Steps in Metagenomics: Let’s Avoid Garbage in and Garbage Out

Authors

Jacques Izard, University of Nebraska–LincolnFollow

ORCID IDs

https://orcid.org/0000-0002-5904-5436

Date of this Version

2015

Citation

Published (as Chapter 1) in Izard, J., & Rivera, M.C., eds., Metagenomics for Microbiology (Academic Press, 2015), pp 1–23. doi 10.1016/B978-0-12-410472-3.00001-4

Online @ https://doi.org/10.1016/B978-0-12-410472-3.00001-4

Comments

Copyright © 2015 Elsevier Inc. Used by permission.

Abstract

Is metagenomics a revolution or a new fad? Metagenomics is tightly associated with the availability of next-generation sequencing in all its implementations. The key feature of these new technologies, moving beyond the Sanger-based DNA sequencing approach, is the depth of nucleotide sequencing per sample.¹ Knowing much more about a sample changes the traditional paradigms of “What is the most abundant?” or “What is the most significant?” to “What is present and potentially sig­nificant that might influence the situation and outcome?” Let’s take the case of identifying proper biomarkers of disease state in the context of chronic disease prevention. Prevention has been deemed as a viable option to avert human chronic diseases and to curb health­care management costs.² The actual implementation of any effective preventive measures has proven to be rather difficult. In addition to the typically poor compliance of the general public, the vagueness of the successful validation of habit modification on the long-term risk, points to the need of defining new biomarkers of disease state. Scientists and the public are accepting the fact that humans are super-organisms, harboring both a human genome and a microbial genome, the latter being much bigger in size and diversity, and key for the health of individuals.^3,4 It is time to investigate the intricate relationship between humans and their associated microbiota and how this relationship mod­ulates or affects both partners.⁵ These remarks can be expanded to the animal and plant kingdoms, and holistically to the Earth’s biome. By its nature, the evolution and function of all the Earth’s biomes are influenced by a myriad of interactions between and among microbes (planktonic, in biofilms or host associated) and the surrounding physical environment.

The general definition of metagenomics is the cultivation-indepen­dent analysis of the genetic information of the collective genomes of the microbes within a given environment based on its sampling. It focuses on the collection of genetic information through sequencing that can target DNA, RNA, or both. The subsequent analyses can be solely fo­cused on sequence conservation, phylogenetic, phylogenomic, function, or genetic diversity representation including yet-to-be annotated genes. The diversity of hypotheses, questions, and goals to be accomplished is endless. The primary design is based on the nature of the material to be analyzed and its primary function.