Search Results (558)

Aptamers are single-stranded DNA or RNA oligonucleotides screened by systematic evolution of ligands by exponential enrichment (SELEX) methods, which are widely used in food analysis. Aptamers have the advantages of low molecular weight, ease of preparation, simplicity of chemical modification, and structural stability. Aptamers generated by SELEX are typically 80–100 bases in length, and the affinity of the aptamer can be improved by sequence optimization. Methods of aptamer optimization commonly include truncation, mutation, and chemical modification, and molecular docking, molecular dynamics, circular dichroism, and isothermal titration to assess often the binding performance of the aptamer to the target. Optimized aptamers usually enhance the affinity of the aptamer for the target and increase its sensitivity in the detection of pesticides, heavy metals, fungal toxins, pathogenic bacteria, and other objects. This paper focuses on truncation, mutation, chemical modification, the introduction of rare nucleotides, and computer-aided design. It provides an overview of non-immobilized optimization metrics. Full article

Background: Salmonella enterica and Escherichia coli are common foodborne pathogens of global concern, particularly due to their antimicrobial resistance, notably to cephalosporins. Objective: This study aimed to evaluate a polymerase chain reaction-based lateral flow strip (PCR-LFS) assay for the detection of Salmonella spp. and E. coli harboring the bla_CTX-M gene, which confers resistance to third-generation cephalosporins. Methods: Two duplex PCRs (dPCR) were established to detect E. coli-harboring bla_CTX-M (set 1) and Salmonella-harboring bla_CTX-M (set 2). 600 bacterial isolates and raw pork mince spiked with bla_CTX-M-harboring E. coli and Salmonella were used to evaluated. Results: Both dPCR assays successfully detected bla_CTX-M-positive E. coli or Salmonella strains, while strains lacking the gene showed no amplification. Non-E. coli and non-Salmonella strains were PCR-negative unless they carried bla_CTX-M. The dPCR-LFS showed 100% validity including accuracy, sensitivity, specificity, positive predictive value, and negative predictive value for both E. coli or Salmonella spp. harboring or lacking bla_CTX-M. The assay accurately detected target strains without cross-reactivity with other bacteria or antimicrobial resistance genes. Cohen’s Kappa coefficient indicated perfect agreement (κ = 1), reflecting the high reliability of the dPCR-LFS. The assay could detect as low as 25 CFU/mL for bla_CTX-M-positive E. coli and 40 CFU/mL for bla_CTX-M-positive Salmonella in spiked raw pork mince. Conclusions: This assay is rapid, easy to interpret, and suitable for large-scale screening in surveillance programs. Full article

Antibiotic resistance is one of the most significant public health issues today. As a consequence, there is an urgent need for novel classes of antibiotics. This necessitates the development of highly efficient screening methods for the rapid identification of antibiotic-producing bacteria. Here, we describe a new method for high-throughput screening of antimicrobial compounds (AMC) producing halophilic bacteria. Our methodology used a newly designed 3D-printed Petri plate replicator used for drop deposition and colony replication. We employed this device in combination with a modified agar overlay assay to screen more than 7400 bacterial colonies. A total of 54 potential AMC producers were discovered at a success rate of 0.7%. Although 40% of them lost their antibacterial activity during the secondary screening, 22 strains retained inhibitory activity and were able to suppress the growth of one or more safe relatives of the ESKAPE group pathogens. The ethyl acetate extract from the most potent strain, Virgibacillus salarius POTR191, demonstrated moderate antibacterial activity against Enterococcus faecalis, Acinetobacter baumanii, and Staphylococcus epidermidis with minimal inhibitory concentrations of 128 μg/mL, 128 μg/mL, and 512 μg/mL, respectively. We propose that our replica plate assay could be used for target-based antimicrobial screening of various extremophilic bacteria. Full article

Biodegradation is a green and efficient method for lignin depolymerization and conversion. In order to screen potential bacterial strains for efficient lignin degradation, composts of cow dung and wheat straw were prepared, and the dynamic changes in the predicted bacterial community structure and function in different periods of the composts were investigated. Then, bacteria with an efficient lignin degradation ability were finally screened out from the compost samples. Based on the monitoring results of the physicochemical indexes of the composting process, it was found that the temperature and pH of the compost firstly increased and then decreased with the extension of time, and the water content and C/N gradually decreased. High-throughput sequencing of compost samples from the initial (DA), high-temperature (DB), and cooling (DC) periods revealed that the number of OTUs increased sharply then stabilized around 2000, and the alpha diversity of the bacterial community decreased firstly and then increased. The predominant phyla identified included Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes, determined by the relative abundance of beta-diversity-associated species. Functional gene analysis conducted using Tax4Fun revealed that the genes were primarily categorized into Metabolism, Genetic Information Processing, Environmental Information Processing, and Cellular Processes. Based on the decolorization of aniline blue and the degradation efficiency of alkali lignin, eight bacterial strains were isolated from compost samples at the three stages. Cupriavidus sp. F1 showed the highest degradation of alkali lignin with 66.01%. Cupriavidus sp. D8 showed the highest lignin degradation potential with all three enzyme activities significantly higher than the other strains. The results provide a strategy for the lignin degradation and utilization of biomass resources. Full article

Background: Lycium chinense has been acknowledged for its substantial nutritional benefits. The “Mengqi No.1” variety of L. chinense is known for its high yield and exceptional quality. Methods: We screened twenty dominant endophytic bacterial genera based on OTUs from L. chinense fruits during three developmental stages. Results: Forty-three differential amino acid metabolites were selected from L. chinense fruits. Five endophytic bacteria (Enterococcus, Escherichia-Shigella, Bacteroides, Pseudomonas, and Bacillus) were dominant genera in green fruit (GF, 16–19 days after flowering), color-changing fruit (CCF, 22–25 days after flowering), and red-ripe fruit (RRF, 31–34 days after flowering). Four endophytic bacterial genera (Enterococcus, Bacillus, Pseudomonas, and Rhodanobacter) showed positive correlation with twenty different amino acid metabolites and negative correlation with seven different amino acid metabolites. Conclusions: Five genes (AST1, ltaE1, TAT1, SHMT2, and SHMT3) indicated positive correlation with seventeen different amino acid metabolites and negative correlation with eight different amino acid metabolites. AST1 gene had a major role in regulating arginine biosynthesis (ko00220); ltaE1, SHMT2, and SHMT3 genes were major in regulating glycine, serine, and threonine metabolism (ko00260); and TAT1 gene had a major role in regulating tyrosine metabolism (ko00350). These findings offer insights into the relationship between amino acid synthesis and endophytic bacteria in L. chinense fruits. Full article

Wine vinegar and wine are traditional Spanish products, obtained from grape must by alcoholic fermentation (wine) and subsequent acetification (vinegar). Although these are established products, there is great interest in the development of new products, particularly new vinegars, and among these, the possibility of vinegars containing gluconic acid stands out. Gluconic acid in vinegar, mainly produced by acetic acid bacteria (AAB), is positively valued by consumers. Its content depends on the availability of glucose in the base wine; however, this hexose is preferentially consumed by the indigenous yeast population which conducts the previous alcoholic fermentation. For this reason, the use of non-conventional fructophilic yeasts, which consume fructose rather than glucose, is required. In this work, we isolated, screened, and identified osmophilic and fructophilic non-Saccharomyces yeasts from sun-dried grape must and tested them under different fermentation conditions in synthetic and natural grape musts, in order to obtain a base wine with ethanol and glucose content for the development of new vinegars containing gluconic acid. The isolate of the species Starmerella lactis-condensi was found to be an ideal candidate due to its fructophilic and osmophilic features, which allowed for the production of a base wine with high ethanol (11% v/v) and glucose (up to 200 g/L) content from a natural concentrated must. In fresh must, inoculation with Starmerella lactis-condensi resulted in faster and preferential fructose consumption over glucose compared to the control. However, both sugars were completely consumed at the end of the alcoholic fermentation; therefore, new fermentation strategies should be tested in this type of must. Furthermore, this strain could be of interest in oenology due to its high glycerol yield and low volatile acid production during alcoholic fermentation. The use of this strain could allow for the production of new wines with unique metabolic profiles suitable for further vinegar production. Full article

The study of antagonistic bacterial strains isolated from the soil around durian tree roots demonstrated their ability to inhibit the growth of Phytophthora palmivora. The pathogens were screened from 30 samples collected around durian trees (leaves, soil around the roots, and debris under the tree) showing symptoms of root and stem rot disease. A total of 17 pathogen strains were isolated and grouped into 3 groups, TNP05, MNP13, and KNP21, originating from Chanthaburi province, Thailand. When P. palmivora isolates were tested for pathogenicity on leaves and durian trees, it was found that the strain MNP13 had the highest capacity to cause root and stem rot disease. A total of 196 beneficial bacteria isolates were collected from several samples around durian trees. The samples included leaves, soil surrounding the roots, and organic debris beneath the trees. Based on their colony characteristics on nutrient glucose agar (NGA), these isolates were divided into 8 groups. The efficacy of the beneficial bacteria against root and stem rot disease was tested using the Dual culture method and arranged in a Completely Randomized Design (CRD) with 5 replications. The experiment showed that bacterial isolates NJTU05, NJTU10, and NJTU13 effectively inhibited the growth of P. palmivora isolate MNP13, with inhibition rates of 76.66, 67.59, and 69.07%, respectively, compared to chemical control using metalaxyl 80% WP. Among the tested strains, NJTU05 was identified as the most effective bacterial strain for controlling major durian diseases. Biochemical identification and 16S rRNA sequencing revealed that bacterial strain NJTU05 was closely related to Brevibacillus formosus with a 99.70% identity. Full article

Urban soils are subject to intense anthropogenic disturbance, often resulting in biodiversity loss and reduced ecosystem functionality. However, rhizospheric microbial communities help maintain critical soil-ecosystem services, supporting urban soil resilience. This study evaluated the diversity of culturable bacteria associated with the rhizospheres of Pennisetum clandestinum and Pseudelephantopus spicatus in green areas of Medellín, Colombia, under contrasting levels of anthropic pressures. Rhizospheric and non-rhizospheric soils were sampled near automotive mechanic sites, and bacterial communities were assessed through plate counting and morphological characterization. Alpha, beta, and rarefaction diversity indices were applied to evaluate culturable morphotypes. P. clandestinum supported a more diverse and complex rhizospheric microbiome, particularly in non-exposed soils, while P. spicatus hosted less diverse communities under similar conditions. Diversity indices effectively distinguished microbial patterns, demonstrating the utility of culture-based methods for microbial community assessment. As a first step in microbial bioprospecting workflows, these methods allow for the rapid screening of culturable diversity and support decision-making for the selection of promising environments, plant species, and microbial isolates. This approach can inform urban soil threats, the promotion of beneficial plant–microbe interactions, and the identification of bioindicator species for soil health monitoring in a framework for the management of green areas. Full article

There is a lack of research on screening new strains of high-efficiency ammonia nitrogen degrading bacteria and treating high-concentration ammonia nitrogen aquaculture wastewater using immobilized composite bacteria. In this study, two strains capable of degrading ammonia nitrogen and nitrite were isolated from surface water. The species of the strains were accurately identified using ITS sequencing technology. Scp1 was identified as Pseudomonas and Scr1 as Rhodococcus erythropolis. Both strains were preserved. When the initial concentration of ammonia nitrogen was 1.50 mg/L, the degradation efficiency of ammonia nitrogen after 4 days of inoculation with Scp1, Scr1, and a combination of Scp1 and Scr1 was 90%, 93.3%, and 99.99%, respectively. Similarly, when the initial concentration of nitrite was 0.25 mg/L, the degradation efficiency after 4 days of inoculation with Scp1, Scr1, and a combination of Scp1 and Scr1 was 60%, 82%, and 97.2%, respectively. In addition, when the initial concentration of COD was 20 mg/L, the degradation efficiency after 6 days of inoculation with Scp1, Scr1, and a combination of Scp1 and Scr1 was 59%, 59.4%, and 93.75%, respectively. The results demonstrated that the combined bacteria, Scp1 and Scr1, had a better degradation effect on ammonia nitrogen, nitrite, and COD. Furthermore, a degradation test was conducted in a Penaeus vannamei breeding base, which showed good degradation effects. These findings provide theoretical support for the treatment of high ammonia nitrogen wastewater in aquaculture and have important practical applications. Full article

The rising prevalence of antibiotic-resistant bacteria demands exploration of alternative antimicrobials. Antimicrobial peptides (AMPs) are a promising group of compounds naturally produced by microorganisms and could serve as potent agents against resistant pathogens. In this study, we evaluated the antimicrobial potential of the cell-free supernatant obtained from Pedobacter silvilitoris—a bacterium originally isolated from decomposing wood—and performed comprehensive genomic screening to uncover novel AMP-encoding genes. The supernatant showed strong inhibitory effects against a diverse selection of pathogens. Scanning electron microscopy (SEM) revealed extensive membrane damage, including pore formation in target bacterial cells, suggesting AMP-mediated activity. A genomic analysis identified 11 candidate AMP genes, named PS_AMP1 to PS_AMP11, based on the significant sequence similarity with known AMPs. Transcriptomic profiling further indicated that several candidates are expressed differentially between the logarithmic and stationary growth phases. Functional assays via gene cloning and peptide synthesis confirmed antimicrobial activity against both Gram-stain-negative and Gram-stain-positive bacteria, with PS_AMP11 emerging as the most effective candidate. Our findings demonstrate that AMPs derived from P. silvilitoris hold substantial promise as alternative antimicrobial agents. Nonetheless, additional structural optimizations may be necessary to fine-tune specificity and to reduce potential host toxicity before clinical deployment. Full article

Streptococcus pneumoniae (S. pneumoniae) Sortase A (SrtA) anchors virulence proteins to the surface of the cell wall by recognizing and cleaving the LPXTG motif. These toxins help bacteria adhere to and colonize host cells, promote biofilm formation, and trigger host inflammatory responses. Therefore, SrtA is an ideal target for the development of new preparations for S. pneumoniae. In this study, we found that phloretin (pht) and phlorizin (phz) exhibited excellent affinities for SrtA based on virtual screening experiments. We analyzed the interactive mechanism between pht, phz, and alnusone (aln, a reported S. pneumoniae SrtA inhibitor) and SrtA based on molecular dynamics simulation experiments. The results showed that these inhibitors bound to the active pocket of SrtA, and the root mean square deviation (RMSD) and distance analyses showed that these compounds and SrtA maintained stable configuration and binding during the assay. The binding free energy analysis showed that both electrostatic forces (ele), van der Waals forces (vdw), and hydrogen bonds (Hbonds) promoted the binding between pht, phz, and SrtA; however, for the binding of aln and SrtA, the vdw force was much stronger than ele, and Hbonds were not found. The binding free energy decomposition showed that HIS141, ILE143, and PHE119 contributed more energy to promote pht and SrtA binding; ARG215, ASP188, and LEU210 contributed more energy to promote phz and SrtA binding; and HIS141, ASP209, and ARG215 contributed more energy to promote aln and SrtA binding. Finally, the transpeptidase activity of SrtA decreased significantly when treated with different concentrations of pht, phz, or aln, which inhibited S. pneumoniae biofilm formation and adhesion to A549 cells without affecting normal bacterial growth. These results suggest that pht, phtz, and aln are potential materials for the development of novel inhibitors against S. pneumoniae infection. Full article

Consumer demand for natural, additive-free foods is increasing. Following the trend, this study evaluated the antifungal potential of lactic acid bacteria (LAB) against Penicillium species commonly found in cheese, using both LAB ferments and hydroxypropylmethylcellulose (HPMC) coatings. LAB strains were first screened with a dual-culture assay. Fermentations in Man–Rogosa–Sharpe (MRS) broth and milk whey were lyophilized and tested, with whey-based ferments showing greater antifungal activity. All whey ferments inhibited fungal growth, with KK₁₃, KB₂, KB₃, and KB₄ being the most effective based on MIC and MFC assays. KB₃-fermented whey had the highest levels of antifungal metabolites, such as phenyllactic acid. A coating containing 5% HPMC and 100 g/L of KB₃-fermented whey was applied to cheese slices, reducing the fungal counts of Penicillium commune by more than 1 Log₁₀ CFU per gram and extending shelf life by 12 days. In whole-cheese trials with natural contamination, this coating delayed visible fungal growth until day 60, extending shelf life by 45 days compared with uncoated samples and 33 days compared with coated controls. These findings support the use of LAB-fermented whey and HPMC coatings as natural preservation strategies, thereby contributing to the sustainable reuse of dairy by-products. Full article

Piroplasmids (Babesia spp., Rangelia spp., Theileria spp., Cytauxzoon spp.) are tick-borne apicomplexan protozoa that infect, depending on the species, erythrocytes and leucocytes in a wide variety of mammals and birds. The genera Bartonella and Borrelia include vector-borne bacteria that can infect and cause disease in both animals and humans. Detection of hemotropic bacteria and piroplasmids in wild animals is often challenging due to low bacteremia or parasitemia. Digital (d)PCR has proven to be an effective modality for the detection and quantification of DNA of hemotropic pathogens with low parasitemia. This study compared dPCR results from 366 biological samples from seven different Brazilian wild animal groups (5 Xenarthra species, 5 deer species, 3 felid species, 1 canid species, 3 rodent species, 1 bat species, 1 tapir species, and 12 bird species) to two other molecular diagnostic techniques: quantitative real-time (qPCR) and nested (nPCR). For this study, DNA extracted from wild animal blood and spleen samples were subjected to a multiplex dPCR assay for piroplasmids, Bartonella spp., and Borrelia spp. For comparison, the same primers and probes for each agent were used in qPCR assays. Additionally, an nPCR based on the 18S rRNA gene for piroplasmids was performed. The proportions of positive results obtained using dPCR were 85.5% for piroplasmids, 33.6% for Bartonella spp., and 16.7% for Borrelia spp. For all tested agents, dPCR proved to be the technique with the highest sensitivity, making it a useful tool for screening vector-borne agents in biological samples from wild animals with low parasitemia. Full article

The gut microbiome has a significant role in general health and well-being. Novel types of prebiotics, such as fungal polysaccharides, show potential for the formulation of new synbiotic formulations. However, little is known about the underlying mechanisms of the prebiotic effects of such compounds. This study investigated the prebiotic properties of fungal glucan extracts from Pleurotus ostreatus, Lentinula edodes, and Saccharomyces cerevisiae, employing a novel high-throughput method based on optical density measurements. This approach enabled the simultaneous screening of the effects of multiple extracts on six different strains of probiotic bacteria. Experiments were conducted to evaluate the effect of the extracts on the growth dynamics (the duration of the lag phase and the growth rate) of probiotic strains of the genera Lactobacillus and Lacticaseibacillus and on pathogenic bacteria. Fungal polysaccharide supplementation, particularly with their β-glucans, significantly shortened the lag phase by an average of 7–8 h in all tested strains and increased the growth rate by 2-fold in four strains of lactic acid bacteria. Different magnitudes of effects were observed across the various strain–extract combinations. This study lays the groundwork for elucidating the mechanism by which fungal β-glucans stimulate growth in probiotic bacteria and for the rapid screening of optimal combinations for formulating innovative synbiotics. Full article

To date, the nitrogen metabolism pathways and salt-tolerance mechanisms of halophilic denitrifying bacteria have not been fully studied, and full-scale engineering trials with saline fly ash-washing wastewater have not been reported. In this study, we isolated and screened a halophilic denitrifying bacterium (Marinobacter sp.), GH-1, analyzed its nitrogen metabolism pathways and salt-tolerance mechanisms using whole-genome data, and explored its nitrogen removal characteristics under both aerobic and anaerobic conditions at different salinity levels. GH-1 was then applied in a full-scale engineering project to treat saline fly ash-washing leachate. The main results were as follows: (1) Based on the integration of whole-genome data, it is preliminarily hypothesized that the strain possesses complete nitrogen metabolism pathways, including denitrification, a dissimilatory nitrate reduction to ammonium (DNRA), and ammonium assimilation, as well as the following three synergistic strategies through which to counter hyperosmotic stress: inorganic ion homeostasis, organic osmolyte accumulation, and structural adaptations. (2) The strain demonstrated effective nitrogen removal under aerobic, anaerobic, and saline conditions (3–9%). (3) When applied in a full-scale engineering system treating saline fly ash-washing wastewater, it improved nitrate nitrogen (NO₃⁻-N), total nitrogen (TN), and chemical oxygen demand (COD) removal efficiencies by 31.92%, 25.19%, and 31.8%, respectively. The proportion of Marinobacter sp. increased from 0.73% to 3.41% (aerobic stage) and 2.86% (anoxic stage). Overall, halophilic denitrifying bacterium GH-1 can significantly enhance the nitrogen removal efficiency of saline wastewater systems, providing crucial guidance for biological nitrogen removal treatment. Full article