The bioBakery help forum

Diversity data from HMP paper (The Human Microbiome Project Consortium 2012 Nature 486 207)

I am a microbial ecologist at the University of Warwick in the UK, working with veterinary epidemiologists to investigate chronic animal diseases, such as mastitis in cows and other ruminants. We are close to finishing a paper on the microbiome of ruminant mammary glands where we challenge the idea that there is a core microbiome at these sites. To help our argument we have compared the diversity we find at these sites to those found in the Human Microbiome Project (specifically from the paper above). These data are used to support our argument as we find far more diversity in ruminant mammary glands than in any of the sites measured in the HMP (26 phyla and nearly 1000 genera, in 1600 milk samples from nearly 100 mammary glands). However, while I could extract some accurate data from Supplementary Figure 1B from the above paper it was not possible to do this accurately at all taxonomic levels or for all sites. Therefore, I wonder is it possible to have the data of clade saturation across all taxonomic levels for the HMP sites reported in that figure so that we can report accurate data as opposed to my reasonable but clearly inaccurate and incomplete derived “data”?

Hi Kevin,

You will be able to get the data across all the taxonomic levels through https://ibdmdb.org/tunnel/public/summary.html. Then navigate to “products” link in the table and select the “taxonomic profiles” tab.

Thanks,
Sagun