July 1, 2014 Ben

download1I’m happy to say that the Liverpool team and I have published a paper in Infection and Immunity. I really enjoyed doing this work and I think I & I is a really good place for it. I hope people enjoy reading it.

The title is “Evidence that intraspecific trait variation among nasal bacteria can shape the distribution of Staphylococcus aureus”

Over the last decade or so, the various -omics fields have exploded. They have allowed us to see detail in biology that was previously impossible. In the field of Microbial Ecology, genomics has allowed for in depth research into microbial community composition which affects everything from human health to global warming. It’s very important!

Our work in this paper is very much a complement to the masses of information produced by genomic and metagenomic analyses. We found that differences in the traits possessed by bacteria found in the microbial communities of human noses were important for colonisation, irrespective of which particular species exhibited those traits. This is an important finding with respect to metagenomics which focusses solely on species identification within microbial communities. Identification is important but it doesn’t necessarily tell us what the organisms are doing or how they contribute to the community structure.

Here, we identify a trait (inhibition/toxin production) that we can measure across bacteria isolated from the noses of 60 healthy volunteers. We tested every strain that we isolated for the ability to inhibit S. aureus in an agar plate based assay. We found that communities that contained more inhibitory strains, were less likely to contain S. aureus. We also found that inhibitory subsets of species were significantly negatively associated with S. aureus when the species as a whole was not negatively associated. Our example shows that Micrococcus luteus is only negatively associated with S. aureus when you consider the inhibitory fraction. No previous papers have shown negative associations between S. aureus and M. luteus before. We believe this is because you would never see a negative association unless you look specifically at this inhibition phenotype.

While this study is relatively small and low throughput, it addresses the need to consider trait variation as well as genotypic variation when trying to understand microbial communities. With exciting new microfluidic technologies on the horizon, it will soon be possible to perform these kinds of assays on much larger microbial communities at a high throughput pace. Until then, we should take care to try to understand trait variation using the high throughput technologies that we have at our disposal. For example, it may be possible to infer traits by looking for toxin genes in metagenomic analyses or by looking for toxins in a parallel proteomic study.

If you’re interested in reading the paper, here is the link.