How urbanization might affect the five-second rule

image from the wikipedia article, ‘the five second rule’

At this point, we know that microbes are everywhere and make up complex communities found all over the place ranging from oceanic hydrothermal vents to lakes, soils, and, yes of course, all over you. It has also become apparent that our human microbiome plays a role in  health, but there’s still plenty to learn about how our relationship with the microbial communities that live with / on / and around us really affects us.
Unraveling the distribution of microbes in the environment, and figuring out if Baas Becking really had it figured out when he said “everything is everywhere, but, the environment selects” is a fascinating challenge that has been investigated, in part using metagenomic approaches. Recently, there has been a growing interest in investigating the diverse microbial communities associated with man-made structures, so turns out we have another type of environment to contemplate when discussing microbial biogeography.

Examining the microbiome of the built environment 
It was pointed out eloquently by Kembel and colleagues in 2012, that studying the microbiology of the built environment is essential to clarify relationships between architecture, biodiversity and human health. They found that architectural design influences the diversity and structure of the built environment microbiome (Kembel et al., 2012). This month, another cool study by Ruiz-Calderon et al., published in Science Advances looked at how the microbiome of the built environment is affected by the architectural shifts associated with urbanization.
The most remote sites chosen for study were in Peru, starting with Checherta, a hunter-gatherer village where everyone lives in open huts, with no electricity, and no potable water. The slightly more urbanized city of Puerto Almendras had houses with walls, but still no potable water. The third community was Iquitos, much more urbanized (i.e. international airport, treated water, electricity) although still lacking access by road. Finally, Manaus in Brazil was chosen as the site most developed, with lots of houses that were the most separated from the environment and a huge population of 1.8 million.
Figure 1

Figure 1 (Ruiz-Calderon et al., 2016)

Interestingly enough, they found a clear influence of urbanization on the microbial community found in homes. The dwellings most exposed to nature were constructed from materials sourced directly from the surrounding environment (like wood and reeds), had dirt floors, consisted of large open living spaces, sheltered larger numbers of people than the more urbanized homes. In the big cities, houses were constructed from man-made materials and divided into different spaces (kitchen, living room, bed rooms), had synthetic floors, and boasted indoor plumbing.
Figure 2.

Figure 2. (Ruiz-Calderon et al., 2016)

The study found that functional spaces in homes could be classified depending on the microbes present, and the significance of this classification increased along with urbanization. While community richness didn’t shift in more urbanized environments, the most abundant community members did. Furthermore, in urban houses the microbes on the walls were the best at pointing out if they came from a kitchen or bathroom. So essentially, the more urbanized your house, the more the microbial community tends to be made up of human associated bugs. In particular, the top 10 bacterial operational taxonomic units (OTUs) were representatives normally found in the human mouth, or, ahem…gut. The authors concluded that:

      “….the presence of walls dividing functional spaces acquires function-dependent microbes, mostly of human origin.”

There are plenty of other questions left and things about the built environment microbiome that are unexplored. The authors suggest that more research is needed to look at how signaling between and among microbial community members might change across different environments, and what the broad implications for human health are. There’s even an interesting site led by Jonathan Eisen and Hal Levin on the microbiology of the built environment. So next time you drop that pretzel on the floor, contemplate which room of the house you’re in and how many walls you have before you decide if the less than 5 seconds it spent picked up a community you’d like to snack on.
Ruiz-Calderon, J.F., Cavallin, H., Song, S.J., Novoselac, A., Pericchi, L.R., Hernandez, J.N., Rios, R., Branch, O.H., Pereira, H., Paulino, L.C. and Blaser, M.J., 2016. Walls talk: Microbial biogeography of homes spanning urbanization. Science Advances, 2(2), p.e1501061. DOI: 10.1126/sciadv.1501061
Kembel, S.W., Jones, E., Kline, J., Northcutt, D., Stenson, J., Womack, A.M., Bohannan, B.J., Brown, G.Z. and Green, J.L., 2012. Architectural design influences the diversity and structure of the built environment microbiome.The ISME journal, 6(8), pp.1469-1479. DOI: 10.1038/ismej.2011.211

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