Fax +41 61 306 12 34 E-Mail karger@karger.ch www.karger.com Dig Dis 2011;29:525–530 DOI: 10.1159/000332966 Metagenomics: Key to Human Gut Microbiota Simone Maccaferri Elena Biagi Patrizia Brigidi  Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy proaches for the characterization of the human gut microbi- ome in health and disease. Recent and promising results in this field are presented, underlining the perspectives and fu- ture research direction of human gut microbial ecology. Copyright © 2011 S. Karger AG, Basel Studying the Human Gut Microbiota: Advantages and Limits of the Classical Approaches Human beings are colonized by several microbial communities which can have an impact on the host’s health. Different human districts, such as skin, mouth, vagina, airways, and gastrointestinal tract (GIT), harbor specific bacterial ecosystems. Among them, the most rich and complex microbial consortium resides in the GIT, reaching a bacterial concentration of 100–200 billion cells/gram of feces (dry weight), so that the number of bacterial inhabitants within the gut lumen can reach 10 14 . The collective genome of the human microbiota, called the ‘microbiome’, contains about 150 times the number of genes represented in the human genome, endowing human hosts with a wide range of metabolic functions which they did not develop on their own. For this reason, humans can be regarded as ‘metaorganisms’ resulting from millennia of coevolution with the incredible num- Key Words Metagenomics  Gut microbiota  Microbiome Abstract The human gastrointestinal tract harbors the most com- plex human microbial ecosystem (intestinal microbiota). The comprehensive genome of these microbial populations (in- testinal microbiome) is estimated to have a far greater ge- netic potential than the human genome itself. Correlations between changes in composition and activity of the gut mi- crobiota and common disorders, such as inflammatory bow- el diseases, obesity, diabetes, and atopic diseases, have been proposed, increasing the interest of the scientific commu- nity in this research field. In this perspective, a comprehen- sive and detailed view of the human gut microbiota, in terms of phylogenetic composition as well as genetic and meta- bolic potential, is essential to understand the dynamics and possible mechanisms of the cause/effect relationships be- tween gut microbiota and pathology. Metagenomics has emerged as one of the most powerful sequence-driven ap- proaches to study the composition and the genetic potential of this complex ecosystem, and efforts in this direction have been smoothed by the implementation of next genera- tion sequencing platforms. Here, we highlight the potential of the newest high-throughput, culture-independent ap- Patrizia Brigidi Laboratory of Microbiology, Department ofPharmaceutical Sciences University of Bologna, Via Belmeloro 6 IT–40126 Bologna (Italy) Tel. +39 051 2099 743, E-Mail patrizia.brigidi  @  unibo.it © 2011 S. Karger AG, Basel 0257–2753/11/0296–0525$38.00/0 Accessible online at: www.karger.com/ddi