[Frontiers in Bioscience 14, 3214-3221, January 1, 2009]

Microbial diversity in the human intestine and novel insights from metagenomics

Marco Ventura1, Francesca Turroni1, Carlos Canchaya1, Elaine E. Vaughan2, Paul W. O'Toole3, Douwe van Sinderen3

1Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Italy, 2Unilever Food and Health Research Institute (UFHRI), 3Alimentary Pharmabiotic Centre and Department of Microbiology, University College Cork, Western Road, Cork, Ireland

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Microbiota diversity of the human git as determined by molecular methods based on 16S rRNA
4. Factors influencing the composition of the gastro intestinal microbiota
5. Development of the human intestinal microbiota
6. Microbial diversity assessed by compositional metagenomics
6.1. Advantages and disadvantages of 16S rRNA- and metagenomic clone library-based diversity approaches
7. Conclusions
8. Acknowledgments
9. Reference

1. ABSTRACT

Bacterial communities reside in very different ecological niches on and within the human host, such as those associated with the alimentary tract. The human gastrointestinal tract is populated with as many as 100 trillion bacterial cells, whose collective genome likely reflects the co-evolution between the microbial community and its host. Recent progress has highlighted the intriguing diversity of these bacterial populations and their important contributions to human physiology. Thus, a thorough understanding of the autochthonous component of the intestinal microbiota is expected to provide crucial information not only on how to develop therapies for various gastrointestinal diseases but also on how to choose the next generation of probiotic bacteria as part of novel functional foods. Recently, novel culture-independent approaches such as metagenomics-based techniques were shown to be crucially important for the exploration of the biodiversity of the human intestinal microbiota.