Abstract: Metagenomics is the comprehensive genomic study of the collective microbial communities retrieved directly from diverse sample types with the purpose of understanding their genetic diversity, population structure, and ecological importance. Over the last two decades, clinical metagenomics has emerged as a new frontier powerful tool that is rapidly transferring from research to clinical laboratories. This emerging approach is widely applied in the field of microbiological diagnostics for etiological diagnosis, antimicrobial resistance, transcriptome, and the microbiome analysis. Here we are presenting national local data highlighting the importance of metagenomic analysis in health/disease and health care environments providing insight into their microbial communities. Thus, clinical microbiologists, infectious disease experts, and epidemiologists can benefit from such studies in the field of medicine by understanding host and microbes interactions and exploring new approaches in managing diseases.