Wednesday, August 01, 2012

Yes Virginia, even the cervix has a #microbiome ........... or does it?

Just read over the following paper: PLoS ONE: The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization

It is interesting and has lots of tidbits worth looking at in more detail including

  • An analysis of methods for classifying sequence reads as to which organism they likely come from
  • comparison of amplification and sequencing methods
  • long time period covered in the sampling
  • and much more
But what struck me more than anything is that, well, they referred to the microbial community that they were sampling as the "cervical microbiome."  And though what they discuss here is fascinating in many ways, I am beginning to wonder if every site on the human body (or sites on other organisms) should have its own microbiome.    Or, another way of looking at this is - where do we draw the line between niches?  Is there a eyebrow microbiome?  A left elbow microbiome?  A testicle microbiome?  Certainly, I view the microbes that live in and on people as part of an ecosystem.  But I think just as biomes in the world around us should be defined by - well - something bigger than just GPS coordinates - so too microbiomes should probably be a bit bigger than just the microbes found in a particular body site.  Starting to wonder if we are going to see a proliferation of microbiomes just as we have seen a proliferation of OMIC words.  Ooh --- this could give me something new to give an award for.  


  1. I think we will absolutely see a proliferation of microbiomes. It is a "hot" field right now and there seems to be an endless list of different microbiomes we could do (e.g. I am looking forward to the reusable coffee cup microbiome with links to its host). It looks as if the microbiome will lose its meaning and simply be where the samples were taken from.

    I agree that it would be nice the term microbiome represented something more akin to a niche. However, I think defining niches should be driven by the data and not just where it was sampled. If there is something unique to the testicle microbiome that clearly separates that region from neighbouring regions then it probably deserves its own special niche (or microbiome) label. However, I presume "clearly" will be hard to define as it seems possible to always detect differences between samples. I think the best measure of a niche, is based on predictability. If I can predict the "source" of an unlabelled sample, given sufficient training data, then it seems to me it deserves a "niche" label.

    As always just my 2 cents.

    1. Yes, agreed - that is what I meant by "something bigger than just GPS coordinates" ... they should be defined as biomes - which are not defined by location but by the organisms that are there ..

  2. Rob Knight has shown data in which he sampled the face of a post-doc in his lab. In the end this indeed showed that there is such a thing as the lip microbiome, the eyebrow microbiome, the chin microbiome etc. Not sure if this study has been published.

    1. I think the point that is trying to be made is that just because you can find differences between two samples doesn't justify calling them different "microbiomes". Differences can also be found between the same location but on different people...does that mean that if I sample my eyebrow I should call it Morgan Langille's Right Eyebrow Microbiome? I think there is lots of work left to be done to hash out these ideas and to see where the boundaries really exist.

    2. Microbiomes can change over time, as well, so you'd have to call it Morgan Langille's Right Eyebrow Microbiome at 2:00PM on July 2nd, 2012!

      In the end, I think the validity of the "-obiome" concept rests in the level of stability of the community, be it taxonomic or functional.