Last week, Pat led us in the examination of a new paper from the Huffnagle group at the University of Michigan. This was the first meeting of McMaster’s HMBJC in a few months which meant a very lively discussion since we were bursting to talk of all things microbe!
As a group, we really enjoyed and appreciated this study. It was great to see researchers going back to their ecological roots with discussions of ecosystems, gradients, niches, and how different anatomical sites can affect one another. We really enjoyed how easy this paper was to follow, even for someone outside of the microbiome research field, using simple-to-read graphs and visuals that any scientist could interpret. This paper also tackled some areas which, historically, have been hard to sample or where sampling has been shrouded in doubt (e.g. BALs). Additionally, for our group, the Θyc statistic was interesting to see in use, and this publication led us down a citation-trail to learn of its advantages over metrics that we more commonly employ such as Bray Curtis and Jaccard.
We did comment on how the nasal swab might have captured a slightly different microbial community compared to a nasal wash, which would me more consistent with the other sample types used in this study. A greater proportion of mucosally-associated species obtained from the “scraping” motion of a swab might account for some of the differences between the nasal communities when compared to other anatomical sites which were sampled by “washing”. Additionally, we were sad to see an opportunity to make more intra- and inter-patient comparisons across all sites not taken, but perhaps that will be the group’s next publication.. we look forward to it!