What is the microbiome?

There has been an explosion in our understanding of the human microbiome (the genome of all our microbes) in the recent years. Advances in genome sequencing technologies and metagenomic analysis (genetic study of genomes taken directly from environmental samples) have enabled scientists to study these microbes and their function and to research microbiome–host interactions both in health and disease. The human microbiome has an estimated 100 trillion microbes, the bulk of which live in our gut. This summary gives an overview about what is known about the microbiota (microbial community) in paediatric practice. This short article is written for the practising paediatrician. For a scientific overview, the reader is referred to reviews.1 ,2 An understanding of this complex ecological community is important as it affects our patients, and manipulation of the gut microbiome has the potential to be used in the treatment of childhood diseases in the future. The human microbiome is composed of communities of bacteria (and viruses and fungi) that have a greater complexity than the human genome itself. Large-scale metagenomic projects (community and environmental genomics), such as the European Metagenomics of the Human Intestinal Tract and the Human Microbiome Project, have reported 3.3 million unique protein-encoding genes as compared with the entire human genome, which has around 23 000 genes. These studies have described the beneficial functions of the normal gut microbiota on health down to the genetic level.3 The human microbiome has extensive functions such as development of immunity, defence against pathogens, host nutrition including production of short-chain fatty acids important in host energy metabolism, synthesis of vitamins and fat storage …