Acinetobacter plasmid genomes.

Discussion: Additional dif-like sites are present in Acinetobacter chromosomes, which are unlikely to play a function in chromosomal dimer resolution, and the modules they form are functionally similar to pdif modules, both of which play an important role in horizontal gene transfer.

Introduction: This study investigated whether probiotics alleviate Endometriosis (EMs)-related inflammation by modulating the gut microbiota and short-chain fatty acids (SCFAs).

Methods: An endometriosis model was established in SD rats, which were randomly divided into a normal diet group (NCD) and a probiotic group (NCD_Pro), with four rats per group. After a 4-week dietary intervention, serum and fecal samples were collected. Tumor Necrosis Factor (TNF)-α and Interleukin (IL)-6 levels were measured by ELISA, gut microbiota composition was analyzed via 16S rRNA sequencing, and fecal levels of nine SCFAs were quantified using GC-MS.

Results: Probiotic supplementation significantly reduced serum levels of TNF-α and IL-6 (P < 0.05), but did not significantly affect body weight, body length, or lesion volume. Beta diversity analysis revealed significant structural differences in gut microbiota between the two groups (P < 0.05), while alpha diversity showed no significant difference. At the phylum level, probiotic intervention decreased the relative abundance of Firmicutes and increased that of Bacteroidota and Proteobacteria. At the family level, certain bacterial families showed opposite abundance patterns between the two groups. At the genus level, Bifidobacterium and Lactobacillus were significantly enriched in the probiotic group. Microbial co-occurrence network analysis indicated increased node number and connectivity along with enhanced network stability in the probiotic group. SCFA profiling showed decreased levels of butyric acid (BA) and caproic acid (CA), and a significant increase in isocaproic acid (4-MVA) in the probiotic group. Correlation analysis revealed a significant negative association between specific differential microbiota and 4-MVA (r < -0.6, P < 0.01).

Conclusion: Probiotic intervention alleviates systemic inflammation in endometriosis by reshaping the gut microbiota structure, enhancing microbial network stability, and modulating the SCFA metabolism. Our findings underscore the role of the gut microbiota-metabolism-immunity axis in EMs pathophysiology and point to 4-MVA as a hypothesis-generating candidate metabolite that requires further validation.

There is a need for dual action anti-virulence and anti-biofilm agents that target the opportunistic pathogen Staphylococcus aureus. Previous research determined that 0.8 mg/mL 4-ethoxybenzoic acid (4EB) reduced S. aureus ATCC 6538 biofilm formation by 88% relative to untreated controls with moderate inhibition of planktonic cell growth. Here we report that 4EB impacted S. aureus virulence phenotypes across all growth phases, including alpha-hemolysin (Hla) and serine protease (SplB/C) exoprotein production (60% reduction), staphyloxanthin pigment accumulation (73% reduction) and alpha-hemolysis (>87% reduction) compared to untreated control cells. RT-qPCR analysis demonstrated that 4EB downregulated virulence gene expression, including >100-fold reduction of alpha-hemolysin (hla) and leukocidins (lukDvEv), and a 35-fold decrease of the response regulator SaeR. Phenol-soluble modulin (PSM) transcription by biofilm-grown cells was upregulated by 4EB more than 4-fold for α1-4psm and β1-2psm genes, while δ-toxin (hld) was unaffected. In silico molecular docking analysis revealed that 4EB has a strong binding affinity (ΔG < -6.0 kcal/mol) for 9 virulence-associated transcriptional regulators, including SaeS, IcaR and CodY. Analysis of gene transcription during late exponential phase growth determined that genes controlled by 7 of the 9 identified regulators were significantly impacted by 4EB. The docking analysis identified putative 4EB binding sites that share common features including valine and tyrosine amino acid residues. The combined in vitro and in silico analyses identified interactions with well-known virulence genes but also implicated an effect of 4EB on proteins less commonly associated with S. aureus pathogenesis. These findings suggested potential alternative targets for anti-virulence and anti-biofilm therapeutics.

Introduction: This study aimed to evaluate the effects of equine-derived Lactobacillus M11 on reproductive performance and metabolic profiles in pregnant Kunming (KM) mice. The objective was to explore the potential of M11 as a safe and effective alternative to antibiotics in antibiotic-free farming systems.

Methods: Specific pathogen-free (SPF) female KM mice were randomly assigned to a blank control group (BC) and three intervention groups (M11-L, M11-M, M11-H). The intervention groups received daily gavage of M11 at low (1.0 × 10⁷ CFU/mL), medium (1.0 × 10⁸ CFU/mL), and high (1.0 × 10⁹ CFU/mL) concentrations for 21 days. Host physiological parameters, metagenomic profiles, and metabolomic signatures were analyzed to assess the impact of M11 supplementation.

Results: (1) Host Physiology and Biochemistry: The M11-H group exhibited a significant elevation in albumin (ALB; 40.30 ± 1.75 g/L), suggesting enhanced nutritional status or hepatic protein synthesis. The M11-L group showed transient increases in alanine aminotransferase (ALT; 59.57 ± 10.34 U/L) and total cholesterol (TC; 2.90 ± 0.24 mmol/L), indicative of adaptive hepatic lipid metabolism. (2) Microbial Community Reconfiguration: Metagenomic analysis revealed significant structural shifts in the gut microbiota between the BC and M11-H groups. Notably, the M11-H group showed enrichment of Bacillota, which correlated with "O-antigen nucleotide sugar biosynthesis," while differences in Pseudomonadota were associated with immune regulation. (3) Metabolomic Profiling: Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated clear separation in the cecal metabolome space. KEGG pathway enrichment analysis highlighted significant alterations in "glycine/serine/threonine metabolism" and "arginine/proline metabolism" pathways. (4) Integrated Multi-Omics Analysis: Correlation analysis identified a significant positive association between s_Clostridiaceae_bacterium (Bacillota) and specific metabolites (3-hydroxy-4-aminopyridine sulfate), suggesting the formation of a regulatory "gut-reproductive axis."

Discussion: The results demonstrate that Lactobacillus M11 improves metabolic support during pregnancy through three primary mechanisms: modulation of the gut microbiota, activation of key metabolic pathways, and enhancement of antioxidant capacity. These findings provide a theoretical basis for the application of probiotic-mediated reproductive support in antibiotic-free farming, highlighting M11 as a promising candidate for improving livestock health and productivity.

Introduction: Predatory bacteria of the Bdellovibrio and like organisms (BALOs) have long been postulated as living antimicrobials, yet their occurrence and ecological roles within human-associated microbiota have remained uncertain due to the absence of culturable human-derived isolates. Here, we report the first successful isolation and comprehensive characterization of viable Bdellovibrio bacteriovorus from human fecal samples.

Methods: Targeted enrichment was applied to five pooled fecal samples to facilitate predator recovery. We performed whole-genome sequencing on the isolates and conducted comparative genomics across 162 publicly available Bdellovibrio genomes. Additionally, pangenome analysis of 22 high-quality genomes and phenotypic assays against clinical pathogens were conducted to assess genomic diversity, prey specificity, and biosafety profiles.

Results: Despite extremely low natural abundance, targeted enrichment recovered predators in two of five pooled samples, which produced characteristic lytic plaques. Sequencing revealed >99% average nucleotide identity to reference strain HD100 with only 26 core single-nucleotide polymorphisms across both isolates, indicating minimal divergence between human-associated and environmental lineages. Comparative genomics showed that only 10.4% of public genomes fulfill criteria for B. bacteriovorus sensu stricto. Pangenome analysis revealed a stable, highly conserved core (~2,500-2,650 genes) and an expanding accessory genome. Phenotypically, the human-derived isolates displayed narrower prey ranges concentrated on Pseudomonas spp., including multidrug-resistant clinical strains, and no acquired virulence factors were detected.

Discussion: Collectively, these findings suggest predation in the human gut and that viable Bdellovibrio could be natural, genomically conserved members of the intestinal ecosystem. This work advances a testable keystone-predator framework for human microbiome ecology and opens an ecologically informed therapeutic pathway in which human-associated Bdellovibrio may help control multidrug-resistant pathogens while supporting microbiota homeostasis.

Traditional Chinese Medicine (TCM) interventions have attracted increasing attention in recent years, with a growing body of evidence supporting their efficacy in the treatment of Alzheimer's disease (AD). Zhinao Capsule (ZNJN), a proprietary TCM formulation, has demonstrated promising clinical outcomes, particularly in enhancing cognitive function and alleviating AD-related pathology in rodent models. This study aimed to evaluate the neuroprotective effects of ZNJN in APP/PS1 transgenic mice. Behavioral assessments indicated that ZNJN, especially at the high dose, significantly improved learning and memory abilities. Histopathological analysis revealed a marked reduction in hippocampal Aβ_1-42 deposition and decreased activation of microglia and astrocytes, as evidenced by lower expression levels of Iba-1 and GFAP. In addition to central effects, ZNJN alleviated colonic inflammation and improved mucosal integrity. Systemic inflammatory responses were also suppressed, with significant reductions in serum levels of TNF-α, IL-6, IL-1β, and LPS. Furthermore, 16S rRNA gene sequencing showed that ZNJN modulated the gut microbiota by decreasing the abundance of pro-inflammatory genera and enriching potentially beneficial. These findings suggest that ZNJN exerts neuroprotective effects by modulating the gut microbiota and reducing neuroinflammation through the gut-brain axis. These findings suggest that ZNJN exerts neuroprotective effects by modulating the gut microbiota and reducing neuroinflammation through the gut-brain axis. This study provides experimental evidence supporting the potential of ZNJN as a multi-target therapeutic agent for AD intervention.

Introduction: Hypervirulent Klebsiella pneumoniae (hvKp) of the K1/ST23 lineage is an emerging global threat associated with invasive community-acquired infections. Increasing reports of virulence-resistance convergence highlight the need for genomic surveillance, particularly within Europe where data remain limited. This study characterizes clinical K1/ST23 KP isolates circulating in the Czech Republic and compares them to a global genomic background to evaluate virulence architecture, resistance acquisition and plasmid evolution.

Methods: From 2017 to 2025, 570 K. pneumoniae isolates from a tertiary-care hospital were screened for hvKp markers. Ninety-six K1/ST23 isolates were subjected to long-read whole-genome sequencing and plasmid reconstruction. Genomes were analyzed alongside 2,463 international ST23 datasets using core-SNV phylogenomics, virulence/resistance profiling, and structural plasmid mapping. Chromosomal integrations were examined through analysis of flanking insertion-sequence contexts.

Results: The Czech K1/ST23 KP population exhibited high virulence uniformity (95/96 isolates scoring 9/9) without evidence of a single-clone outbreak, instead forming multiple phylogenetic lineages consistent with recurrent introductions. Eighty-three isolates carried pLVPK-like virulence plasmids; however, structural plasticity was prominent. The iro cluster was relocated to conjugative IncFII/rep_cluster_1418 plasmids in two isolates-one carrying additional AMR genes-and was chromosomally integrated via IS1-mediated recombination in three others. Iut was chromosomally integrated via IS903 (IS5 family) with either classical target-site duplication or recombination-associated insertion. Nine virulence-resistance fusion plasmids (IncFIB-IncFII-IncHI1B or IncC-based) were identified, representing early convergence toward MDR-hvKp.

Conclusion: K1/ST23 KP circulating in the Czech Republic is highly virulent yet genomically diverse, driven by active plasmid exchange, insertion-sequence-mediated chromosomal integration, and emerging virulence-resistance fusion plasmids. Although carbapenemase genes were absent, ESBL determinants and transmissible virulence loci indicate strong evolutionary potential toward MDR-hvKp. Continuous genomic surveillance and early intervention strategies are essential to mitigate future clinical impact.