The continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated with several species that are antibiotic producers. In this study, combination of conventional screening methods with Liquid chromatography- Mass spectroscopy (LC/MS) and metagenomic nanopore sequence analysis have been conducted for the deciphering the active metabolites produced by soil isolate(s). Preliminary soil screening resulted in a Gram-negative isolate identified via 16S ribosomal RNA as Alcaligenes faecalis isolate MZ921504 with promising antimicrobial activities against wide range of MDR gram-positive and gram-negative pathogens. The LC/MS analysis of the metabolites of A. faecalis isolate MZ921504 confirmed the presence of ectoine, bacillibactin, quinolobactin and burkholderic acid. Metagenomics sequence analysis of the soil sample (NCBI GenBank accession PRJNA771993) revealed the presence of conserved biosynthetic gene clusters of ectoine, bacteriocin, bacillibactin, quinolobactin, terpene and burkholderic acid of A. faecalis. In conclusion, A. faecalis isolate MZ921504 is a promising source for antimicrobial metabolites. LC/MS spectral analysis and third generation sequencing tools followed by secondary metabolite gene clusters analysis are useful methods to predict the nature of the antimicrobial metabolites.

The continuous emergence of multidrug-resistant (MDR) pathogens poses a global threat to public health. Accordingly, global efforts are continuously conducted to find new approaches to infection control by rapidly discovering antibiotics, particularly those that retain activities against MDR pathogens. In this study, metagenomic nanopore sequence analysis coupled with spectroscopic methods has been conducted for rapid exploring of the various active metabolites produced by Paenibacillus ehimensis soil isolate. Preliminary soil screening resulted in selection of a Gram-positive isolate identified via 16S ribosomal RNA gene sequencing as Paenibacillus ehimensis MZ921932. The isolate showed a broad range of activity against MDR Gram-positive, Gram-negative, and Candida spp. A metagenomics sequence analysis of the soil sample harboring Paenibacillus ehimensis isolate MZ921932 (NCBI GenBank accession PRJNA785410) revealed the presence of conserved biosynthetic gene clusters of petrobactin, tridecaptin, locillomycin (β-lactone), polymyxin, and macrobrevin (polyketides). The liquid chromatography/mass (LC/MS) analysis of the Paenibacillus ehimensis metabolites confirmed the presence of petrobactin, locillomycin, and macrobrevin. In conclusion, Paenibacillus ehimensis isolate MZ921932 is a promising rich source for broad spectrum antimicrobial metabolites. The metagenomic nanopore sequence analysis was a rapid, easy, and efficient method for the preliminary detection of the nature of the expected active metabolites. LC/MS spectral analysis was employed for further confirmation of the nature of the respective active metabolites.

Human immunodeficiency virus (HIV ) is one of the pathogenic viruses that enter the human body and replicate in T-cells, leading to acquired immunodeficiency syndrome ( AIDS). On the other hand, GB-virus C (GBV-C) is a virus that enters the human body without known pathogenic effects on the human body. It is mostly related to the Flaviviridae family, especially hepatitis C (HCV).To our knowledge, studies show that this virus is not associated with any disease. The viral composition differs from most known RNA viruses as it encodes a single polyprotein. The virus could be transmitted through blood and sexual contact. The GBV-C includes three different strains: GBV-C, Hepatitis G virus (HGV), and non-studied one. HGV strain has been detected in patients with liver cirrhosis. However, there is no evidence that it causes liver disease. GBV-C reduces immunity activation in HIV-infected patients. It has been found that it has a marked effect on the target cell receptors for HIV indicating that it could be studied to design a vaccine against HIV. However, there is a lack of information and studies concerning the virus. Many challenges are faced when developing a vaccine based on a virus. These challenges include safety and efficacy, mechanism of action for GBV-C, immunogenicity, variability in HIV Strains, ethical and regulatory issues, production and delivery, long-term outcomes, and public perception and acceptance. However, bioinformatics techniques can play a crucial role in overcoming these challenges by several methods that are: comparative genomics, epitope mapping, structural bioinformatics, and vaccine design and optimization.

Human immunodeficiency virus (HIV) is a pathogenic virus capable of entering the human body and replicating within T cells, ultimately leading to acquired immunodeficiency syndrome. In contrast, GB-virus C (GBV-C), a member of the Flaviviridae family, also infects humans but, according to current studies, is not associated with any known pathogenic effects. Unlike most RNA viruses, GBV-C encodes a single polyprotein. It is primarily transmitted through blood and sexual contact. GBV-C comprises three strains: GBV-C, hepatitis G virus (HGV), and other less-studied strains. The HGV strain has been detected in patients with liver cirrhosis; however, there is no evidence that it causes liver disease. Notably, GBV-C reduces immune activation in HIV-infected patients. It has been shown to have a significant effect on the target cell receptors for HIV, indicating its potential as a model for vaccine development against HIV. However, there is a lack of information and studies concerning this virus. GBV-C-based vaccine development faces many challenges, such as concerns about safety and efficacy, limited understanding of its mechanisms of action and immunogenicity, HIV strain variability, ethical and regulatory considerations, production and delivery logistics, long-term outcomes, and public perception and acceptance. Nevertheless, bioinformatic techniques can play a crucial role in overcoming these challenges through approaches such as comparative genomics, epitope mapping, structural bioinformatics, and vaccine design and optimization.