Metagenomics in Microbial Diversity Studies: Advances and Challenges

Abstract

The advent of metagenomics has proven to be an invaluable tool in studying microbial diversity in an effort to understand the collective genetic information of microbial communities without having to culture them. In this review, I will highlight some of the developments, applications, and challenges in using metagenomics to understand human microbial diversity with regards to taxonomic and functional diversity, geographic and demographic variation, uncultured microorganisms, metagenome-assembled genomes, strain-level diversity, sequencing technology, and bioinformatics. With the emergence of metagenomics, human-based studies such as the Human Microbiome Project and gut microbiome investigations have shown great microbial diversity among anatomical regions, individuals, and different populations and have led to the discovery of many unknown microorganisms and microbial genes. Further advancements in shotgun metagenomics, long-read sequencing, genome assembly, and metatranscriptomics have provided even better tools for characterizing microbial genomes and their metabolisms and functions. However, there are still important challenges such as incomplete databases, host DNA contamination, geographic and demographic biases, sequencing and computational needs, methodology variations, and differentiating between microbial genetic capacity and biological activities. The review highlights the need for standardized methodologies, diverse and longitudinal human-based datasets, improved microbial genome resources, strain-resolved analysis, and integration of multi-omics approaches. Overall, metagenomics provides an essential framework for advancing the comprehensive understanding of human microbial diversity and its functional significance.