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Title: Exploring Antibiotic resistance genes, mobile Gene elements, and virulence gene factors in an urban freshwater sample using metagenomic analysis
Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people’s lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.
Title: GLOBAL ANALYSIS OF NON-SYNONYMOUS SNPs IN MONKEYPOX VIRUS
In May of 2022, it was determined that a virus known as monkeypox (MPX) had spread over the world. The MPXV strain responsible for 87000 illnesses and 112 fatalities has been identified. This strain had a global average of 38.35 mutations per virus sample, with the 2022 epidemic seeing the highest MPXV mutation rate. Our aim was to use publicly accessible NCBI (National Center for Biotechnology Information) data to explore the genetic diversity and evolutionary history of monkeypox viruses (MPXVs). In-depth comparisons of the genomic characteristics of 376 publicly available complete MPXV genome sequences were performed. Nucleotide sequence variation, gene order, mapping, alignment, and mapping accuracy were among these features. A large amount of sequence conservation was discovered in the MPXV genomes by the meta-analysis, with only a few minor changes between isolates. Multiple genomic regions were discovered to be highly conserved among all MPXV strains, suggesting an essential function in viral replication and persistence. The use of phylogenetic analyses to trace the evolutionary relationships of MPXV strains revealed that the virus has diverged into several subgroups with distinct genetic makeups.
Title: Complete Genome Sequence and Comparative Analysis of Bifidobacterium bifidum Strains Reveal Insight into Probiotic Properties
Despite the widespread use of probiotic supplements for their beneficial health effects, there have recently been some concerns expressed over the absorption and potential colonization of the intestinal tract by the bacteria that these products contain. One of the bacterial species of the genus Bifidobacterium is the strain Bifidobacterium bifidum. One of the most prevalent probiotic bacteria in the bodies of mammals, including humans, is called Bifidobacterium bifidum. Recently, probiotics like Bifidobacterium bifidum have become more and more well-liked. However, it has been the focus of a few studies that demonstrate its efficacy in treating a number of ailments, including dyspepsia and malnutrition. The Bifidobacterium bifidum strain has genes that let the organism tolerate and be resistant to hazardous toxins and some medications, which helps with their capacity to cling to the host. Specialty genes, such as those encoding for vitamins, DNA repair, stress response, amino acids, bacteriocins, phages, and antibiotic tolerance and resistance, are responsible for certain bodily processes in hosts. In our study, eight sequencing datasets produced from Bifidobacterium bifidum sample were subjected to bioinformatic analysis. A particular number of ARGs were connected to integrated mobile genomic elements or prophages that assisted the HGT. In this study, we identified the genes that code for fundamental and significant properties of probiotics in the host, such as the production of bacteriocin and vitamins.
Title: Probiotics, their action modality and the use of multi-omics in metamorphosis of commensal microbiota into target-based probiotics
This review article addresses the strategic formulation of human probiotics and allows the reader to walk along the journey that metamorphoses commensal microbiota into target-based probiotics. It recapitulates what are probiotics, their history, and the main mechanisms through which probiotics exert beneficial effects on the host. It articulates how a given probiotic preparation could not be all-encompassing and how each probiotic strain has its unique repertoire of functional genes. It answers what criteria should be met to formulate probiotics intended for human use, and why certain probiotics meet ill-fate in pre-clinical and clinical trials? It communicates the reasons that taint the reputation of probiotics and cause discord between the industry, medical and scientific communities. It revisits the notion of host-adapted strains carrying niche-specific genetic modifications. Lastly, this paper emphasizes the strategic development of target-based probiotics using host-adapted microbial isolates with known molecular effectors that would serve as better candidates for bioprophylactic and biotherapeutic interventions in disease-susceptible individuals.
DRUG DESIGN & DISC0VERY
Title: Molecular Dynamics Simulation and Pharmacoinformatic Integrated Analysis of Bioactive Phytochemicals from Azadirachta indica (Neem) to Treat Diabetes Mellitus
Diabetes mellitus is a chronic hormonal and metabolic disorder in which our body cannot generate necessary insulin or does not act in response to it, accordingly, ensuing in discordantly high blood sugar (glucose) levels. Diabetes mellitus can lead to systemic dysfunction in the multiorgan system, including cardiac dysfunction, severe kidney disease, lowered quality of life, and increased mortality risk from diabetic complications. To uncover possible therapeutic targets to treat diabetes mellitus, the in silico drug design technique is widely used, which connects the ligand molecules with target proteins to construct a protein-ligand network. To identify new therapeutic targets for type 2 diabetes mellitus, Azadirachta indica is subjected to phytochemical screening using in silico molecular docking, pharmacokinetic behavior analysis, and simulation-based molecular dynamic analysis. This study has analyzed around 63 phytochemical compounds, and the initial selection of the compounds was made by analyzing their pharmacokinetic properties by comparing them with Lipinski’s rule of 5. The selected compounds were subjected to molecular docking. The top four ligand compounds were reported along with the control drug nateglinide based on their highest negative molecular binding affinity. The protein-ligand interaction of selected compounds has been analyzed to understand better how compounds interact with the targeted protein structure. The results of the in silico analysis revealed that 7-Deacetyl-7-oxogedunin had the highest negative docking score of −8.9 Kcal/mol and also demonstrated standard stability in a 100 ns molecular dynamic simulation performed with insulin receptor ectodomain. It has been found that these substances may rank among the essential supplementary antidiabetic drugs for treating type 2 diabetes mellitus. It is suggested that more in vivo and in vitro research studies be carried out to support the conclusions drawn from this in silico research strategy.