PLoS has made it’s first foray into ‘book’ publishing, with it’s new collection from PLOS Computational Biology called Translational Bioinformatics.
I think this is a great idea, and as founding editor Phil Bourne points out, are a far better option for both readers and authors than the ‘traditional’ science books made up of contributed chapters, which are hard to access, expensive and rarely cited.
Of particular interest to us in the microbial world is Chapter 12: Human Microbiome Analysis by Xochitl C. Morgan, Curtis Huttenhower from Harvard.
Being a book-chapter-style document, it includes some really useful ‘extras’ including questions to get you thinking about what you’ve learnt from the article (and answers in the supplementary), a useful glossary and pointers for further reading.
Because it is PLoS, I can show you exactly what is in it:
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, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.
Citation: Morgan XC, Huttenhower C (2012) Chapter 12: Human Microbiome Analysis. PLoS Comput Biol 8(12): e1002808. doi:10.1371/journal.pcbi.1002808
What to Learn in This Chapter
- An overview of the analysis of microbial communities
- Understanding the human microbiome from phylogenetic and functional perspectives
- Methods and tools for calculating taxonomic and phylogenetic diversity
- Metagenomic assembly and pathway analysis
- The impact of the microbiome on its host
2. A Brief History of Microbiome Studies
3. Taxonomic Diversity
4. Shotgun Sequencing and Metagenomics
5. Computational Functional Metagenomics
6. Host Interactions and Interventions