Abstract:
The development of genome-sequencing technologies, especially the application of next-
generation sequencing (NGS), has accelerated the study of complex microbiota.
Metagenomics plays a crucial role in expanding our knowledge of the microbial world, has
numerous applications across various fields, and holds the potential to address pressing global
challenges in health, the environment, and biotechnology.
This new approach has the potential to uncover novel enzymes, pathways, and molecules with
industrial applications. Furthermore, by analyzing metagenomic data, researchers can identify new
natural products with therapeutic potential. Many antibiotics, antivirals, and other pharmaceuticals
have been discovered through metagenomic approaches.
This work is intended to introduce different research methods to study complex microbiota, with
a specific focus on the current progress and application of metagenomics.
We discuss here computer programs used in metagenomics such as MEGAN, Kraken and MePIC
that allow analysis of large data sets by a single scientist.
We also highlight the necessity to begin studying complex infections using metagenomics
approach, which is essential for better understand the host–bacterial interactions
