Education Chapter 12: Human Microbiome Analysis

Abstract: Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, ar-chaeal, fungal, and viral. Under normal circumstances, these mi-crobes help us to digest our food and to maintain our immune sys-tems, but dysfunction of the hu-man microbiota has been linked to conditions ranging from inflamma-tory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioin-formatic tools provide a powerful means of understanding the con-tribution of the human microbiome to health and its potential as a target for therapeutic interven-tions. This chapter will first discuss the historical origins of microbiome studies and methods for determin-ing the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metage-nomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable micro-biome analysis. Finally, it will con-clude with examples of the func-tional genomics of the human microbiome and its influences up-on health and disease. This article is part of the ‘‘Transla-tional Bioinformatics’ ’ collection fo