Stromatinia cepivora (Berk.) Whetzel, the causal agent of onion white rot, is a devastating disease globally affecting onion crop production, leading to considerable losses. Control of S. cepivora is difficult due to its sclerotial high survival rate that can extend for decades in the soil. In this study, forty-nine Trichoderma species were isolated from the rhizosphere and tissues of 25 plant species collected from different sites across four Egyptian governorates. The antagonistic activity of all isolated Trichoderma strains was screened against S. cepivora BYAN1 in vitro. Microscopic examination showed that isolate B3R12 (identified as T. afroharzianum B3R12) has the greatest mycoparasitic level. Moreover, this isolate showed high in vitro inhibitory effect on S. cepivora BYAN1 growth by the production of both volatile and nonvolatile antifungal metabolites, recording inhibition of 74.32 % and 71.68 %, respectively. In the greenhouse experiment, T. afroharzianum B3R12 culture filtrate led to complete reduction in disease severity in the pretreated onion plants. In addition, pretreating onion plants with T. afroharzianum B3R12 enhanced several plant growth parameters and photosynthesis pigments, and increased total protein, carbohydrates, phenols, and flavonoid contents. Our results suggested that T. afroharzianum B3R12 represents a promising bioagent for biocontrol of onion white rot and promoting the plant growth; however, field evaluation in the future studies is necessary before the final recommendation.

Metagenomics is an important technique for discovering and screening significant bioactive compounds such as polyketide synthases, non-ribosomal peptide synthetases, antibiotics, and biocatalysts. The enormous potential of microbial diversity in coastal lagoons remains untapped because of the difficulty of culturing many microorganisms under laboratory conditions. Therefore, this study aimed to decipher the structural and functional diversity of microbial communities, including un-culturable species in lagoon sediments collected from Tam Giang, Nai, and Thi Nai lagoons, which were located in the central coast of Vietnam using metagenomics approach. The results showed that all three large lagoons exhibited a high diversity of fungal species among the eukaryotic species and a high diversity of bacterial and archaeal species. Among them, the most prominent phyla included Ascomycota (fungal phyla), Firmicutes and Proteobacteria (bacterial phyla), and Thaumarchaeota (archaeal phyla). Sequencing of the metagenome samples of microbiome in the three lagoons of Tam Giang, Nai, and Thi Nai using shotgun sequencing technology revealed the existence of 126 potential gene sequences from the Tam Giang lagoon, 346 sequences from the Nai lagoon, and 341 sequences from the Thi Nai lagoon. These sequences participated in various metabolic processes and belonged to more than 30 groups of biologically active compounds. Most of these genes were related to antibacterial, antifungal, antiviral, cancer cell inhibition, and antioxidant activities. This is the first study conducted on lagoon microorganisms in Vietnam, opening up prospects and potential in exploiting microorganisms and biologically active substances with important applications in life from the lagoon ecosystems of Vietnam in particular and the overall world in general.

During analyzing morbidity data, it is obvious that the ratio of infections has decreased significantly since the beginning of the 20th century, but the proportion of metabolic and inflammatory diseases has increased. This may be related to the degradation of soils. At the same time, mobilization of nutrient elements primarily depends on the activity of soil microbiota, which is subjected to negative anthropogenic impact. Although plant nutritional value has a direct impact on human health; however, modern agricultural practices that aimed at deep cultivation are causing disturbances in the soil microbiota composition. Subsequently, this resulted in maladaptation of the human immune system, as contacts with xenobiotics occur instead of evolutionarily calibrated interactions; potentially endangering the gut microbiota. This review aims to represent recent data on the relationships among human intestinal, soil, and plant microbiota. Nowadays, it is evident that there is a broad range of influences on human health not only from intestinal microbiota but also from its connection with the environmental microbiota (i.e., soil microorganisms in particular). Today, with respect to the background of active use of modern technologies, including genetical ones, we have the opportunity to examine such volumes of data that will allow us to fully analyze microbiological diversity of the different ecological niches in terms of their common features, differences, and mutual influences. Such studies will make it possible to identify potential factors determining the composition of microbiota in different loci, assess their potential impact on human health, and adjust methods to diagnose and restore the optimal composition of human, plant, and soil microbiota.

Bimetallic nanoparticles (BNPs) have garnered a great interest rather than monometallic nanoparticles (NPs) in terms of biotechnological applications due to their enhanced properties. They have a growing interest as promising biomedical agents for drug delivery, antibacterial, and anticancer treatments due to their significant permeability and retention effects. Both of nano-size copper (Cu) and selenium (Se) exhibited a significant activity in biological treatment and drug delivery systems. Consequently, the present work aimed to focus on the novel biogenic synthesis of Cu-Se BNPs using cell-free extract of a marine bacterium, and studying their anticancer and antioxidant activities. Based on 16S rDNA sequencing, the isolated marine bacterium was identified Bacillus amyloliquefaciens by phylogenetic analysis. Biogenic synthesis of Cu-Se BNPs was optimized by studying the effect of some physiological factors such as reaction time, pH, and temperature. Based on the reaction conditions, the biologically synthesized Cu-Se NPs was obtained with different particle size that ranged from 15.7-106.0 nm. The spherical small sized (15.7 nm) bimetallic Cu-Se BNPs displayed anticancer activity against HepG2 and MDA cell lines, while the cell viability was reduced by 87 % and 81 %, respectively. The estimated IC 50 values were 696.4 µg/ ml for HepG2 and 273.9 µg/ ml for MDA, while scavenging capacity (SC) of Cu-Se BNPs (SC 50 = 305.3 µM) showed lower ability to 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) scavenging compared to ascorbic acid (SC 50 = 95.9 µM).

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The Enterobacteriaceae is a large family of bacteria that includes many important bacterial pathogens known for their high virulence and contributions to the global antimicrobial resistance threat. We aimed, through this study, to provide a comparative overview of the genomes, resistance determinants, and stress signaling pathway of 22 enterobacterial clinical isolates. Our results showed that Escherichia coli harbored the lowest percentage of core genes (44 % versus 58 % in Salmonella enterica, and 52 % in Klebsiella pneumoniae) and the highest percentage of strain-specific genes (31 % versus 18 % in S. enterica and 24 % in K. pneumoniae). All bacterial strains included in the analysis encoded genes for resistance to commonly used antibacterials, including cell envelope acting antibiotics, aminoglycosides, quinolones, and sulphonamide. The resistance genes showed different distributions among the core, dispensable and/or strain-specific genomes, ranging from an almost equal distribution in E. coli and S. enterica to higher occurrence in the dispensable/ strain specific genome in K. pneumoniae. Depending on the bacterial genus, cell envelope acting antibiotics occupied between 15 % -30 % of the core genome resistome. In addition, the sequence diversity of different proteins of the signalling pathway "the regulator of colanic acid capsule synthesis" (Rcs), which is involved in sensing and responding to cell envelope threats was examined. High diversity of two domains in Rcs system proteins (i.e., IgaA first cytosolic domain and RcsD pseudokinase) was observed despite high conservation of all other proteins. All these differences might point out to specific adaptation strategies of the studied bacterial isolates to antibiotic exposure and ecological niche variation.

In recent decades, microbial resistance to antimicrobial drugs has emerged as a global health crisis. Therefore, it is crucial to develop alternative therapeutic strategies to address the growing threat of multi-drug resistant (MDR) pathogens. Researchers and clinicians are increasingly focusing on plant-based products due to their antibiotic properties and lack of associated antibiotic resistance. Plant-based nanoparticles present several benefits, including their natural origin, biocompatibility, and potential for targeted delivery. Our aims in this review were exploration of the complexities and limitations of plant-based phytochemical extraction processes and addressing the challenges of synthesizing nanoparticles for combating multidrug-resistant (MDR) pathogens. It also examined the effectiveness of phytobased nanoparticles in drug delivery systems to treat MDR infections; both alone and in combination with antibiotics, and provided a critical assessment of their potentials as a research avenue. For this, we have taken the diverse methodologies that were previously used to select the best possible process to tackle MDR pathogens using plant extracts. Although using plant-derived products and nanoparticles is a novel approach to address the antimicrobial drug resistance; however, detailed researches are necessary to explore their antibacterial attributes. Specifically, transcriptome profiling should be employed to identify therapeutic molecules from plant-based products that can effectively combat MDR bacteria before synthesis of nano-drugs. The outcomes of this study will enable the researchers to obtain the best approaches to tackle MDR pathogens through using the nano-based phytochemicals.

Numerous common human disorders, including cancer, high blood pressure, high cholesterol, inflammatory bowel diseases, obesity, and oral health issues, have been linked to changes in the composition and activity of the gut microbiota. This review aimed to highlight the significance of probiotics due to their positive impacts on gut microbiota, overall human health, cancer prevention, and production of bioactive compounds. Therefore, modifying the gut microbiota's balance can be highly beneficial for maintaining the human health. Probiotics are live microbial supplements, when consumed with meals; they help the host by harmonizing his/ her intestinal microflora. Supplements containing these good bacteria can be used up, or they can be added to dairy-free or non-dairy foods and drinks. Probiotics are mainly categorized into two main genera; mainly Lactobacillus spp. and Bifidobacterium spp. Probiotics are vital for maintaining a healthy microbiota; especially in cancer patients. They enhance the production of anticancer enzymes, apoptosis, autophagy, immunology, and other processes. Additionally, probiotics produce various bioactive molecules such as short-chain fatty acids, enzymes, vitamins, and exopolysaccharides with antibacterial attributes. Consequently, probiotics are utilized in food technology to develop the functional foods that promote the human health.

The emergence of multidrug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), poses a significant threat to the global public health. Streptomyces species have been recognized as a prolific source of bioactive secondary metabolites, including antimicrobial compounds. In this study, we aimed to optimize the production of anti-MRSA compounds by Streptomyces sp. AR05; a strain isolated from hydrocarbon-contaminated soil, using an integrated approach combining response surface methodology (RSM), artificial neural networks (ANN), and genetic algorithms (GA). The strain was identified through 16S rRNA gene sequencing and exhibited significant genetic similarity to Streptomyces kurssanovii and Streptomyces ostreogriseus. Using the PlackettBurman design, the most important variables affecting the anti-MRSA activity were found to be peptone, CaCO3, and pH. These factors were optimized using Box-Behnken design, while RSM and ANN were utilized for modeling the experimental data. The predicted accuracy of ANN model was higher than that of the RSM model, with lower values of mean absolute percentage error (MAPE) and root mean square error (RMSE). Sensitivity analysis of the ANN model identified peptone as the most influential factor, followed by pH and CaCO3. The ANN model was further optimized using GA, and the optimized conditions (5.34 g/ l peptone, 1.54 g/ l CaCO3, pH 6.07) were experimentally validated, resulting in a 48.87 % increase in anti-MRSA activity compared to the initial conditions. The developed RSM-ANN-GA approach demonstrated the potential for enhancing the production of valuable antibacterial compounds from Streptomyces species and contributed to the global efforts to combat antimicrobial resistance.

Helicobacter pylori, a bacterial pathogen that causes severe gastric diseases, has developed antibiotics resistance; mainly against clarithromycin. Consequently, the latest international recommendations have advised clarithromycin susceptibility testing before prescribing the first line of therapy. This resistance is predominantly related to the A2143G point mutation of 23S rRNA. The aim of this study was to develop a highly sensitive and cheap molecular technique to detect H. pylori clarithromycin resistant strains. For that, plasmids of H. pylori 23S rRNA region harboring A2143G point mutation were constructed and used to develop polymerase chain reaction coupled with a high-resolution melting technique (PCR-HRM). Then, this method was applied on 233 gastric H. pylori positive samples. The obtained results showed that the developed PCR-HRM technique allowed specific identification of clarithromycin resistant and heteroresistant H. pylori samples, even if the ratio of resistant/ sensitive samples was low. In this series, the detected rate of H. pylori clarithromycin resistance was 7.6 %, which concord with the resistance rate determined using molecular sequencing. So, the developed PCR-HRM represents a good tool for detecting resistant and sensitive H. pylori samples and can be used in routine clinical practices. This will help in managing H. pylori infection, increase its eradication rate, and avoid the use of therapeutic protocols that have serious side effects.