Traditional microbiology focused on clonal cultures of single microorganism. However, it is now well established that majority of the microbes existing in the world could not be laboratory cultivated while playing essential roles in human life. Therefore, the newly emerged metagenomic method poses an important approach to explore the fantastic world of unculturable microorganisms. With the power of modern genomic techniques the metagenomic approach directly analyze the collective nucleotide contents of the entire microbial community (i.e. the metagenome), bypassing the need for isolation and lab cultivation of individual species the metagenomic method was easily applicable only after the advent of next-generation sequencing (NGS) technologies, which have dramatically improved the speed and cost-effectiveness of DNA sequencing some associated techniques need substantial improvements to facilitate further applications of metagenomic approach for microbial identification. Efficient methods for microbe enrichment are essential to circumvent the high human contamination as currently encountered in many studies. In addition, optimized bioinformatics tools for accurate binning, assembly and annotation from the metagenomic data are also urgently required