Genome-resolved metagenomics: a game changer for microbiome medicine

Abstract

Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones. The human body houses numerous microbes, tiny organisms, that are vital for our health. This research aims to overcome limitations using genome-resolved metagenomics, a method that assembles complete genomes from complex microbial communities without needing to grow the organisms in a lab. The study focuses on the gut microbiome, using advanced computer methods to build metagenome-assembled genomes from DNA sequencing data. The research successfully increased the genetic diversity of the human gut microbiome by adding many new genomes to the existing database. The main findings include identifying new microbial species and expanding the genetic repertoire of known species, providing deeper understanding of the microbial diversity within the human gut. Researchers conclude that genome-resolved metagenomics is a significant advancement in microbiome research, offering understanding of microbial communities and their functions. This summary was initially drafted using artificial intelligence, then revised and fact-checked by the author.