Metagenomic studies have truly revolutionised biology and medicine, and changed the way we study genomics. As genome sequencing becomes cheaper, it is being applied to study complex metagenomes. 'Metagenome' is the genetic material recovered directly from an environmental sample or niche. By delivering fast, cheap, and large volumes of data Next Generation Sequencing (NGS) platforms have facilitated a deeper understanding of the fundamentals of genomes, gene functions and regulation. Metagenomics, also referred to as environmental or community genomics, has brought about radical changes in our ability to analyse complex microbial communities by direct sampling of their natural habitat paving the way for the creation of innovative new areas for biomedical research. Many metagenomic studies involving the 'human microbiome 'have been undertaken to date. Samples from of a number of diverse habitats including different human body sites have been subject to metagenomic examinations. Huge national and international projects with the purpose of elucidating the biogeography of microbial communities living within and on the human body, are well underway. The analysis of human microbiome data has brought about a paradigm shift in our understanding of the role of resident microflora in human health and disease and brings non-traditional areas such as gut ecology to the forefront of personalised medicine. In this chapter, we present an overview of the state-of-the-art in current literature and projects pertaining to human microbiome studies.
Keywords: microbiome, metagenome, biomarkers, genome sequencing, human health, omics
The human microbiome--the complex population of microbial species including bacteria, archaea, viruses and micro-eukaryotes that reside on and in the human body--has recently come to the forefront as being integral for human health and disease. Diet, age and environmental factors have been shown to be important in regulating the microbiome which, in turn, can exert both positive and negative effects on the host. The study of microbiomes has stimulated work on several other aspects of microbial communities and launched fields of study such as metaproteomics and metatranscriptomics. Many of the earlier studies on microbial diversity on the human body employed 16S rRNA gene diversity studies as the preferred tool--this was driven primarily by the high costs associated with sequencing technologies. As sequencing became cheaper, whole genome shotgun (WGS) approaches also known as metagenomic surveys became a dominant force in the evaluation of microbial diversity in any environment of choice. Metagenomics has considerably enhanced our understanding of the extent and role of microbial diversity in natural habitats and in ecologically important environments with far greater implications on human health and disease.
Building on the early diversity surveys, and one that showed extensive diversity in two individuals (1), two large international studies and several smaller ones have been launched to investigate the microbiota associated with the human.
1. The National Institutes of Health Human Microbiome Project (2) has only recently completed a survey of the human microbiome (2-4) (https://commonfund.nih.gov/hmp/). This survey of the healthy microbiome revealed extensive diversity between body sites and between people. The final publications from this study represented a population of 242 healthy adults sampled at 15 or 18 body sites and provided 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 terabases of metagenomic sequence. The study design allowed for a streamlined sample collection, DNA extraction, sequencing and data analysis across all the sequencing centres that were involved (Baylor College of Medicine, The J. Craig Venter Institute (JCVI), Broad Institute, Washington University). As a result of extensive quality control and standardisation the data that was being released to the public databases were of the highest quality possible (5). …