Breakthrough: The Relationship Between Urbanization, Lifestyle, the Microbiome(s) and Autoimmune and Allergic Problems is Complex

Recently, the news has been awash with stories of the links between the biodiversity outside of peoples’ homes, the diversity of bacteria and other microbes inside peoples’ homes and autoimmune disorders (Crohn’s, IBD, autism, you name it). The general idea is less biodiversity outside = less inside = a dysfunctional immune system. Personally, the existence of such links seems likely. I have written about them lovingly elsewhere. But given the flurry of recent news stories about microbe biodiversity studies, it seems worth calling attention to something that seems to be getting missed. We are ignorant.

I don’t mean this in any offensive way. I mean it more simply. I mean that if all of the things that could be known were the size of the universe (they are), what we so far know is just a star-prick of light. I believe this to be generally, but especially with regard to the microbiome, if for no other reason than that while we have studied the microbiomes of termites and many other organisms for more than a century, we have only fully begun to dive into microbiomes of humans in the last decade and in many ways even more recently.

I could elaborate the aspects of our microbiomes about which we remain ignorant. They are legion (and fascinating, I love a gap in knowledge more than most. Frankly, I delight in the gaps in knowledge as much as I enjoy the things we have discovered). But rather than detail them, I’ll just offer one measure of our ignorance. Recently, we have been working on what I think is probably the biggest study ever of the microbiomes of homes. In this study, supported by the Sloan foundation, we have worked with the public to sample microscopic organisms and bits of organisms in four sites in and on houses. To date, we have been able to identify the bacteria and fungi at two of these sites, in the dust on the outside of doorframes and in the dust on the inside of doorframes. Amazingly, working with collaborators at the University of Colorado (including Noah Fierer, Shelly Miller, and their rockin’ lab groups), it appears that the diversity and composition of the microbes we detect in these simple samples reflect what can be found using a much more intensive microbe sampling approach in each house through time (that, on its own, is interesting).

The resulting data are thrilling. Every time I open the data set to begin to understand what we are seeing, I get excited. But the data are not simple. This is even the case for the simplest thing we might consider, which houses have diverse microbes and which don’t. We might predict in advance that houses that are more tropical (or simply, in the U.S., more southern) would have more species. We’d predict the same for a more rural house. This is the model everyone seems to implicitly be talking about, one that says by living in urban centers in the low diversity north we have deprived ourselves of the richness of microbial living available in, say, the subtropical rural south. Well, what do the data say? Below, you can find two maps that highlight how little we know. They depict, respectively, the number of kinds of bacteria and fungi found in each of the houses we sampled.

Bacterial diversity_2

Figure 1. The number of bacterial species in a sample from an inner door frame. Predictions are obtained via Gaussian kernel smoothing, which locally weights observed values (indicated by the points on the map) and creates a smoothed prediction map across the US. Prepared by Neal Grantham.

Fungal diversity_2Figure 2. The number of fungal species in a sample from an inner door frame. Predictions are obtained via Gaussian kernel smoothing, which locally weights observed values (indicated by the points on the map) and creates a smoothed prediction map across the US. Prepared by Neal Grantham.

What do these maps mean? What does explain bacterial or fungal diversity and how it varies among houses? We don’t know yet. That is the point. The delicious, terrifying, inescapable point.

By | 2016-11-22T13:47:04+00:00 June 19th, 2014|

About the Author:

Rob Dunn
Rob Dunn is a biologist and writer in the Department of Biological Sciences at North Carolina State University. Central to all of his work is the sense that big discoveries lurk not only in faraway tropical forests, but also in our backyards and even bedrooms. The unknown is large and wonderful and Dunn and his collaborators, students, and postdocs love to spend their days in it.


  1. Jonathan Eisen June 19, 2014 at 11:12 am - Reply

    In case people are not aware of the problems with much of the reporting and discussion on microbiome studies, I would like to point everyone to the “Overselling the Microbiome” awards I give out on my blog. If I had time I would give out one or more of these a day, there is so much out there that is misleading. See for more information.

  2. […] “Aspects of our microbiomes about which we remain ignorant..are legion (but fascinating).” Quote by Rob Dunn from a super assessment of what we do, and don't, know about microbiomes. […]

Leave A Comment