Journal of microbiology and biotechnology最新文献

Inflammation is a fundamental immune response that protects the host against infection and tissue injury. However, it can also contribute to the pathogenesis of various chronic diseases. In this study, we investigated the anti-inflammatory effects of Cornus controversa leaf and stem (CC-LS) extract in RAW 264.7 macrophages as well as the underlying mechanisms. Our results showed that CC-LS attenuated lipopolysaccharide (LPS)-induced inflammatory responses in RAW 264.7 macrophages in a dose-dependent manner without cytotoxicity even at high concentrations. Specifically, CC-LS significantly suppressed nitric oxide production and downregulated the expression of inducible nitric oxide synthase and cyclooxygenase-2 in the LPS-stimulated cells. It also attenuated intracellular reactive oxygen species accumulation, inhibited NF-κB p65 phosphorylation, and downregulated the expression of pro-inflammatory cytokines, including tumor necrosis factor-α, interleukin-6, and interleukin-1β. Moreover, it inhibited the phosphorylation of mitogen-activated protein kinases, ERK, JNK, and p38, while promoting the activation of AMP-activated protein kinase (AMPK) and its downstream substrate, acetyl-CoA carboxylase. These findings indicate that CC-LS exerts potent anti-inflammatory effects in macrophages by targeting the NF-κB, MAPK, and AMPK signaling pathways, suggesting its potential as a natural source for developing anti-inflammatory therapeutic agents.

Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.

Dysbiosis of the gut microbiota plays a key role in the pathogenesis of rheumatoid arthritis (RA). However, it is still unclear whether the classic prescription Er Miao San (EMS) can exert therapeutic effects on RA by regulating the gut microbiota. In this study, we investigated whether EMS alleviates collagen-induced arthritis (CIA) by modulating the gut microbiota and its metabolites. We demonstrated that EMS significantly reduced arthritis severity, paw swelling, and systemic inflammation in CIA mice. In addition, 16S rRNA sequencing analysis revealed that EMS restored gut microbiota homeostasis, as evidenced by an increased abundance of Bacteroidetes, and a decreased Bacteroidetes/Firmicutes ratio. Crucially, antibiotic depletion of the gut microbiota abolished the protective effects of EMS, whereas fecal microbiota transplantation (FMT) from EMS-treated donors replicated its anti-arthritic efficacy, confirming the indispensable role of the microbiota. Measurement of short-chain fatty acids (SCFAs) further revealed a significant increase in the microbial metabolite butyrate following EMS treatment. Subsequent supplementation with sodium butyrate mimicked the therapeutic effects of EMS, ameliorating joint inflammation and cartilage damage. Mechanistically, butyrate enhanced the expression of intestinal tight junction proteins (ZO-1 and occludin), thereby restoring intestinal barrier integrity. Collectively, our results demonstrate that EMS exerts its anti-arthritic effects by modulating the gut microbiota-butyrate-intestinal barrier axis, highlighting the critical value of microbial metabolites in RA treatment. This study provides novel insights into the mechanism of EMS and suggests the therapeutic potential of butyrate for RA.

COVID-19 demonstrates distinct clinical heterogeneity, ranging from mild symptoms to severe acute respiratory distress syndrome (ARDS). Neutrophil extracellular traps (NETs), which are web-like structures consisting of decondensed DNA adorned with cytotoxic proteins such as myeloperoxidase (MPO) and citrullinated histone H3 (CitH3), play a crucial role in pathogen containment. However, they may also promote immunothrombosis and tissue injury. This research aimed to explore the association between NET formation and the severity of COVID-19. Plasma samples were collected from 99 patients diagnosed between 2022 and 2023. NET remnants were quantified through cell-free DNA (cfDNA), MPO-DNA, neutrophil elastase (NE)-DNA complexes, histone-DNA complexes, and CitH3. The levels of all NET biomarkers were significantly increased in COVID-19 patients and were positively correlated with disease severity. Notably, patients who required mechanical ventilation or high-flow oxygen had significantly higher concentrations of cfDNA, histone-DNA, and CitH3, indicating a strong connection between NETs and respiratory deterioration. Specifically, the combined model incorporating three NETs-related biomarkers demonstrated superior performance in discriminating disease severity, as evidenced by receiver operating characteristic (ROC) analysis. These findings suggest that excessive NET formation contributes to the pathogenesis of COVID-19, potentially via pro-inflammatory and pro-thrombotic pathways. Consequently, the combined model (histone-DNA, MPO-DNA, and CitH3) is identified as a promising biomarker signature for reflecting neutrophil-mediated immunopathology.

Systemic bacteriophage therapy against multidrug-resistant (MDR) Escherichia coli is fundamentally limited by rapid immune-mediated clearance, complement activation, and phagocytic sequestration, collectively constituting pharmacological barriers that restrict systemic bioavailability, shorten circulation half-life, and attenuate therapeutic efficacy. We hypothesized that PEGylation, by sterically shielding phage capsids from host immune clearance mechanisms, would enhance systemic stability, improve pharmacokinetic (PK) behavior, and augment therapeutic efficacy in vivo. Four lytic E. coli phages were covalently conjugated with 5-kDa mPEG-S-NHS, achieving >60% surface amine modification as confirmed by fluorescamine assay. PEGylation resulted in a ~1.5-5 log₁₀ reduction in infectious titer and modestly slowed adsorption kinetics but preserved latent period and burst size, confirming intact replication competence. In serum, wild-type phages were undetectable within 24-48 h, whereas PEGylated phages retained ~2-3 log₁₀ PFU ml^-1 at 24 h and persisted longer within RAW264.7 macrophages and HT-29 epithelial cells. In mice, PEGylation markedly increased systemic exposure (AUC₀-∞ up to 50-fold), prolonged circulation, and reduced clearance >15-fold. In infected hosts, PEG-EC.W2-6 and PEG-EC. W15-4 achieved plasma titers up to 100-fold higher with >30-fold lower clearance, accelerating bacterial elimination (72 h vs 96 h). Despite partial IgG induction upon repeated dosing, PEGylated phages maintained superior PK and significantly suppressed infection-driven IL-6, IFN-γ, TNF-α, and IL-1β, normalizing cytokine profiles toward baseline. Overall, PEGylation markedly improves systemic persistence, intracellular stability, and immunomodulatory efficacy, representing a robust strategy to overcome PK barriers and optimize systemic phage therapy against MDR E. coli.

A synthetic promoter is an artificially designed DNA sequence based on naturally occurring promoter elements, enabling more precise control of gene expression than natural promoters. Design of synthetic promoters with tunable expression levels is key to precise genetic regulation in microbes, supporting metabolic engineering, natural product biosynthesis, and diverse biotechnological applications. Recent advances in deep learning have made it possible to generate functional synthetic promoters using deep generative models (DGMs). Such approaches dramatically accelerate the traditionally labor-intensive and time-consuming process of experimental promoter design, enabling the efficient discovery of synthetic promoters. In synthetic promoter generation, three major types of DGMs have been predominantly employed: variational autoencoders (VAEs), generative adversarial networks (GANs), and diffusion models. VAEs reconstruct promoters through latent feature learning, GANs create realistic promoter sequences via adversarial training, and diffusion models iteratively denoise random inputs to generate high-fidelity synthetic promoters. This review outlines deep learning-based strategies for synthetic promoter design, encompassing data acquisition, promoter generation, and validation of promoters generated by DGMs.

The rising need for new antibiotics and antioxidants highlights endophytic bacteria as promising sources of bioactive compounds. Medicinal plants such as Azadirachta indica harbour diverse endophytes, yet their potential in southwest Nigeria remains largely underexplored. This study investigated the antimicrobial, biofilm inhibitory, and antioxidant activities of bioactive compounds produced by the bacterial endophyte Serratia marcescens AI-N-1, isolated from A. indica. Crude extracts of S. marcescens showed strong antimicrobial activity against Bacillus subtilis (79.79% inhibition) and Salmonella typhi (77.04% inhibition) at 5 mg/ml. In addition, most extracts also displayed potent biofilm inhibition (>80%) against both pathogens, comparable to the positive control baicalein (P < 0.05). Antioxidant assays revealed high radical scavenging activity, with the supernatant extract obtained after 2 days of culture exhibiting the strongest effect (DPPH: 86.61% at 0.1 mg/ml; ABTS: 99.64% at 0.1 mg/ml). Online HPLC-ABTS⁺ analysis identified serranticin as a major contributor to these antioxidant effects. HR-MS/MS profiling further revealed prodigiosin, serratamolides, and serranticin, along with putative novel lipopeptides and other metabolites, as key bioactive compounds. To our knowledge, this is the first report of a Serratia endophyte from A. indica in southwest Nigeria with combined antimicrobial, antibiofilm, and antioxidant activities, as well as the discovery of putative new lipopeptides. These findings highlight endophytic bacteria from Nigerian medicinal plants as promising sources of novel antimicrobial and antioxidant agents for pharmaceutical development.

Dry eye disease (DED) is a multifactorial ocular disorder characterized by tear film instability, inflammation, and ocular surface damage. Although various therapeutic approaches are available, there remains a strong need for safer and more effective agents with clearly defined mechanisms of action. This study examined the protective effects of Misgurnus mizolepis protein hydrolysate (MMH) in both in vitro and in vivo models of DED. In vitro, pretreatment of air-dried human corneal epithelial cells with MMH attenuated oxidative stress and apoptosis. In vivo, oral administration of MMH to rats with atropine-induced DED restored tear secretion, preserved ocular tissue architecture, reduced immune cell infiltration, and downregulated inflammatory mediators in the cornea. Furthermore, MMH maintained tight junction proteins, suppressed pro-apoptotic signaling in the lacrimal gland, improved meibomian gland and goblet cell integrity, and mitigated neovascularization. Collectively, MMH demonstrated anti-inflammatory, anti-apoptotic, and tissue-protective effects, supporting its potential as a novel therapeutic candidate for DED.

Probiotics play a crucial role in promoting host health by modulating the composition of the gut microbiota through the production of their own bioactive metabolites. The aim of the study was to investigate the anti-atrophic effects of Lacticaseibacillus paracasei EFEL6501 (EFEL6501) in dexamethasone (DEX)-treated C2C12 myotubes and a mouse model. In vitro experiments demonstrated that specific bioactive metabolites present in the cell culture supernatant (CS) and lysate supernatant (LS) of EFEL6501 alleviated muscle degradation and restored muscle protein synthesis in DEX-induced C2C12 myotubes. Similarly, EFEL6501 supplementation in mice significantly enhanced muscle thickness (6.09 mm), grip strength (117.87 g), and the cross-sectional area (CSA) (34.11 μm²) of the gastrocnemius muscle, compared to the DEX group (5.70 mm, 106.87 g and 29.79 μm², respectively), by suppressing protein degradation pathways and improving muscle differentiation. Furthermore, EFEL6501 positively modulated the gut microbiota composition by increasing the abundance of beneficial bacteria, including Lactobacillus reuteri (7.19%), Bifidobacterium choerinum (25.66%), Bacteroides uniformis (0.29%), Allobaculum (0.63%), and Faecalibaculum (18.00%) compared to the DEX group (3.44%, 0.75%, 0.14%, -0.63%, and 8.53%, respectively), while also elevating acetate concentrations from 1.57 ± 0.27 mM to 1.97 ± 0.16 mM. Taken together, EFEL6501 may serve as a potential functional probiotic for preventing muscle atrophy by regulating muscle metabolism and gut microbiota composition.

Vancomycin-resistant Enterococcus (VRE) has demonstrated increasing global prevalence in recent years. Clinical detection currently relies on phenotypic methods including agar screening, minimum inhibitory concentration (MIC) testing, Kirby-Bauer disk diffusion, and Etest. In addition, molecular approaches such as polymerase chain reaction (PCR) and quantitative PCR (qPCR) can be applied for VRE identification. Nevertheless, these methods cannot achieve point-of-care detection (POCT). Thus, novel rapid diagnostic platforms have become urgently needed for curbing VRE transmission and containing nosocomial outbreaks. Recombinase polymerase amplification (RPA) and lateral flow strips (LFS) are effective tools for achieving rapid POCT. In this study, RPA was combined with LFS to establish a fast, sensitive, and specific detection method. This study established a multiplex RPA-LFS (mRPA-LFS) that delivers results within 30-40 min, with detection limits of 10² copies/μl for vanA, vanB, and vanM. Notably, the assay demonstrated high specificity without cross-reactivity to common bacterial/fungal pathogens, and showed 100% concordance with conventional PCR in 30 clinical samples. In this study, a rapid detection assay for vanA, vanB, and vanM genes in VRE was developed using mRPA-LFS technology. Characterized by high sensitivity, specificity, operational simplicity, and cost-effectiveness, this method is suitable for on-site detection.