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Abstract: Many methods have been developed for studying and comparing bacterial diversity. These methods suffer from a number of drawbacks. Culture-dependent methods have a drawback that only a small number of bacteria can be cultured. Although many modifications in the traditional cultivation approach have been made, such as the use of gellan instead of agar and high throughput dilution to extinction culturing, but a large fraction of microbes still remain uncultured. Culture-independent methods were developed to explore uncultured bacterial diversity but they have their own drawbacks. PCR-based methods have biases during DNA extraction and the removal of substances that may inhibit polymerase activity during PCR and digestion with restriction enzymes. “Omics” approach, i.e., metagenomics, metatranscriptomics, and metaproteomics, aim to link bacterial community structure with function. Different combinations of methods can be used to know more precisely about the bacterial diversity. To date, no known method can reveal the exact bacterial diversity of different environments. This lacuna needs to be filled and newer methods must be developed that can help in exploring the immense bacterial diversity created by nature.