Answering questions about microbes in the built environment

Laura Williams recently posted a great writeup of some of the materials she covered with her microbiology class – specifically focused on microbes in the built environment. It turns out they were reading one of the papers we recently published (!) about how humans can influence the microbes indoors by the way we interact with surfaces.  I’m glad this stuff is making it into a microbiology course! Here is a response to some of the questions that came up during the class, and I hope this can add to the BE microbiome discussion.

Why should we care about all of this?

This is a great question, and one we constantly debate. Of course we should care about how we disperse pathogens, bioterrorism threats, and the sorts of microbes that degrade our building materials or otherwise influence our health. But being able to detect those types of microbes (sometimes at a very low abundance threshold), requires an in-depth understanding of what ‘normal’ should look like.

The new NYC subway paper (which blew up in the media) is an excellent example. They found lots of things that seem troubling at first glance, but almost certainly are not dangerous to people riding the subway, and might not even exist. And anytime we sequence from surfaces in buildings, like classrooms, we pretty much always find microbes that are closely related to pathogens. But that, again, is teaching us what normal should look like. That way we will be better able to distinguish real threats when they do show up. It is probably shocking to most people the first time they learn that chairs are covered in gut and vaginal microbes, but it turns out that is pretty normal, so now we know what to look for.

Another reason I think all of this is really important it to constantly keep an eye on the future of sequencing technology. When we do studies, like the classroom microbiome or the subway study, it takes months to process, analyze and interpret the data. That is an unacceptable turnaround if we really care about detecting threats in real time. However, I tend to approach all of these studies as a way to calibrate our understanding of the built environment, as well as the tools we use, because we are likely only a few years from essentially real time sequencing and detection. When we get there, we will have a better handle on the sequencing technology and on the ecology of the built environment because of these early studies. In other words, these early studies are laying the foundation for what is coming soon — the ability to make sense of the built environment microbiome in real time.

How can we influence the types of microbes that grow in the BE?

There are two parts of this question: how to influence what grows in the BE, and how to influence what shows up in the BE.

Almost all of these high-throughput bacterial studies are mostly detecting microbes (or their leftover DNA) that are just hanging out in relatively dry conditions. So they dispersed in from other environments and now they have a chance to interact with us and our indoor environments. From that perspective, we now know of lots of ways to influence the microbes indoors.

Ventilation is one major way to influence the BE microbiome. Ventilated air carries around lots of microbes, either from outdoors (e.g., soils, plant leaves, ag fields, marine environments, …) or from other rooms (e.g., human-associated microbes floating in from the hallway). The simple choice of opening a window vs mechanically filtering air through an HVAC system can have a major influence on the sorts of microbes in the air, on surfaces, and accumulated in dust.

Our group (BioBE Center) has thought quite a bit about ventilation and the BE microbiome. Here are three papers about that:

Carpet vs hard floors have huge influence on the microbes you breath. Carpets are just kind of nasty. They accumulate lots and lots of skin cells, pet dander, and other particles from inside and out. When we move around indoors, we stir these up, and then we have a chance to breath them in. Hard floors are easier to clean, so less dust and particulate matter (and therefore microbes) accumulates.

Here are two interesting papers about that:

There has also been some really cool research lately about how incredibly influential dogs are to the BE microbiome! Some would even argue that dogs create a ‘healthier’ BE microbiome, especially for babies (and those in utero) in the house. This might be true, and is certainly something to continue studying.

The seminal paper in this area, and I think one of the most important in our field:

Light might be a effective way to influence the microbes indoors. Many bacteria have little ability to survive in dry, well-lit conditions. So in dry buildings, we tend to see desiccation-resistant microbes accumulating over time.

Notice, however, that although we can influence the microbes inside, none of these controls really tells us much about health. Except to say that indoor air quality scientists have been telling us for decades that breathing tiny particles is bad for our health. We don’t really know yet whether it is good or bad to encounter most of these bugs inside our buildings. That is where lots of researchers are focusing now — health implications of the indoor microbiome.

However, when we consider what grows inside, there are a few really important features of buildings that influence the BE microbiome. Moisture in buildings is the biggest. A moist building will generally become unhealthy because excessive moisture encourages things like mildew and mold, which do influence our health. And ventilation can help here too, as a way to get rid of excessive humidity. Materials matter too, because different materials can trap moisture and develop biofilms, especially in the unventilated spaces behind walls and such. There is really not much research about whether biofilms on our walls are necessarily good or bad inside buildings, but most building scientists and health experts will tell you that biofilms in buildings should be avoided at all costs, and I tend to agree :)

How do you see your research being implemented in the future?

Several directions:

  • Dig into the health effects of the microbes we commonly find, both good and bad.
  • Technological advances toward real-time sequencing and interpretation.
  • Materials that influence the BE microbiome.
  • Find out what matters for early childhood exposure.

Here is a very good piece about that:

Would there be a large difference between the microbiome of a built environment in a developing country versus a built environment in a developed country? What types of differences might we see in these microbiomes? What effects might these differences have on the people living in them and could you argue that one is better than the other based on these effects?

Yes. Big difference regarding connectivity to the outdoor environment, human microbiome, cleanliness, fecal contamination, materials, and dispersal from livestock/agriculture/pets, just to name a few. However, whether this is ‘good’ or not is a matter of very active debate. The hygiene hypothesis would argue that we have lost connection to some of the beneficial microbes and challenges our bodies need to develop properly. While this might be true in some ways, there is still so much to be learned, and no one can tell definitively which is necessarily better. I tend to think there must be a happy medium between cholera and asthma. In other words, our houses have probably become too clean and sterile, and this has a negative effect on our health, but there is almost certainly a way to encourage the ‘good’ bugs and discourage the ‘bad’ ones. We’re not there yet.

But, lots of scientists have been thinking about this from a different perspective for a very long time: in the fields of indoor air and building science. If you want to know how to design your indoor environment to benefit human health, you can definitely think about things like the VOCs given off by our plastics, carpets, paints, couches, and whatnot.

Brent Stephens recently posted his take on the 20 most important papers when considering building science, which include some fantastic papers on indoor air pollution:

I think in the near future, we’ll see some of the same health information for the BE microbiome. Or maybe we should curate the 20 most important MicroBE papers to date …

I am curious if there is any research about how built environment manipulation can aid or facilitate the eradication of an outbreak in a confined space such as a college campus.

This is an area of very active research. Ventilation is the biggest way to influence indoor airborne threats, but then you have to think about the quality of the air being brought in. In Beijing or Delhi, maybe ventilation is a really bad solution because the air outside is often terrible. Here in Eugene, Oregon, we enjoy terrific air quality, except if you have pollen allergies. If so, outdoor air can put you in the hospital. So we always have to weight the benefits and sources of ventilation. But there are many different ways we can design and alter buildings to get to this goal. Stay tuned …


There are so many different types of material that make up our infrastructure. Are there any particulars types of material that are better at inhibiting bacterial growth than others?

This can be controvercial. Yes, surfaces made of copper, for instance, are probably effective as antimicrobial, but is that necessarily a good thing? Maybe in some places, but certainly not in all built environments. And since the 1960s we’ve been embedding antimicrobial compounds like Triclosan in our household items, soaps, cutting boards and kids toys (wtf!?!?). It turns out that this is probably a very bad thing for our health in the long run, and drives resistance to antimicrobials. Indiscriminately killing all microbes in the name of health is … well … probably not fully thought out.

The future most likely holds surface technology that can encourage the bugs we want and discourage the ones we don’t. But we’re not there yet.

Is there a way for scientists to create a faux outdoor environment that would change the state of built environments? For example — outdoor microorganisms in something like a Glade Plug-In (for lack of a better example).

Certainly there is a way, but no one is there yet. One theoretical way to maybe accomplish this is an indoor plant. The thought is that a plant will put more soil- and leaf-associated microbes in our indoor air. BUT plants tend to increase humidity in buildings, which is ultimately bad for indoor health and materials. And they might actually make air quality worse in some cases. So plants are probably a bad idea in some situations. Plants might be good for your own mental health in buildings, but there is really no good evidence that they are good for our physical health. Opening a window can do wonders if outdoor air quality is good enough to want it inside. Whoever asked this question should probably start thinking about patents :)

Would someone who cooks more or smokes cigars and/or cigarettes in their home have a noticeably different microbiome in their home?

Maybe. Good question. Cooking definitely increases humidity indoors, and that will change microbial communities. It also coats the walls with tiny oil particles that might be attractive for some microbes, so kitchen biofilms might accumulate. What we do know for certain is that cooking (and especially smoking!) is detrimental to indoor air quality. If you search through hundreds of papers from people like Richard Corsi or Bill Nazaroff, you will soon find that these questions have been answered for IAQ for a very long time, but the rest of us are just starting to notice.

I was curious to know whether researchers account for their own microbes that they may bring into the built environment. That is to say — is it significant enough where a team of researchers may have to account for microbes that could show up from their lab or themselves?

It depends on the microbial load already in the building or room. So in a heavily trafficked classroom, we didn’t worry too much about it. However, we have ongoing studies where we experimentally remove all of the background dust and biomass we possibly can. In that case, we sometimes wear Tyvek suits and face masks to reduce our own influence. It feels crazy but every little bit helps to see the very small signal we are after.

Here is a movie about how that looks:

That being said, laboratory contamination is always a big issue for any sequencing study involving low biomass (especially BE samples). So this is something that most labs now approach very carefully with negative sequencing control samples to see what bugs live in the reagents, and which are really from the samples.

A very important paper really explains the problem:

Ed Yong wrote a great piece about it here:

I hope this is useful when digesting some of these built environment studies!

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James Meadow

Research Associate at the University of Oregon BioBE Center.