[VanBUG] Thursday, Sept 13, 6pm - Katherine Pollard, Quantifyin
http://www.ncbi.nlm.nih.gov/pubmed/19383763
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges.
High-throughput sequencing studies and new software tools are revolutionizing microbial community analyses, yet the variety of experimental and computational methods can be daunting. In this review, we discuss some of the different approaches to community profiling, highlighting strengths and weaknesses of various experimental approaches, sequencing methodologies, and analytical methods. We also address one key question emerging from various Human Microbiome Projects: Is there a substantial core of abundant organisms or lineages that we all share? It appears that in some human body habitats, such as the hand and the gut, the diversity among individuals is so great that we can rule out the possibility that any species is at high abundance in all individuals: It is possible that the focus should instead be on higher-level taxa or on functional genes instead.
Environmental Shotgun Sequencing
http://www.plosbiology.org/
In this essay I focus on one particularly promising area of metagenomics—the use of shotgun genome methods to sequence random fragments of DNA from microbes in an environmental sample. The randomness and breadth of this environmental shotgun sequencing (ESS)—first used only a few years ago [10,11] and now being used to assay every microbial system imaginable from the human gut [12] to waste water sludge [13]—has the potential to reveal novel and fundamental insights into the hidden world of microbes and their impact on our world. However, the complexity of analysis required to realize this potential poses unique interdisciplinary challenges, challenges that make the approach both fascinating and frustrating in equal measure.
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