Search Results (91)

Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant clinical challenge due to its resistance to multiple antibiotics. The urgent need for new therapeutic approaches has led to the exploration of natural compounds as potential treatments, particularly those targeting the key bacterial proteins involved in antibiotic resistance. This study focused on the multidrug ABC transporter and MecA proteins, which play crucial roles in MRSA′s pathogenicity and resistance mechanisms. Using computational techniques and molecular docking methods, we assessed the interactions of 80 natural compounds with S. aureus multidrug ABC transporter SAV1866 (SAV1866) and MecA proteins. Our analysis revealed 14 compounds with robust binding to SAV1866 and one compound with a strong affinity for MecA. Notably, these compounds showed weaker affinities for the MgrA, MepR, and arlR proteins, suggesting specificity in their interactions. Among the 15 promising compounds identified, 1′,2-Binaphthalen-4-one-2′,3-dimethyl-1,8′-epoxy-1,4′,5,5′,8,8′-hexahydroxy-8-O-β-glucopyranosyl-5′-O-β-xylopyranosyl(1→6)-β-glucopyranoside; Cis-3,4-dihydrohamacanthin b; and Mamegakinone exhibited the highest binding affinities to S. aureus SAV1866. These compounds represent diverse chemical classes, including alkaloids, indole derivatives, naphthalenes, and naphthoquinones, offering a range of structural scaffolds for further drug development. Our findings provide valuable insights into potential new antibacterial agents targeting S. aureus SAV1866 and MecA proteins. These results lay the groundwork for future in vitro and in vivo studies to validate these compounds′ efficacy for combating MRSA infections, potentially leading to the development of novel therapeutic strategies against antibiotic-resistant bacteria. Full article

Escherichia coli and Klebsiella pneumoniae are major contributors to the global challenge of antimicrobial resistance, posing serious threats to public health. Among current preventive strategies, conjugate vaccines that utilize bacterial surface polysaccharides have emerged as a promising and effective approach to counter multidrug-resistant strains. In this study, both the Wzy/Wzx-dependent and ABC transporter-dependent biosynthetic pathways for antigenic polysaccharides were introduced into E. coli W3110 cells. This dual-pathway engineering enabled the simultaneous biosynthesis of two structurally distinct polysaccharides within a single host, offering a streamlined and potentially scalable strategy for vaccine development. Experimental findings confirmed that both polysaccharide types were successfully produced in the engineered strains, although co-expression levels were moderately reduced. A weak competitive interaction was noted during the initial phase of induction, which may be attributed to competition for membrane space or the shared use of activated monosaccharide precursors. Interestingly, despite a reduction in plasmid copy number and transcriptional activity of the biosynthetic gene clusters over time, the overall polysaccharide yield remained stable with prolonged induction. This suggests that extended induction does not adversely affect final product output. Additionally, two glycoproteins were efficiently generated through in vivo bioconjugation of the synthesized polysaccharides with carrier proteins, all within the same cellular environment. This one-cell production system simplifies the workflow and enhances the feasibility of generating complex glycoprotein vaccines. Whole-cell proteomic profiling followed by MFUZZ clustering and Gene Ontology analysis revealed that core biosynthetic genes were grouped into two functional clusters. These genes were predominantly localized to the cytoplasm and were enriched in pathways related to translation and protein binding. Such insights not only validate the engineered biosynthetic routes but also provide a molecular basis for optimizing future constructs. Collectively, this study presents a robust synthetic biology platform for the co-expression of multiple polysaccharides in a single bacterial host. The approach holds significant promise for the rational design and production of multivalent conjugate vaccines targeting drug-resistant pathogens. Full article

Prebiotics are food ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefits upon host health. Xylooligosaccharides (XOS) are prebiotic fibers made from xylan. Commercial XOS are mixtures of oligosaccharides containing β-1,4–linked xylose residues. Though they are widely added to foods at different doses, the molecular mechanisms of the catabolism and growth promotion of XOS in the innate gut microbes Lactobacillus spp. remain unknown. In this study, we evaluated the growth-promoting effect using a human fecal isolate, Lactiplantibacillus plantarum strain B20 (Lb. plantarum B20). Assays of bacterial growth and lactic acid production showed stronger growth promotion of XOS than other oligosaccharides did, in a dose- and fraction-dependent pattern. Using the Lb. plantarum strain SK151 genome as a reference, bioinformatic analysis failed to identify any previously characterized genes responsible for the uptake and catabolism of XOS. However, transcriptomic analysis of Lb. plantarum B20 yielded numerous differentially expressed genes (DEGs) during fermentation of XOS. Among these, an oligopeptide ABC transporter (RS03575-03595, composed of five proteins) and a hydrolase (RS06170) were significantly upregulated. Molecular docking analysis indicated that the substrate-binding protein RS03575 may mediate the import of XOS into the cell. Enzymatic assays further demonstrated that RS06170 possesses β-xylosidase activity and can effectively degrade XOS. In addition, functional enrichment analysis suggested that the growth-promoting effect of XOS may be attributed to the upregulation of genes involved in cellular component biogenesis and cell division, potentially through modulation of ribosome function and carbohydrate metabolism in Lb. plantarum B20. These results provide valuable insights into the mechanisms by which XOS promote growth and highlight potential targets for enhancing prebiotic–probiotic interactions. Full article

Gaseous chlorine dioxide (ClO₂) is a potent antimicrobial agent used to control microbial contamination in food and water. This study evaluates the bactericidal activity of gaseous ClO₂ released from a sodium chlorite (NaClO₂) pad against Campylobacter jejuni. Exposure to a low concentration (0.4 mg/L) of dissolved ClO₂ for 2 h resulted in a >93% reduction of C. jejuni, highlighting the bacterium’s extreme sensitivity to gaseous ClO₂. To elucidate the molecular mechanism of ClO₂-induced bactericidal action, transcriptomic analysis was conducted using RNA sequencing (RNA-seq). The results indicate that C. jejuni responds to ClO₂-induced oxidative stress by upregulating genes involved in reactive oxygen species (ROS) detoxification (sodB, ahpC, katA, msrP, and trxB), iron transport (ceuBCD, cfbpABC, and chuBCD), phosphate transport (pstSCAB), and DNA repair (rdgB and mutY). Reverse transcription-quantitative PCR (RT-qPCR) validated the increased expression of oxidative stress response genes but not general stress response genes (spoT, dnaK, and groES). These findings provide insights into the antimicrobial mechanism of ClO₂, demonstrating that oxidative damage to essential cellular components results in bacterial cell death. Full article

Tetrodotoxin (TTX) is a potent marine neurotoxin found in pufferfish, causing severe poisoning or death if consumed improperly. Studies have indicated that intestinal symbiotic microbiota are associated with the production and accumulation of TTX in pufferfish. However, the specific symbiotic microorganisms involved in these processes and their respective functions remain unclear. This study explored differences in intestinal microbiota related to the TTX content between toxic and non-toxic tiger puffer Takifugu rubripes. We found that the dominant phyla exhibiting significant abundance differences between the two groups were Proteobacteria and Bacteroidota, with the core bacterial genera being Rikenella, Vibrio, Photobacterium, and Bacteroides. Moreover, the genera Marinimicrobium, Idomarina, Galbibacter, and Brumimicrobium were reported for the first time to be potentially associated with TTX bioaccumulation in T. rubripes. In addition, an integrated analysis with our previous study indicated that the “ABC transporters” pathway may play significant roles in the production and transport of TTX in both symbiotic microorganisms and T. rubripes. This study preliminarily investigated the intestinal symbiotic bacteria associated with the accumulation and metabolism of TTX in T. rubripes, as well as screening potential microbial biomarkers for assessing the safety of pufferfish. Full article

Background and Objectives: The imminent threat of antibiotic resistance has spurred studies of nonconventional antimicrobial approaches. Gallium utilization is a promising and emerging approach to treating a variety of resistant bacteria using “Trojan horse” strategies to disrupt iron-dependent processes and biofilms. This study utilized experimental evolution to test the evolvability of gallium resistance in Staphylococcus aureus and resistance traits potentially correlated with metals, antibiotics and polyfluorinated compounds, as well as its genomics foundations. Methods: Whole-genome sequencing was utilized to reveal functional networks of mutations associated with gallium resistance. Additionally, scanning electron microscopy (SEM) observation was utilized to visualize distinct morphological changes on the surface of gallium-resistant populations and compare with the control populations. Results: As demonstrated by these studies, S. aureus evolved resistance to gallium after 20 days of selection. Furthermore, these populations displayed resistance traits correlated with heavy metals and polyfluorinated compounds. In contrast, the gallium-resistant populations were very sensitive to antibiotics. Whole-genome analysis revealed significant polymorphisms in the gallium (III)-resistant populations for example, polymorphisms in staphyloferrinA export MFS transporter/D ornithine citrate ligase (sfaA/sfaD), teichoic acid D Ala esterase (fmtA), DUF3169 family protein (KQ76_RS01520) and adenine phosphoribosyltransferase (KQ76_RS08360), while polymorphisms in the ABC transporter permease subunit (pstC) and acyltransferase family protein (KQ76_RS04365) were unique to the control populations. The polymorphisms directly affected the cells’ morphology. SEM images showed significant external ultrastructural changes in the gallium-selected bacterial cells compared to the control cells. Conclusions: Our study confirmed that using gallium as an antimicrobial can have significant health and environmental implications. Full article

Soda lakes are extreme saline–alkaline environments that harbor metabolically versatile microbial communities with significant biotechnological potential. This study employed shotgun metagenomics (NovaSeq PE150) to investigate the functional diversity and metabolic potential of microbial communities in Ethiopia’s Chitu and Shala Lakes. An analysis of gene content revealed 554,609 and 525,097 unique genes in Chitu and Shala, respectively, in addition to a substantial fraction (1,253,334 genes) shared between the two, underscoring significant functional overlap. Taxonomic analysis revealed a diverse phylogenetic composition, with bacteria (89% in Chitu Lake, 92% in Shala Lake) and archaea (4% in Chitu Lake, 0.8% in Shala Lake) as the dominant domains, alongside eukaryotes and viruses. Predominant bacterial phyla included Pseudomonadota, Actinomycetota, and Gemmatimonadota, while Euryarchaeota and Nitrososphaerota were prominent among archaea. Key genera identified in both lakes were Nitriliruptor, Halomonas, Wenzhouxiangella, Thioalkalivibrio, Aliidiomarina, Aquisalimonas, and Alkalicoccus. Functional annotation using the KEGG, eggNOG, and CAZy databases revealed that the identified unigenes were associated with various functions. Notably, genes related to amino acid, carbohydrate, and energy metabolism (KEGG levels 1–2) were predominant, indicating that conserved core metabolic functions are essential for microbial survival in extreme conditions. Higher-level pathways included quorum sensing, two-component signal transduction, and ABC transporters (KEGG level 3), facilitating environmental adaptation, stress response, and nutrient acquisition. The eggNOG annotation revealed that 13% of identified genes remain uncharacterized, representing a vast untapped reservoir of novel enzymes and biochemical pathways with potential applications in biofuels, bioremediation, and synthetic biology. This study identified 375 unique metabolic pathways, including those involved in pyruvate metabolism, xenobiotic degradation, lipid metabolism, and oxidative stress resistance, underscoring the microbial communities’ ability to thrive under fluctuating salinity and alkalinity. The presence of carbohydrate-active enzymes (CAZymes), such as glycoside hydrolases, polysaccharide lyases, and oxidoreductases, highlights their role in biomass degradation and carbon cycling. Enzymes such as alkaline proteases (Apr), lipases (Lip), and cellulases further support the lakes’ potential as sources of extremophilic biocatalysts. These findings position soda lakes as reservoirs of microbial innovation for extremophile biotechnology. Future research on unannotated genes and enzyme optimization promises sustainable solutions in bioenergy, agriculture, and environmental management. Full article

The escalating global health crisis of antibiotic resistance, driven by the rapid emergence of multidrug-resistant (MDR) bacterial pathogens, necessitates urgent and innovative countermeasures. This review comprehensively examines the diverse mechanisms employed by bacteria to evade antibiotic action, including alterations in cell membrane permeability, efflux pump overexpression, biofilm formation, target site modifications, and the enzymatic degradation of antibiotics. Specific focus is given to membrane transport systems such as ATP-binding cassette (ABC) transporters, resistance–nodulation–division (RND) efflux pumps, major facilitator superfamily (MFS) transporters, multidrug and toxic compound extrusion (MATE) systems, small multidrug resistance (SMR) families, and proteobacterial antimicrobial compound efflux (PACE) families. Additionally, the review explores the global burden of MDR pathogens and evaluates emerging therapeutic strategies, including quorum quenching (QQ), probiotics, postbiotics, synbiotics, antimicrobial peptides (AMPs), stem cell applications, immunotherapy, antibacterial photodynamic therapy (aPDT), and bacteriophage. Furthermore, this review discusses novel antimicrobial agents, such as animal-venom-derived compounds and nanobiotics, as promising alternatives to conventional antibiotics. The interplay between clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) in bacterial adaptive immunity is analyzed, revealing opportunities for targeted genetic interventions. By synthesizing current advancements and emerging strategies, this review underscores the necessity of interdisciplinary collaboration among biomedical scientists, researchers, and the pharmaceutical industry to drive the development of novel antibacterial agents. Ultimately, this comprehensive analysis provides a roadmap for future research, emphasizing the urgent need for sustainable and cooperative approaches to combat antibiotic resistance and safeguard global health. Full article

The prevalence of antimicrobial resistance (AMR) in bacterial pathogens resulting from the intensive usage of antibiotics and antibiotic compounds is acknowledged as a significant global concern that impacts both human and animal health. In this study, we sequenced and analyzed the genomes of two emergent onion-pathogenic species of Burkholderia, B. cenocepacia CCRMBC56 and B. orbicola CCRMBC23, focusing on genes that are potentially associated with their high level of antibiotic and copper resistance. We also identified genes contributing to the copper resistance of B. cenocepacia CCRMBC56 through high-throughput analysis of mutated genes in random transposon mutant populations that were differentially enriched in a copper-containing medium. The results indicated that genes involved in DNA integration, recombination, and cation transport are important for the survival of B. cenocepacia CCRMBC56 in copper-stressed conditions. Furthermore, the fitness effect analysis identified additional genes crucial for copper resistance, which are involved in functions associated with the oxidative stress response, the ABC transporter complex, and the cell outer membrane. In the same analysis, genes related to penicillin binding, the TCA cycle, and FAD binding were found to hinder bacterial adaptation to copper toxicity. This study provides potential targets for reducing the copper resistance of B. cenocepacia and other copper-resistant bacterial pathogens. Full article

Salt stress poses a significant constraint on rice production, so further exploration is imperative to elucidate the intricate molecular mechanisms governing salt tolerance in rice. By manipulating the rhizosphere microbial communities or targeting specific microbial functions, it is possible to enhance salt tolerance in crops, improving crop yields and food security in saline environments. In this study, we conducted rice rhizospheric microbial amplicon sequencing and metatranscriptome analysis, revealing substantial microbiomic differences between the salt-tolerant rice cultivar TLJIAN and the salt-sensitive HUAJING. Fungal taxa including Hormiactis, Emericellopsis, Ceriosporopsis, Dirkmeia, and Moesziomyces predominated in the rhizosphere of salt-tolerant rice, while bacterial genera such as Desulfoprunum and Hydrogenophaga exhibited notable differences. Metatranscriptomic analysis identified 7192 differentially expressed genes (DEGs) in the two rice varieties, with 3934 genes being upregulated and 3258 genes being downregulated. Enrichment analyses in KEGG and GO pathways highlighted the majority of DEGs were associated with the “two-component system”, “sulfur metabolism”, and “microbial metabolism in diverse environments”. The interaction network of DEGs and microbial taxa revealed upregulation of transporters, transcriptional factors, and chaperones, such as ABC transporters and chaperonin GroEL, in the rhizosphere microbiomes of salt-tolerant varieties. Our multi-omics network analysis unveiled that fungi like Ceriosporopsis and Dirkmeria, along with bacteria such as Desulfoprunum, Rippkaea, and Bellilinea, showed a positive correlation with flavonoid synthesis in salt-tolerant rice. This study provides an in-depth exploration of the distinctive microbial communities associated with the rhizosphere of salt-tolerant rice varieties, shedding light on the complex interactions between these microbial consortia and their host plants under stress conditions. Full article

Pseudomonas cannabina pv. alisalensis (Pcal) causes bacterial blight on cabbage. In a previous study, we screened for reduced virulence using Tn5 transposon mutants and identified a LysR-type transcriptional regulator (LTTR) as a potential virulence factor in Pcal. However, the role of LTTR in Pcal virulence has not been thoroughly investigated. In this study, we demonstrated that the Pcal NN14 mutant (with Tn5 insertion in the LTTR-encoding gene) showed reduced disease symptoms and bacterial populations in cabbage, indicating that LTTR contributes to Pcal virulence. RNA-seq analysis identified 39 LTTR-dependent genes. Genes associated with 13 of the type three secretion system (T3SS), two of flagellar apparatus, ABC transporters, and transcription factors were expressed at lower levels in the NN14 mutant compared to the wild type. Conversely, tssH and hcp, type six secretion system (T6SS)-related genes, showed higher expression in NN14. Furthermore, these differences in gene expression were observed in minimal medium, but not in nutrient-rich medium, suggesting that LTTR acts as a global regulator responsive to nutrient conditions. Additionally, LTTR activated the expression of T3SS-related genes during Pcal infection. We also demonstrated that NN14 showed a reduced ability to induce hypersensitive reaction (HR) cell death in non-host plants. Collectively, these results suggest that LTTR contributes to Pcal virulence by regulating T3SS in response to environmental changes. Full article

Aquatic ecosystems, including rivers, estuaries, and coastal environments, are crucial for maintaining biodiversity, regulating nutrient cycles, and supporting human livelihoods. However, these ecosystems are increasingly being threatened by urbanization, making it essential to understand their microbial communities and their ecological roles. This study employed high-throughput 16S rRNA gene sequencing to characterize the bacterial communities within the riverine, estuarine, and coastal sediments of Adyar Creek, Chennai, India. Proteobacteria were the dominant phylum across most samples, with proportions ranging from 39.65% to 72.09%. Notably, the estuarine environment exhibited a distinct taxonomic profile characterized by a significant abundance of Firmicutes (47.09% of the bacterial population). Distinct bacterial classes were observed across sediment types: Alphaproteobacteria (30.07–34.32%) in riverine sediments, Bacilli dominated estuarine sediments (40.17%), and Gammaproteobacteria (15.71–51.94%) in coastal sediments. The most significant environmental factors influencing the bacterial community composition across these samples were pH, salinity, phosphate, and nitrate. LEfSe (Linear discriminant analysis Effect Size) analysis identified specific genera within the estuary, including Bacillus (20.26%), unclassified_Paenibacillus (12.87%), Clostridium (3.81%), Gailella (3.17%), Paenibacillus (3.02%), Massilia (1.70%), Paraburkholderia (1.42%), and Pantoea (1.15%), as potential biomarkers for habitat health. Functional analysis revealed an elevated expression of the genes associated with ABC transporters and carbon metabolism in the estuary, suggesting a heightened nutrient cycling capacity. Furthermore, co-occurrence network analysis indicated that bacterial communities exhibit a strong modular structure with complex species interactions across the three sediment types. These findings highlight bacterial communities’ critical role and the key drivers in estuarine ecosystems, establishing a baseline for further investigations into the functional ecology of these vulnerable ecosystems. Full article

(1) Background: The unique geographical and climatic conditions of the Antarctic Peninsula contribute to distinct regional ecosystems. Microorganisms are crucial for sustaining the local ecological equilibrium. However, the variability in soil microbial community diversity across different regions of the Antarctic Peninsula remains underexplored. (2) Methods: We utilized metagenome sequencing to investigate the composition and functionality of soil microbial communities in four locations: Devil Island, King George Island, Marambio Station, and Seymour Island. (3) Results: In the KGI region, we observed increased abundance of bacteria linked to plant growth promotion and the degradation of pollutants, including PAHs. Conversely, Marambio Station exhibited a significant reduction in bacterial abundance associated with iron and sulfur oxidation/reduction. Notably, we identified 94 antibiotic resistance genes (ARGs) across 15 classes of antibiotics in Antarctic soils, with those related to aminoglycosides, β-lactamase, ribosomal RNA methyltransferase, antibiotic efflux, gene regulatory resistance, and ABC transporters showing a marked influence from anthropogenic activities. (4) Conclusions: This study carries substantial implications for the sustainable use, advancement, and conservation of microbial resources in Antarctic soils. Full article

To solve the problem of large-scale growth of wetland reeds, wood vinegar, a by-product of pyrolysed reed wood vinegar, can be used as a natural antimicrobial agent. In this study, we compare the changes in growth and bacterial morphology of Escherichia coli (E. coli) treated with reed wood vinegar at different pyrolysis temperatures (300 °C, 500 °C and 700 °C) and reveal the bacterial inhibition mechanism of reed wood vinegar by RNA-Seq. The results of bacteria inhibitory activity showed that 1/2MIC 500 °C wood vinegar had the most prominent bacteria inhibitory activity. qPCR results showed that reed wood vinegar was able to significantly inhibit the expression of E. coli biofilm and genes related to the cell membrane transporter proteins. Electron microscopy observed that the wood vinegar disrupted the cellular morphology of E. coli, resulting in the crumpling of E. coli cell membranes. RNA-Seq showed the multifaceted antimicrobial effects of wood vinegar and demonstrated that the inhibitory effect of wood vinegar on E. coli was mainly realized through the inhibition of the expression of malE, which is an ATP-binding cassette (ABC) transporter complex of E. coli. In conclusion, our study provides an effective method and a theoretical basis for the mechanism of reed wood vinegar as a natural antimicrobial agent and its pathway of bacterial inhibition. Full article

The contamination of soil with the heavy metal cadmium (Cd) is increasingly prominent and severely threatens food security in China. Owing to its low cost, suitable efficacy, and ability to address the shortcomings of plant remediation by enhancing the ability of plants to take up Cd, plant–microbe combination remediation technology has become a research hotspot in heavy metal pollution remediation. A pot experiment was performed to examine the effects of inoculation with the plant-growth-promoting bacterium Brevibacillus sp. SR-9 on the biomass, Cd accumulation, and soil nutrients of hybrid Pennisetum. The purpose of this study was to determine how Brevibacillus sp. SR-9 alleviates stress caused by heavy metal contamination. High-throughput sequencing and metabolomics were used to determine the effects of inoculation on the soil bacterial community composition and microbial metabolic functions associated with hybrid Pennisetum. The results suggest that mutation of Brevibacillus sp. SR-9 effectively alleviates Cd pollution stress, leading to increased biomass and accumulation of Cd in hybrid Pennisetum. The aboveground biomass and the root weight increased by 12.08% and 27.03%, respectively. Additionally, the accumulation of Cd in the aboveground sections and roots increased by 21.16% and 15.50%, respectively. Measurements of the physicochemical properties of the soil revealed that the strain Brevibacillus sp. SR-9 slightly increased the levels of available phosphorus, total nitrogen, total phosphorus, and available potassium. High-throughput DNA sequencing revealed that Brevibacillus sp. SR-9 implantation modified the composition of the soil bacterial community by increasing the average number of Actinobacteria and Bacillus. The total nitrogen content of the soil was positively correlated with the Actinobacteria abundance, total phosphorus level, and available phosphorus level. Metabolomic analysis revealed that inoculation affected the abundance of soil metabolites, and 59 differentially abundant metabolites were identified (p < 0.05). Among these, 14 metabolites presented increased abundance, whereas 45 metabolites presented decreased abundance. Fourteen metabolic pathways were enriched in these metabolites: the folate resistance pathway, the ABC transporter pathway, D-glutamine and D-glutamic acid metabolism, purine metabolism, and pyrimidine metabolism. The abundance of the metabolites was positively correlated with the levels of available phosphorus, total potassium, total phosphorus, and total nitrogen. According to correlation analyses, the development of hybrid Pennisetum and the accumulation of Cd are strongly associated with differentially abundant metabolites, which also impact the abundance of certain bacterial populations. This work revealed that by altering the makeup of microbial communities and their metabolic processes, bacteria that promote plant development can mitigate the stress caused by Cd. These findings reveal the microbiological mechanisms through which these bacteria increase the ability of hybrid Pennisetum to take up the Cd present in contaminated soils. Full article