Food Science and Technology Department


Date of this Version



Published in Izard, J., & Rivera, M.C., eds., Metagenomics for Microbiology (Academic Press, 2015), pp xi-xii.

doi 10.1016/B978-0-12-410472-3.00015-4

Online @


Copyright © 2015 Elsevier Inc. Used by permission.


It is well known that only a small fraction of extant microbial life has been identified. Metagenomics, the direct sequencing and characterization of genes and genomes present in complex microbial ecosystems (e.g., metagenomes), has revolutionized the practice of microbiology by bypassing the hurdle of pure culture isolation. Metagenomics shows promise of advancing our understanding of the diversity, function, and evolution of the uncultivated majority.

Metagenomics as a field arose in the 1990s after the application of molecular biology techniques to genomic material directly extracted from microbial assemblages present in diverse habitats, including the human body. The application of metagenomic approaches allows for the acquisition of genetic/genomic information from the viruses, bacteria, archaea, fungi, and protists forming complex assemblages. The field of metagenomics addresses the fundamental questions of which microbes are present and what their genes are potentially doing.

In the mid-2000s, the availability of high-throughput or next-generation sequencing technologies propelled the field by lowering the monetary and time constraints imposed by traditional DNA sequencing technologies. These advances have allowed the scientific community to examine the microbiome of diverse environments/habitats, follow spatial and temporal changes in community structure, and study the response of the communities to treatment or environmental modifications. In 2012, the publication of the large-scale characterization of the microbiome of healthy adults created high expectations about the influence of the microbiota in human health and disease. With the publication of the results of the Human Microbiome Project, metagenomics has emerged as a major research area in microbiology, particularly, when it comes to the characterization of the role of microbiota in complex disorders, such as obesity. With contributions by leading researchers in the field, we provide a series of chapters describing best practices for the collection and analysis of metagenomic data, as well as the promises and challenges of the field. The chapters have been dedicated to different aspects of metagenomics.