Health Research and Policy

Abstract

DATE: January 16, 2014
TIME: 1:15 - 3:00 pm
LOCATION: Medical School Office Building, Rm x303
TITLE: An Introduction to Current Methods for Understanding (Human) Microbiomes
SPEAKER: Paul J. McMurdie, Postdoctoral Fellow
Computational Microbiology,
Department of Statistics, Stanford

The term `microbiome' refers to the ecosystem of microorganisms that live in a defined environment. The development of culture-independent methods in microbiology coupled with the decreasing cost and increasing speed of DNA sequencing technology has revolutionized our understanding about the role of microbiomes inhabiting our planet as well as our own bodies, whether healthy or sick. Indeed, we now consider microorganisms to play an important role in virtually every known ecosystem, from the open ocean to plant roots; from wastewater treatment tanks to numerous sites in the human body. In the opening portion of this workshop I will summarize key technological and biological breakthroughs in our understanding of microbiomes. After the coffee break, I will transition from this foundation and motivation into an overview of the most common statistical procedures in the field, as well as some drawbacks and alternatives. Special emphasis will be on available data resources, software tools, and improved practices for normalization, independent filtering, and integrating heterogenous datasets in the context of reproducible (microbiome) research.

Suggested readings:
The NIH Human Microbiome Project. http://genome.cshlp.org/content/19/12/2317.full

Prokaryotes: The unseen majority. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC33863/

Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible. http://arxiv.org/abs/1310.0424

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. http://dx.plos.org/10.1371/journal.pone.0061217

Stanford Medicine Resources:

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