Streptococcus suis (S. suis) is an important zoonotic pathogen that often forms biofilm, leading to persistent clinical infections and exacerbation of antibiotic resistance. There is an urgent need to develop novel antibiofilm strategies. In this study, for the first time, lactate dehydrogenase (LDH) was targeted with the aim of reactivating the metabolic activity of bacteria embedded in biofilm using natural product molecules, thereby disrupting mature biofilm. Through virtual screening based on the TCMSP database, molecular docking, and molecular dynamics simulations, two potential molecules, ginkgolide B and daidzein were identified. The results showed that ginkgolide B significantly eradicated mature biofilm of S. suis at 160 µg/mL, whereas daidzein did not exhibit such an effect. Ginkgolide B treatment led to a marked accumulation of tricarboxylic acid (TCA) cycle intermediates (pyruvate, malate, fumarate, and isocitrate), a substantial downregulation of the pentose phosphate pathway product ribose-5-phosphate, and a global upregulation of NADH as well as various high energy phosphate compounds and amino acids. These findings suggest that ginkgolide B may interfere with TCA cycle, leading to reduced lactate fermentation, enhanced accumulation of TCA cycle-related metabolites, and broader metabolic changes in biofilm-associated S. suis. This metabolic disturbance may contribute to the disruption of mature biofilm. This study validates the feasibility of a 'metabolic activation' strategy in eradicating mature biofilm of S. suis and provides ginkgolide B as a candidate molecule for the development of novel antibiofilm agents.

Staphylococcus caprae, a coagulase-negative staphylococcus (CoNS), is an opportunistic microorganism increasingly identified in clinical specimens. However, its genomic and functional characterization in human infection have not yet been fully elucidated. In this study, we characterized the genomic and phenotypic diversity of two clinical S. caprae isolates, M89 and S13, to elucidate their opportunistic traits. Whole-genome sequencing was performed to evaluate genomic differences in antimicrobial resistance, virulence determinants, and protein-coding sequences, while their pathogenic potential was assessed using a murine subcutaneous catheter model. Our results revealed that both isolates harbored core resistance genes, such as mecA and blaZ; however, the healthcare-associated strain S13 displayed a broader antimicrobial resistance profile. Although virulence profiling identified conserved factors shared by both strains, including icaABCR, atl, and clfB, a key genomic differentiator was the presence of the accessory Sec (aSec) secretion system in M89, which was absent in S13. Functionally, M89 exhibited significantly greater adherence to endothelial cells and higher colonization efficiency in vivo. Furthermore, M89 infection induced epidermal thickening and elevated proinflammatory cytokine expression in mouse skin tissue. These findings demonstrate significant intra-species heterogeneity in S. caprae regarding host interaction capabilities and underscore the importance of integrating genomic and phenotypic analyses to delineate the pathogenic mechanisms of this emerging opportunistic pathogen.

We report a bloodstream Burkholderia arboris isolate from a 75-year-old man without cystic fibrosis. The organism was recovered from both aerobic bottles of two separately collected blood-culture sets and was initially assigned to the Burkholderia cepacia complex (Bcc) by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Whole-genome sequencing yielded three circular chromosomes and one circular plasmid. DFAST_QC identified B. arboris as the only type-strain match above the species threshold, with an average nucleotide identity of 99.48%; the next-highest match was B. seminalis at 93.33%. Multilocus sequence typing identified ST-2575, and ResFinder detected no acquired antimicrobial resistance genes. The patient improved after 14 days of meropenem therapy without recurrent B. arboris bacteremia. This report adds a clinically supported bloodstream infection, a complete genome resource, and detailed susceptibility data, while illustrating the importance of up-to-date reference genomes for species-level interpretation of unusual Bcc isolates.

The accumulation of potentially toxic metals (PTMs) poses a threat to the cellular integrity of soil microorganisms as well as ecological stability, driving the selection of resistant microorganisms with biotechnological potential. This study aimed to evaluate the behavior of the Rhizobium sp. LBMP-C04 isolate under PTM stress, focusing on adaptive resistance mechanisms and intracellular bioaccumulation. The bacterium, which was isolated from Arachis pintoi root nodules and had previously undergone genomic characterization, was subjected to antibiotic-resistance assays, growth-curve analysis in the presence of Cd[2+], Cu[2+], Cr[3+], Cr[6+], Zn[2+], and Ni[2+], metal-removal analyses, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and thermogravimetric analysis. The results revealed resistance to multiple antibiotics and differential tolerance to metals, with Cr[3+] notably allowing sustained bacterial growth. Correlation analyses indicated associations between population dynamics and metal-concentration changes, indicating active involvement in bioaccumulation processes. TEM images showed intracellular metal accumulation without severe structural damage, while FTIR analyses identified functional groups potentially involved in metal ion interactions. Thermogravimetric analysis confirmed changes in biomass composition associated with metal exposure. Overall, the findings demonstrate that the isolate shows efficient adaptive and intracellular sequestration mechanisms for PTMs, although removal efficiency from the medium was limited. Nevertheless, the plant growth-promoting traits and metal resistance of the isolate highlight its potential for application in phytoremediation strategies in contaminated environments.

Thymol, a monoterpenoid phenolic compound, exhibits broad-spectrum antibacterial activity and is gaining increasing attention as a natural alternative to synthetic agents. Thymol appears to demonstrate high antibacterial efficacy against Gram-negative and Gram-positive bacteria, particularly resistant pathogens, through disruption of bacterial cell membranes, protein and enzyme inhibition, influencing DNA synthesis, and triggering oxidative stress mechanisms. Given these reported mechanisms and its broad-spectrum activity, thymol has been the subject of increasing research interest in recent years. The aim of this review is to comprehensively evaluate the antibacterial effects of thymol based on studies published between 2020 and 2025, identified through major databases including PubMed, Scopus, and Web of Science. Based on current literature, thymol appears to have strong potential as an antibacterial agent in diverse fields such as dermatological products, veterinary treatments, oral health formulations, food preservative systems, and agricultural biopesticide applications. In recent years, various encapsulation and controlled-release strategies have been developed to overcome the limiting characteristics of thymol, such as low water solubility, volatility, and chemical instability, which restrict its direct use in clinical and industrial applications. Studies using thymol in combination with various carrier systems, nanoparticles, and phenolic extracts have shown that the bioavailability of the compound is increased and, in some cases, synergistic antimicrobial effects can be achieved. However, the data indicates that studies have not progressed beyond the in vitro and in vivo levels. This finding reveals the need for more detailed clinical data to support the research on such valuable molecules, which are essential in today's world where resistant pathogens are dramatically developing. Current research shows that thymol is a promising natural agent with antibacterial properties and potential applications. Despite the promising in vitro and in vivo evidence, thymol lacks clinical validation data and standardized formulation protocols. The primary bottleneck appears to be its pharmacokinetic profile, low oral bioavailability (~ 16%) and a short plasma half life (~ 1.5 h), which must be addressed before meaningful human trials can be designed.

Salinity imposes severe osmotic and ionic challenges that require coordinated adaptive responses in microorganisms. Although numerous studies have characterized salt-stress responses in individual Bacillus species, the extent to which these responses are conserved across phylogenetically distinct taxa remains poorly understood. Here, we performed an orthology-based comparative transcriptomic analysis of Bacillus velezensis and Bacillus paralicheniformis using publicly available RNA-seq datasets comparing low- and high-salinity conditions within each species. Publicly available RNA-seq datasets were analyzed using Salmon for transcript quantification and DESeq2 for differential expression analysis, followed by reciprocal best-hit orthology inference and functional annotation through KEGG Orthology assignments. Differential expression analysis identified 1,893 and 1,879 genes with significant expression changes (padj < 0.05, |log2FC|≥ 1) in B. velezensis and B. paralicheniformis, respectively. Reciprocal best-hit analysis recovered 2,963 orthologous gene pairs, of which 725 orthologous pairs met the differential-expression criteria in both species and were retained for comparative response classification. Among these, 234 orthologs were consistently upregulated and 230 were consistently downregulated under salt stress. Conserved induction was dominated by genes associated with compatible-solute metabolism, transport systems, and sodium homeostasis, with additional contributions from oxidative-stress-related functions. Notably, proline biosynthesis genes (proB and proC), glycine betaine-related genes (betB and gbsB), compatible-solute transporters (opuAA and opuAB), and the sodium/proton antiporter nhaC exhibited coordinated activation in both species. Conversely, conserved repression primarily affected biofilm-associated functions and extracellular matrix-related genes. Although KEGG Orthology enrichment analyses did not retain significance after false-discovery-rate correction, functional annotations consistently supported osmoadaptation-related processes as the dominant shared response. These results support the presence of conserved osmoadaptive transcriptional responses shared between Bacillus velezensis and Bacillus paralicheniformis and highlight orthology-guided comparative transcriptomics as an effective approach for identifying candidate conserved stress-response mechanisms.

A commensal organism has transformed into the leading multidrug resistant (MDR) hospital acquired pathogen, with serious implication on global public health. The ability of Enterococcus faecium to rapidly adapt through its great genomic plasticity, horizontal gene transfer and under selective pressures created by heavy antibiotic application both clinically and non-clinically is responsible for the phenomenon. Comparative genome studies have reported the presence of different community acquired and hospital acquired clades; hospital acquired clones being particularly the clonal complex 17 have enriched antibiotic resistant genes, mobile genetic elements, virulence factors. Therapeutic choices are now restricted, while mortality and morbidity increase due to lack of adequate drug targets, resistant to penicillin, vancomycin, linezolid and daptomycin. This review critically discuss the finding about the evolutionary history, diversity of genome, resistant mechanisms and global resistant trends of E. faecium's evolution into the hospital associated strain. The clinical and public health importance of MDR E. faecium is reviewed within the context of one health including the integrated roles of human, animal, and environment as reservoirs. Lastly, the review highlights the importance of integrated genomic surveillance, novel therapy approaches and an enhanced antimicrobial stewardship program according to World Health Organization priorities in the global fight against MDR E. faecium.

Flavonoids are important components of plant root exudates and key chemical signals mediating cross-kingdom interactions between plants and rhizosphere microorganisms. Based on the theory of chemical communication in the plant rhizosphere, this article systematically reviews the biosynthesis and secretion characteristics of flavonoids, as well as their major regulatory roles in plant-microbe interactions, including symbiotic signal induction in legume-rhizobium associations, arbuscular mycorrhizal fungal colonization, recruitment of plant growth-promoting rhizobacteria, inhibition of pathogenic microorganisms, and interference with quorum sensing. In addition, flavonoids are also involved in host nutrient acquisition and stress-response regulation, affecting the uptake of mineral elements such as phosphorus and iron, as well as plant adaptation to biotic and abiotic stresses. Although significant progress has been made in related research, current evidence remains largely confined to legume model systems. Systematic understanding is still lacking regarding receptor recognition, spatiotemporal dynamic regulation, and field ecological functions of flavonoid signals in non-leguminous staple crops. Future studies should integrate multi-omics analyses, in situ imaging, and functional gene validation to further elucidate the general principles and ecological specificity of flavonoid-mediated rhizosphere interactions. This article aims to provide a theoretical basis for elucidating the mechanisms underlying flavonoid-mediated plant-rhizosphere microbial interactions, advancing the precise regulation of the rhizosphere microecology, and supporting the development of sustainable agriculture.

Coal mining creates coupled physicochemical stresses, including extreme pH, nutrient depletion, metal enrichment, compaction, and loss of plant-derived carbon, that reduce microbial biomass, simplify interaction networks, and suppress biogeochemical functions. This review synthesizes recent evidence on microbial community restoration in abandoned coal mine lands, with emphasis on community assembly, stress adaptation, functional genes, and the interpretive value of high-throughput sequencing and meta-omics. During natural recovery, microbial propagule dispersal interacts with strong habitat filtering and rhizosphere selection. Pioneer plants and biological soil crusts progressively add carbon and nitrogen, stabilize surfaces, and recruit bacterial, fungal, and phototrophic guilds. Active interventions accelerate these processes by correcting substrate constraints and by inoculating soils, planting holes, seeds, or carriers with locally adapted microorganisms. However, field performance is often limited by competition with resident communities, host mismatch, environmental heterogeneity, and declining inoculant persistence. Restoration assessment should therefore combine taxonomic composition with functional-gene abundance, gene expression, enzyme activity, microbial biomass, and ecosystem-level indicators. Across sites, no single strategy is consistently superior: amendments act rapidly but may require repeated inputs, vegetation-based approaches are slower but potentially self-sustaining, and inoculation is most effective after major physicochemical barriers have been removed. Future research should prioritize replicated field trials, standardized and activity-resolved measurements, locally adapted consortia, and early-stage interventions that influence microbiome composition and function without assuming complete control. These priorities provide a practical basis for precision restoration of mine-affected soils.

Helicobacter pylori (H. pylori) is a major cause of chronic gastritis and gastric cancer. Macrophages are key regulators of gastric immunity, yet the mechanisms by which H. pylori reprogram macrophage activation and suppresses host immune responses remain unclear. RAW264.7 macrophages were infected with H. pylori PMSS1. Macrophage polarization, cytokine secretion, and JAK3/STAT5-SOCS3 signaling were examined by qRT-PCR, Western blotting, flow cytometry, and ELISA. Ritlecitinib was used to inhibit JAK3. Primary naive CD4[+] T cells were treated with macrophage-conditioned medium to assess proliferation, CD25/CD69 activation, and FoxP3[+] Treg differentiation. SOCS3 knockdown was used to evaluate rescue effects. H. pylori significantly promoted M1 macrophage polarization, with increased CD86, iNOS, MHC II, TNF-α, and IFN-γ and decreased CD163, Arg1, TGF-β, and IL-10 (p < 0.05). H. pylori also upregulated JAK3, STAT5, and SOCS3, while Ritlecitinib attenuated inflammatory gene expression (p < 0.05). Hp-CM significantly inhibited primary CD4[+] T-cell proliferation, CD25/CD69 activation, and CD4[+]CD25[+]FoxP3[+] Treg differentiation (p < 0.05). SOCS3 knockdown partially restored these CD4[+] T-cell responses (p < 0.05). H. pylori promotes M1 macrophage polarization and impairs CD4[+] T-cell immunity through JAK3/STAT5-SOCS3-mediated immune dysregulation. This mechanism contributes to chronic immune dysregulation and supports bacterial persistence, identifying JAK3/SOCS3 as potential therapeutic targets.

Adenoviral infection has been implicated in spontaneous abortion, but the relationship between adenovirus-associated pregnancy loss and systemic apoptotic activation remains incompletely understood. This study investigated serum caspase-3 (CASP3) concentrations and cleaved caspase-3 protein expression in women with adenovirus-associated spontaneous abortion and evaluated the diagnostic performance of serum CASP3. A comparative cross-sectional study was conducted including 90 pregnant women: 46 with adenovirus-associated spontaneous abortion and 44 healthy pregnant controls. Serum CASP3 concentrations were quantified by ELISA, and cleaved caspase-3 expression was evaluated by Western blot in an exploratory sub-cohort. Pearson correlation, multivariable linear regression, and receiver operating characteristic (ROC) analyses were performed. Serum CASP3 was significantly elevated in the spontaneous abortion group relative to controls (5.60 ± 1.21 vs. 2.17 ± 0.49 ng/mL; p < 0.001). Western blot analysis revealed a 28.66 ± 4.80-fold upregulation of cleaved caspase-3 in the abortion cohort (relative expression: 4.30 ± 0.72 vs. 0.15 ± 0.01; p < 0.001). BMI was an independent positive predictor of serum CASP3, whereas hemoglobin demonstrated a significant inverse association. ROC analysis yielded an area under the curve of 0.844 (95% CI: 0.765-0.922), with an optimal diagnostic threshold of 3.45 ng/mL conferring 76.9% sensitivity and 88.6% specificity. Serum CASP3 concentrations and cleaved caspase-3 expression were significantly increased in women with adenovirus-associated spontaneous abortion, supporting an association with enhanced systemic apoptotic activity. Serum CASP3 demonstrated promising discriminatory performance within the study cohort; however, these findings require validation in larger prospective studies before clinical application.

Aspergillus fungi are rich in secondary metabolites, yet their biosynthetic potential remains underexplored. Nonribosomal peptides (NRPs), an important class of natural products with diverse biological activities, are synthesized by nonribosomal peptide synthetases (NRPSs). In this study, we performed a large-scale bioinformatic analysis of NRPS adenylation (A) domains from 1,162 Aspergillus genomes to predict their substrate specificities. Using AdenylPred, we analyzed 40,684 A-domain sequences and found that large phenyl-derivative amino acids and small hydrophobic amino acids are the predominant substrates, accounting for 66% of all predictions. Focused genome mining of Aspergillus spinosus 2437 revealed a biosynthetic gene cluster (BGC 29.2) showing high similarity to known non-proteinogenic amino acid-containing cyclic dipeptide BGCs. Fermentation of this strain led to the isolation of three tryptophan-anthranilic acid cyclic dipeptides, namely asperdiazapinone G (1), 6-hydroxyaszonalenin (2), and aszonalenin (3), thereby providing support for the functional assignment of the identified gene cluster and suggesting the utility of A-domain substrate prediction for targeted genome mining. Enzyme similarity analysis further indicated that NRPSs responsible for cyclic dipeptide biosynthesis are predominantly distributed within the Aspergillus genus. This study indicates that combining A-domain substrate prediction with genome mining is an effective strategy for discovering NRPs in Aspergillus, expanding our understanding of their biosynthetic potential.

Achromobacter xylosoxidans is an emerging opportunistic pathogen related to cystic fibrosis (CF). Its clinical impact is variable among patients depending on strain-specific genomic diversity and interaction with co-infecting pathogens. Hence, genomic analysis plays a key role in understanding its pathogenic potential and adaptation in the CF disease. This study included a clinical strain isolated from sputum of a patient with CF. The strain was evaluated for its antimicrobial susceptibility using VITEK 2 and biofilm formation / inhibition using crystal violet assay in the presence and absence of PAβN. Whole-genome sequencing was conducted using Illumina technology, followed by genome assembly and annotation. The resistome and virulence profiling of MICB25 was achieved using BV-BRC and PGAP pipelines. The clinically strain (MICB25) was identified as Achromobacter xylosoxidans. Our study shows that secretion systems, multidrug efflux systems are functionally linked to biofilm formation in a CF-associated A. xylosoxidans MICB25, as evidenced by PAβN-mediated biofilm inhibition. The whole-genome sequencing revealed a multifaceted resistome including β-lactamases, aminoglycoside-modifying enzymes, and other resistance determinants in addition to an exceptionally broad and varied efflux repertoire covering ABC, MFS, RND, and SMR families. The application of whole-genome sequencing in this study provides crucial insights into the persistence-oriented pathogenic strategy of this emerging CF pathogen A. xylosoxidans. The coexistence of multidrug efflux determinants and PAβN-sensitive biofilm formation suggests that efflux activity could be involved in persistence and warrants addditional mechanistic investigation.

Plant growth-promoting rhizobacteria are promising tools for agricultural management. We previously identified Achromobacter sp. 5B1, Bacillus sp., Micrococcus luteus, and Pseudomonas brassicae strains that influence the growth of Arabidopsis seedlings in highly contrasting manners. Here, pairwise combinations of these four bacterial isolates were tested to identify single or additive traits influenced by cocultivation with Arabidopsis seedlings in vitro. Root architectural modifications, such as primary root growth and lateral root formation, as well as root and shoot biomass production were correlated with expression of gene promoters involved in phytohormone responses using auxin, cytokinin and jasmonic acid-inducible DR5:GUS, ARR5:GUS, and JAZ1:GUS constructs, respectively. Noteworthy, the presence of P. brassicae in all consortia led to the exhaustion of the root meristem that coincided with high expression of jasmonic acid-inducible JAZ1:GUS in primary root tips, whereas Achromobacter sp. 5B1 induced cytokinin-signaling in roots. These effects were prevalent over other bacteria when grown together. Additive effects in expression of JAZ1:GUS were observed in primary and lateral roots of P. brassicae - Achromobacter sp. 5B1 consortium indicating elicitation of the jasmonic acid response. Transfer of plants to soil with and without pairwise inoculum showed that early interaction with Bacillus sp. - Achromobacter sp. 5B1 promoted the transition to flowering and increased fruit and seed production. These results advance our understanding of how mixed consortia of plant growth-promoting rhizobacteria affect plant growth and reveal dominant effects of particular strains in mixed populations.

This study explored the immunomodulatory properties of the probiotic strains Lacticaseibacillus rhamnosus LR-32 and Lactobacillus acidophilus LA-5 by evaluating their effects on human dendritic cell (DC) responses. Immature DCs were obtained from human CD14[+] monocytes and challenged with E. coli LPS and/or probiotic lactobacilli at a DC ratio of 1:10. Relative transcription of inflammatory mediators and pattern-recognition receptors was assessed by RT-qPCR. Cytokine production and surface marker expression were evaluated by ELISA and flow cytometry, respectively. DC function was further assessed after interaction with CD4[+] T lymphocytes, followed by analysis of T cell phenotype by flow cytometry and cytokine production by ELISA. LPS upregulated the transcription of intracellular receptors AIM2, NOD1, and NOD2 and increased COX-2, TNF-α, IL-1β, IL-6, CXCL-8, IL-12, and IL-18 mRNA levels compared with immature DCs (p < 0.001). Exposure to probiotics downregulated most genes encoding receptors and inflammatory mediators compared with LPS-stimulated DCs. In LPS-stimulated DCs, LA-5 reduced intra- and extracellular receptor gene expression, increased COX-2, TNF-α, IL-1β, IL-6, CXCL-8, and IL-10 transcription, and decreased IL-12 mRNA levels. LR-32 upregulated TLR2, COX-2, IL-6, CXCL-8, and IL-10, while reducing IL-12 expression, although these effects were less pronounced than those induced by LA-5. LA-5-exposed DCs induced a higher frequency of CD25highFOXP3highCD127low CD4[+] T cells than LR-32. These findings indicate that LA-5 and LR-32 modulate human DC responses in a strain-dependent manner. Rather than acting as broadly anti-inflammatory stimuli, these probiotics reshaped LPS-induced activation by modulating pattern-recognition receptor pathways, cytokine responses, and a Treg-associated CD4[+] T cell phenotype, suggesting a potential role in controlled mucosal immune regulation.