Monday, February 29, 2016

Why Design Matters

Recently an article resulting from some of my research at the University of Pennsylvania was published.  It highlights how methods, approach, and experimental design can heavily influence the conclusions of studies on microbial communities.  Specifically, it shows that the most common primers used for microbiome studies (amplifying the 16S-V4 region) do a poor job of amplifying DNA from certain crucial microbes in the skin microbiome (such as Propionibacterium), biasing results and giving an overall inaccurate picture of skin microbial diversity.  A related observation was that the species of Staphylococcus could not be reliably identified using the V4 region, as shown here:

Relative abundance of Staphylococcus sequences able to be classified at the species level. (Top) Staphylococcus species in the Whole Metagenomic Sequence dataset were classified using MetaPhlAn. (Middle and Bottom) 16S-V1-V3 and 16S-V4 species level classifications were determined by pplacer. Pie charts depict the percentage of sequences classified as Staphylococcus at the genus level that were further classified at the species level.

To read a lengthier summary of the article, check out my friend and co-author Geof Hannigan's blog post!

- Brendan



Meisel, J., G. D. Hannigan, A. Tyldsley, A. J. SanMiguel, B. P. Hodkinson, Q. Zheng, and E. A. Grice. 2016. Skin microbiome surveys are strongly influenced by experimental design. Journal of Investigative Dermatology DOI: 10.1016/j.jid.2016.01.016.
Download manuscript (PDF file)