# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 7488 | 0 | 0.8963 | Metagenomic insights into microorganisms and antibiotic resistance genes of waste antibiotic fermentation residues along production, storage and treatment processes. Antibiotic fermentation residue (AFR) is nutrient-rich solid waste generated from fermentative antibiotic production process. It is demonstrated that AFR contains high-concentration of remaining antibiotics, and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals. However, the dominate microorganisms and antibiotic resistance genes (ARGs) in AFRs have not been adequately explored, hampering understanding on the potential antibiotic resistance risk development caused by AFRs. Herein, seven kinds of representative AFRs along their production, storage, and treatment processes were collected, and multiple methods including amplicon sequencing, metagenomic sequencing, and bioinformatic approaches were adopted to explore the biological characteristics of AFRs. As expected, antibiotic fermentation producer was found as the predominant species in raw AFRs, which were collected at the outlet of fermentation tanks. However, except for producer species, more environment-derived species persisted in stored AFRs, which were temporarily stored at a semi-open space. Lactobacillus genus, classified as Firmicutes phylum and Bacilli class, became predominant bacterial taxa in stored AFRs, which might attribute to its tolerance to high concentration of antibiotics. Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species (e.g., Lactobacillus genus) tended to carry ARGs conferring resistance to the remaining antibiotic. However, after thermal treatment, remaining antibiotic could be efficiently removed from AFRs, and microorganisms together with DNA could be strongly destroyed. In sum, the main risk from the AFRs was the remaining antibiotic, while environment-derived bacteria which tolerate extreme environment, survived in ARFs with high content antibiotics, and may carry ARGs. Thus, hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry. | 2024 | 37923454 |
| 8432 | 1 | 0.8903 | A 0D-2D Heterojunction Bismuth Molybdate-Anchored Multifunctional Hydrogel for Highly Efficient Eradication of Drug-Resistant Bacteria. Due to the increasing antibiotic resistance and the lack of broad-spectrum antibiotics, there is an urgent requirement to develop fresh strategies to combat multidrug-resistant pathogens. Herein, defect-rich bismuth molybdate heterojunctions [zero-dimensional (0D) Bi(4)MoO(9)/two-dimensional (2D) Bi(2)MoO(6), MBO] were designed for rapid capture of bacteria and synergistic photocatalytic sterilization. The as-prepared MBO was experimentally and theoretically demonstrated to possess defects, heterojunctions, and irradiation triple-enhanced photocatalytic activity for efficient generation of reactive oxygen species (ROS) due to the exposure of more active sites and separation of effective electron-hole pairs. Meanwhile, dopamine-modified MBO (pMBO) achieved a positively charged and rough surface, which conferred strong bacterial adhesion and physical penetration to the nanosheets, effectively trapping bacteria within the damage range and enhancing ROS damage. Based on this potent antibacterial ability of pMBO, a multifunctional hydrogel consisting of poly(vinyl alcohol) cross-linked tannic acid-coated cellulose nanocrystals (CPTB) and pMBO, namely CPTB@pMBO, is developed and convincingly effective against methicillin-resistant Staphylococcus aureus in a mouse skin infection model. In addition, the strategy of combining a failed beta-lactam antibiotic with CPTB@pMBO to photoinactivation with no resistance observed was developed, which presented an idea to address the issue of antibiotic resistance in bacteria and to explore facile anti-infection methods. In addition, CPTB@pMBO can reduce excessive proteolysis of tissue and inflammatory response by regulating the expression of genes and pro-inflammatory factors in vivo, holding great potential for the effective treatment of wound infections caused by drug-resistant bacteria. | 2023 | 37531599 |
| 8765 | 2 | 0.8902 | Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack. INTRODUCTION: The rhizosphere microbiome is critical to plant health and resistance. PGPR are well known as plant-beneficial bacteria and generally regulate nutrient utilization as well as plant responses to environmental stimuli. In our previous work, one typical PGPR strain, Pseudomonas chlororaphis IRHB3, isolated from the soybean rhizosphere, had positive impacts on soil-borne disease suppression and growth promotion in the greenhouse, but its biocontrol mechanism and application in the field are not unclear. METHODS: In the current study, IRHB3 was introduced into field soil, and its effects on the local rhizosphere microbiome, disease resistance, and soybean growth were comprehensively analyzed through high-throughput sequencing and physiological and molecular methods. RESULTS AND DISCUSSION: We found that IRHB3 significantly increased the richness of the bacterial community but not the structure of the soybean rhizosphere. Functional bacteria related to phosphorus solubilization and nitrogen fixation, such as Geobacter, Geomonas, Candidatus Solibacter, Occallatibacter, and Candidatus Koribacter, were recruited in rich abundance by IRHB3 to the soybean rhizosphere as compared to those without IRHB3. In addition, the IRHB3 supplement obviously maintained the homeostasis of the rhizosphere microbiome that was disturbed by F. oxysporum, resulting in a lower disease index of root rot when compared with F. oxysporum. Furthermore, JA-mediated induced resistance was rapidly activated by IRHB3 following PDF1.2 and LOX2 expression, and meanwhile, a set of nodulation genes, GmENOD40b, GmNIN-2b, and GmRIC1, were also considerably induced by IRHB3 to improve nitrogen fixation ability and promote soybean yield, even when plants were infected by F. oxysporum. Thus, IRHB3 tends to synergistically interact with local rhizosphere microbes to promote host growth and induce host resistance in the field. | 2024 | 38380096 |
| 7947 | 3 | 0.8900 | Molecular insights into linkages among free-floating macrophyte-derived organic matter, the fate of antibiotic residues, and antibiotic resistance genes. Macrophyte rhizospheric dissolved organic matter (ROM) served as widespread abiotic components in aquatic ecosystems, and its effects on antibiotic residues and antibiotic resistance genes (ARGs) could not be ignored. However, specific influencing mechanisms for ROM on the fate of antibiotic residues and expression of ARGs still remained unclear. Herein, laboratory hydroponic experiments for water lettuce (Pistia stratiotes) were carried out to explore mutual interactions among ROM, sulfamethoxazole (SMX), bacterial community, and ARGs expression. Results showed ROM directly affect SMX concentrations through the binding process, while CO and N-H groups were main binding sites for ROM. Dynamic changes of ROM molecular composition diversified the DOM pool due to microbe-mediated oxidoreduction, with enrichment of heteroatoms (N, S, P) and decreased aromaticity. Microbial community analysis showed SMX pressure significantly stimulated the succession of bacterial structure in both bulk water and rhizospheric biofilms. Furthermore, network analysis further confirmed ROM bio-labile compositions as energy sources and electron shuttles directly influenced microbial structure, thereby facilitating proliferation of antibiotic resistant bacteria (Methylotenera, Sphingobium, Az spirillum) and ARGs (sul1, sul2, intl1). This investigation will provide scientific supports for the control of antibiotic residues and corresponding ARGs in aquatic ecosystems. | 2024 | 38653136 |
| 8128 | 4 | 0.8895 | Recognize and assessment of key host humic-reducing microorganisms of antibiotic resistance genes in different biowastes composts. Humic-reducing microorganisms (HRMs) can utilize humic substance as terminal electron mediator promoting the bioremediation of contaminate, which is ubiquitous in composts. However, the impacts of HRMs on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in composts and different HRMs community composition following the types of biowastes effected the spread of ARGs have not been investigated. Herein, the dynamics and mobility of ARGs and HRMs during protein-, lignocellulose- and lignin-rich composting were investigated. Result show that ARGs change significantly at the thermophilic phase, and the relative abundance of most ARGs increase during composting. Seven groups of HRMs communities are classified as primary host HRMs of ARGs, and most host HRMs groups from protein-rich composts. Conclusively, regulating methods for inhibiting ARGs spread for different composts are proposed. HRMs show a higher ARGs dissemination capacity in protein-rich composts than lignocellulose- and lignin-rich composts, but the spread of ARGs can be inhibited by regulate physicochemical parameters in protein-rich composts. In contrary, most HRMs have inhibitory effects on ARGs spread in lignocellulose- and lignin-rich composts, and those HRMs can be used as a new agent that inhibits the spread of ARGs. Our results can help in understanding the potential risk spread of ARGs by inoculating functional bacteria derived from different biowastes composts for environmental remediation, given their expected importance to developing a classification-oriented approach for composting different biowastes. | 2022 | 34600985 |
| 8187 | 5 | 0.8891 | Racial disparities in metastatic colorectal cancer outcomes revealed by tumor microbiome and transcriptome analysis with bevacizumab treatment. Background: Metastatic colorectal cancer (mCRC) is a heterogeneous disease, often associated with poor outcomes and resistance to therapies. The racial variations in the molecular and microbiological profiles of mCRC patients, however, remain under-explored. Methods: Using RNA-SEQ data, we extracted and analyzed actively transcribing microbiota within the tumor milieu, ensuring that the identified bacteria were not merely transient inhabitants but engaged in the tumor ecosystem. Also, we independently acquired samples from 12 mCRC patients, specifically, 6 White individuals and 6 of Black or African American descent. These samples underwent 16S rRNA sequencing. Results: Our study revealed notable racial disparities in the molecular signatures and microbiota profiles of mCRC patients. The intersection of these data showcased the potential modulating effects of specific bacteria on gene expression. Particularly, the bacteria Helicobacter cinaedi and Sphingobium herbicidovorans emerged as significant influencers, with strong correlations to the genes SELENBP1 and SNORA38, respectively. Discussion: These findings underscore the intricate interplay between host genomics and actively transcribing tumor microbiota in mCRC's pathogenesis. The identified correlations between specific bacteria and genes highlight potential avenues for targeted therapies and a more personalized therapeutic approach. | 2023 | 38357363 |
| 8809 | 6 | 0.8889 | Comparison of corrosion behaviour in presence of oral bacteria. The aim of this study was to compare the resistance of the corrosion of dental alloys in a solution containing oral bacteria named Actinomyces viscosus (ATCC19246). In this paper, we explain the choice of this precise species of bacteria, then specify its culture in artificial saliva and the experimental precautions needed to avoid the pollution by other bacteria. The electrochemical behaviour of two dental alloys (Ni-Cr alloy and gold-based alloy) was investigated by electrochemical means in sterile Fusayama artificial saliva (AS), AS enriched with sterile yeast extract (YE) and YE modified by introducing bacteria (AV). Open-circuit potentials, potentiodynamic curves, polarization resistance and impedance spectroscopy are the electrochemical procedures selected for this work. It has thus been shown that the open-circuit potential of the non-precious alloy is always lower than that of the gold precious alloy, and the colonization of metal surface by bacteria caused a drop in open circuit potential. The electrochemical impedance spectroscopy results have shown that the electrolyte resistance decreased between the AS, YE and AV milieu, in the presence of bacteria a slight decrease in polarization resistance was observed with the precious alloy and an increase with the non-precious alloy. The drop in the electrolyte resistance cannot explain the change in polarization resistance. The influence of Actinomyces viscosus might be essentially due to the consumption of oxygen at the metal/electrolyte interface of the specimen. For the non-precious alloy, the absence of oxygen (instigator of corrosion) led to an increase in polarization resistance whereas the slight decrease for the precious alloys might be justified by the organic and inorganic metabolites released by bacteria in to the electrolyte. The scanning electron micrography after electrochemical analysis, confirmed the absence of contaminants. These preliminary results demonstrate the unquestionable influence of this bacteria on the corrosion behaviour of the alloys studied, however, further studies are necessary. | 2001 | 11456067 |
| 7873 | 7 | 0.8887 | Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than hydrochar in an agricultural soil. Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems. | 2023 | 36996986 |
| 9108 | 8 | 0.8886 | Learning from losers. Bacteria can overcome environmental challenges by killing nearby bacteria and incorporating their DNA. | 2017 | 29148975 |
| 9079 | 9 | 0.8885 | Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth. | 2019 | 31749830 |
| 7674 | 10 | 0.8885 | Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing. The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics. | 2024 | 38374282 |
| 8163 | 11 | 0.8885 | Green materials science and engineering reduces biofouling: approaches for medical and membrane-based technologies. Numerous engineered and natural environments suffer deleterious effects from biofouling and/or biofilm formation. For instance, bacterial contamination on biomedical devices pose serious health concerns. In membrane-based technologies, such as desalination and wastewater reuse, biofouling decreases membrane lifetime, and increases the energy required to produce clean water. Traditionally, approaches have combatted bacteria using bactericidal agents. However, due to globalization, a decline in antibiotic discovery, and the widespread resistance of microbes to many commercial antibiotics and metallic nanoparticles, new materials, and approaches to reduce biofilm formation are needed. In this mini-review, we cover the recent strategies that have been explored to combat microbial contamination without exerting evolutionary pressure on microorganisms. Renewable feedstocks, relying on structure-property relationships, bioinspired/nature-derived compounds, and green processing methods are discussed. Greener strategies that mitigate biofouling hold great potential to positively impact human health and safety. | 2015 | 25852659 |
| 8484 | 12 | 0.8883 | Deciphering the acidophilia and acid resistance in Acetilactobacillus jinshanensis dominating baijiu fermentation through multi-omics analysis. Lactic acid bacteria (LAB) are pivotal in constructing the intricate bio-catalytic networks underlying traditional fermented foods such as Baijiu. However, LAB and their metabolic mechanisms are partially understood in Moutai flavor Baijiu fermentation. Here, we found that Acetilactobacillus jinshanensis became the· dominant species with relative abundance reaching 92%, where the acid accumulated rapidly and peaked at almost 30 g/kg in Moutai flavor Baijiu. After separation, purification, and cultivation, A. jinshanensis exhibited pronounced acidophilia and higher acid resistance compared to other LAB. Further integrated multi-omics analysis revealed that fatty acid synthesis, cell membrane integrity, pHi and redox homeostasis maintenance, protein and amide syntheses were possibly crucial acid-resistant mechanisms in A. jinshanensis. Structural proteomics indicated that the surfaces of A. jinshanensis proteases contained more positively charged amino acid residues to maintain protein stability in acidic environments. The genes HSP20 and acpP were identified as acid-resistant genes for A. jinshanensis by heterologous expression analysis. These findings not only enhance our understanding of LAB in Baijiu, providing a scientific basis for acid regulation for production process, but also offer valuable insights for studying core species in other fermentation systems. | 2025 | 39448165 |
| 8553 | 13 | 0.8882 | Unveiling the power of nanotechnology: a novel approach to eliminating antibiotic-resistant bacteria and genes from municipal effluent. The increasing global population and declining freshwater resources have heightened the urgency of ensuring safe and accessible water supplies.Query The persistence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in municipal effluents poses a significant public health threat, exacerbated by the widespread use of antibiotics and the inadequate removal of contaminants in wastewater treatment facilities. Conventional treatment methods often fail to eliminate these emerging pollutants, facilitating their entry into agricultural systems and natural water bodies, thereby accelerating the spread of antimicrobial resistance. To address these challenges, interdisciplinary strategies in water treatment are essential. Nanotechnology has emerged as a promising approach due to its unique physicochemical properties, biocompatibility, and high efficiency in detecting and removing biological and chemical contaminants. Various nanomaterials, including graphene-based structures, Carbon nanotubes (CNTs), noble metal nanoparticles (gold (Au) and silver (Ag)), silicon and chitosan-based nanomaterials, as well as titanium and Zinc oxide (ZnO) nanomaterials, demonstrate potent antimicrobial effects. Moreover, nanosensors and photocatalysts utilizing these nanomaterials enable precise detection and effective degradation of ARB and ARGs in wastewater. This review examines the mechanisms by which nanotechnology-based materials can mitigate the risks associated with antibiotic resistance in urban effluents, focusing on their applications in pathogen detection, pollutant removal, and wastewater treatment. By integrating nanotechnology into existing treatment frameworks, we can significantly enhance the efficiency of water purification processes, ultimately contributing to global water security and the protection of public health. | 2025 | 40512401 |
| 8554 | 14 | 0.8882 | Nanomaterial-Enhanced Hybrid Disinfection: A Solution to Combat Multidrug-Resistant Bacteria and Antibiotic Resistance Genes in Wastewater. This review explores the potential of nanomaterial-enhanced hybrid disinfection methods as effective strategies for addressing the growing challenge of multidrug-resistant (MDR) bacteria and antibiotic resistance genes (ARGs) in wastewater treatment. By integrating hybrid nanocomposites and nanomaterials, natural biocides such as terpenes, and ultrasonication, this approach significantly enhances disinfection efficiency compared to conventional methods. The review highlights the mechanisms through which hybrid nanocomposites and nanomaterials generate reactive oxygen species (ROS) under blue LED irradiation, effectively disrupting MDR bacteria while improving the efficacy of natural biocides through synergistic interactions. Additionally, the review examines critical operational parameters-such as light intensity, catalyst dosage, and ultrasonication power-that optimize treatment outcomes and ensure the reusability of hybrid nanocomposites and other nanomaterials without significant loss of photocatalytic activity. Furthermore, this hybrid method shows promise in degrading ARGs, thereby addressing both microbial and genetic pollution. Overall, this review underscores the need for innovative wastewater treatment solutions that are efficient, sustainable, and scalable, contributing to the global fight against antimicrobial resistance. | 2024 | 39591087 |
| 8767 | 15 | 0.8882 | Poly-γ-glutamic acid enhanced the drought resistance of maize by improving photosynthesis and affecting the rhizosphere microbial community. BACKGROUND: Compared with other abiotic stresses, drought stress causes serious crop yield reductions. Poly-γ-glutamic acid (γ-PGA), as an environmentally friendly biomacromolecule, plays an important role in plant growth and regulation. RESULTS: In this project, the effect of exogenous application of γ-PGA on drought tolerance of maize (Zea mays. L) and its mechanism were studied. Drought dramatically inhibited the growth and development of maize, but the exogenous application of γ-PGA significantly increased the dry weight of maize, the contents of ABA, soluble sugar, proline, and chlorophyll, and the photosynthetic rate under severe drought stress. RNA-seq data showed that γ-PGA may enhance drought resistance in maize by affecting the expression of ABA biosynthesis, signal transduction, and photosynthesis-related genes and other stress-responsive genes, which was also confirmed by RT-PCR and promoter motif analysis. In addition, diversity and structure analysis of the rhizosphere soil bacterial community demonstrated that γ-PGA enriched plant growth promoting bacteria such as Actinobacteria, Chloroflexi, Firmicutes, Alphaproteobacteria and Deltaproteobacteria. Moreover, γ-PGA significantly improved root development, urease activity and the ABA contents of maize rhizospheric soil under drought stress. This study emphasized the possibility of using γ-PGA to improve crop drought resistance and the soil environment under drought conditions and revealed its preliminary mechanism. CONCLUSIONS: Exogenous application of poly-γ-glutamic acid could significantly enhance the drought resistance of maize by improving photosynthesis, and root development and affecting the rhizosphere microbial community. | 2022 | 34979944 |
| 9078 | 16 | 0.8880 | MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. MOTIVATION: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens. RESULTS: We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent. COTANCT: ulyantsev@rain.ifmo.ru. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. | 2018 | 29092015 |
| 8134 | 17 | 0.8877 | Sweet scents from good bacteria: Case studies on bacterial volatile compounds for plant growth and immunity. Beneficial bacteria produce diverse chemical compounds that affect the behavior of other organisms including plants. Bacterial volatile compounds (BVCs) contribute to triggering plant immunity and promoting plant growth. Previous studies investigated changes in plant physiology caused by in vitro application of the identified volatile compounds or the BVC-emitting bacteria. This review collates new information on BVC-mediated plant-bacteria airborne interactions, addresses unresolved questions about the biological relevance of BVCs, and summarizes data on recently identified BVCs that improve plant growth or protection. Recent explorations of bacterial metabolic engineering to alter BVC production using heterologous or endogenous genes are introduced. Molecular genetic approaches can expand the BVC repertoire of beneficial bacteria to target additional beneficial effects, or simply boost the production level of naturally occurring BVCs. The effects of direct BVC application in soil are reviewed and evaluated for potential large-scale field and agricultural applications. Our review of recent BVC data indicates that BVCs have great potential to serve as effective biostimulants and bioprotectants even under open-field conditions. | 2016 | 26177913 |
| 7868 | 18 | 0.8876 | A double-quenching paperclip ECL biosensing platform for ultrasensitive detection of antibiotic resistance genes (mecA) based on Ti(3)C(2) MXene-Au NPs as a coreactant accelerator. The global spread of environmental biological pollutants, such as antibiotic-resistant bacteria and their antibiotic resistance genes (ARGs), has emerged as a critical public health concern. It is imperative to address this pressing issue due to its potential implications for public health. Herein, a DNA paperclip probe with double-quenching function of target cyclic cleavage was proposed, and an electrochemiluminescence (ECL) biosensing platform was constructed using Ti(3)C(2) MXene in-situ reduction growth of Au NPs (TCM-Au) as a coreactant accelerator, and applied to the sensitive detection of ARGs. Thanks to the excellent catalytic performance, large surface area and Au-S affinity of TCM-Au, the ECL performance of CdS QDs have been significantly improved. By cleverly utilizing the negative charge of the paperclip nucleic acid probe and its modification group, double-quenching of the ECL signal was achieved. This innovative approach, combined with target cyclic amplification, facilitated specific and sensitive detection of the mecA gene. This biosensing platform manifested highly selective and sensitive determination of mecA genes in the range of 10 fM to 100 nM and a low detection limit of 2.7 fM. The credible detectability and anti-interference were demonstrated in Yangtze river and Aeration tank outlet, indicating its promising application toward pollution monitoring of ARGs. | 2023 | 37666010 |
| 8436 | 19 | 0.8876 | NIR-Activated Hydrogel with Dual-Enhanced Antibiotic Effectiveness for Thorough Elimination of Antibiotic-Resistant Bacteria. Antibiotic resistance has become a critical health crisis globally. Traditional strategies using antibiotics can lead to drug-resistance, while inorganic antimicrobial agents can cause severe systemic toxicity. Here, we have developed a dual-antibiotic hydrogel delivery system (PDA-Ag@Levo/CMCS), which can achieve controlled release of clinical antibiotics levofloxacin (Levo) and classic nanoscale antibiotic silver nanoparticles (AgNPs), effectively eliminating drug-resistant P. aeruginosa. Benefiting from the photothermal (PTT) effect of polydopamine (PDA), the local high temperature generated by PDA-Ag@Levo/CMCS can quickly kill bacteria through continuous and responsive release of dual-antibiotics to restore sensitivity to ineffective antibiotics. Moreover, AgNPs could significantly improve the efficiency of traditional antibiotics by disrupting bacterial membranes and reducing their toxicity to healthy tissues. A clever combination of PTT and drug-combination therapy can effectively eliminate biofilms and drug-resistant bacteria. Mechanism studies have shown that PDA-Ag@Levo might eliminate drug-resistant P. aeruginosa by disrupting biofilm formation and protein synthesis, and inhibit the resistance mutation of P. aeruginosa by promoting the expression of related genes, such as rpoS, dinB, and mutS. Collectively, the synergistic effect of this dual-antibiotic hydrogel combined with PTT provides a creative strategy for eliminating drug-resistant bacteria in chronic infection wounds. | 2025 | 39760335 |