Citizen Microbiology Book Chapter: Lessons Learned

Back in September 2014 I was invited to write a book chapter on citizen science in microbiology.  After several iterations of the book, the chapter, and the licensing agreement here is the final version.  The book came out yesterday, here’s a link to the entire book on Amazon (“The Rightful Place of Science: Citizen Science“)  I’m posting the chapter here both in the hopes that it might be of interest to some people and for licensing reasons that I’ll explain in another post.  Here’s a PDF of the chapter which has much better formatting.

Chapter 6:
CITIZEN MICROBIOLOGY: A CASE STUDY IN SPACE
David Coil

At 3:25 PM on April 18, 2014, I stood on the viewing platform at Cape Canaveral,
Florida, watching a massive rocket carry a nationwide citizen science microbiology
project into space. This project would catalog hundreds of types of bacteria living
on the space station, survey thousands more bacteria from participants around
the country, and measure the growth of common bacteria in space. Mixed with
the excitement and relief was a feeling of amazement that we live in a time where
such things are possible. New and cheaper technology has completely changed
our understanding of microbiology in the last decade or two. We can relatively
cheaply ask questions that weren’t even conceivable in the recent past. These
changes, along with rapidly growing public interest in microbiology, have created
the perfect conditions for an explosion of what we call “citizen microbiology.”
Our project involving microbes in space is but one example of this new and
exciting field.

Over the last decade, microbiology has seen a renewed surge of interest in
popular media, books, and films. While some of this relates to topics such
as global pandemics and new diseases, increasing attention is being paid to
subjects like the importance of beneficial human-associated microbes or the
problem of antibiotic resistance. Given the current level of public interest in
both microbiology and citizen science, it is perhaps no surprise to hear that
citizen microbiology is taking off. In this chapter I’ll discuss the idea of citizen
microbiology, the opportunities and challenges therein, a few examples, and one
detailed case study.

Before going into the details of citizen microbiology, a few definitions might be
in order. A “microbe” is traditionally defined as a living organism too small
to be seen with the naked eye. For our purposes this includes viruses, bacteria,
fungi, and various other tiny creatures. “Microbiology” is the study of microbes
and a “microbiome” is the collection of microbes found in a particular habitat
(e.g., on a person or in a house).

A few microbiology citizen science projects that involved culture-based monitoring
(i.e., growing microbes on plates in the lab) go back decades. For example, the
State of the Oyster project in Washington State has helped volunteers monitor
edible shellfish populations for harmful bacteria since 1987. However, the ease
and low cost of DNA sequencing has been a major force for change. The majority
of citizen microbiology projects today are less than ten years old, and rely in some
way on cheap and easy DNA sequencing. This sequencing allows researchers to
quickly and accurately identify most of the microbes in a given sample.
Microbes are hard to see, often viewed negatively, and have large impacts
(good and bad) on human health. These features create both opportunities and
challenges in conducting citizen microbiology.

Opportunities & Challenges of Citizen Microbiology

Every human being carries a complex and unique collection of microbes, making
each person a valuable data point in understanding the human microbiome. Given
our increasing understanding of the critical role played by microbes in human
health, this understanding may transform numerous aspects of healthcare at an
individual level. In addition to human-associated microbes, citizen microbiology
efforts involving environmental and water monitoring can be extremely helpful
in understanding microbial ecology.

Beyond the scientific benefits, there is a tremendous educational opportunity
with microbiology. Many people react negatively to words like “microbes” and
“bacteria.” It is far more common to find the term “germs” in the media,
usually portrayed in a health-influencing and negative way. Engaging the public
through actually doing microbiology provides an opening to discuss the fact
that microbes are everywhere, and the vast majority of them are harmless or
beneficial. Increased awareness of this fact has important implications for human
health, both directly (e.g., through reduced use of unnecessary antibiotics) and
indirectly (e.g., shifting away from “kill all the microbes” that is probably
counterproductive for health).

Another opportunity with citizen microbiology is the accessibility of samples: to
get started all you often need is a sterile swab. Citizen microbiology can also be
adapted in a hands-on manner in the classroom in a way that might be difficult
with, say, endangered birds. An excellent example is the Phage Hunters project
run by Graham Hatfull at the University of Pittsburgh, where students actually
discover and characterize novel bacteriophages (viruses that infect bacteria).
Citizen microbiology also presents a number of challenges, some of which are
shared with other citizen science projects but many of which are unique to, or
more problematic, when dealing with microbes. There is often, for instance,
a very strong negative association with microbiology and microbes. This is
really both a challenge and an opportunity, since educating the public about
microbiology should be a primary goal of any citizen micro-biology project. Many
people are both surprised and interested to learn how important microbes are to
the world around us and our own health. In our experience, many times all that
is needed is a couple examples of how “germs” aren’t all bad to get people to be
more open-minded about microbiology.

For the researchers, the logistics of organizing sample collections with citizen
scientists can be quite complex. For example, samples collected for DNA analysis
need to be protected from contamination and often kept frozen or otherwise
preserved. This can be particularly difficult in the absence of electricity, which
would require sub-optimal chemical preservation methods or lugging around
crates of dry ice. Human-associated microbes run into issues related to privacy,
informed consent, and human-subject research. Solutions to this problem range
from pretending it doesn’t exist, to anonymizing all data, to (for example)
collecting microbes from a cell phone instead of a person directly. Actually
growing microbes as part of citizen microbiology (or in an educational setting)
can present biosafety concerns. When microbes are given rich growth conditions
(lots of food, warmth, liquid, etc.) it can be hard to predict what will appear. In
particular, growth of human-associated microbes typically requires specialized
equipment and training to ensure a minimal risk of either contamination or
spread. Government regulations, and transportation/collection permits are other
potential snags. In one frustrating example from our own lab, we recently
discovered that while we could have mailed animal feces (rich with microbes)
internationally without permits, once we had extracted DNA from the same
samples it was considered highly regulated “biological material from a protected
species.”

Beyond the considerations in the field, one of the challenges with citizen
microbiology–particularly that associated with humans is in not overinterpreting
the data. Conversations about the human microbiome tend to
range between “kill all the germs” and “I take three kinds of probiotics and am
considering a fecal transplant to get a more healthy microbiome.” Scientists
involved in citizen microbiology need to be very careful about how they present
information about the human microbiome. Along these lines, there is a lot of
concern about “self-experimentation” with projects that measure the microbiomes
of participants. There’s nothing to prevent people from radically changing their
diet or lifestyle just to see what that does to their microbiome. The problem is
mainly with interpretation: surely, for instance, if you eat nothing but beets for
two weeks you’ll observe changes in your gut microbiome, but no one can really
say (yet) what those changes mean.

Another challenge is that of communicating the data back to the public. Traditional
outputs of bacterial surveys include statistics and graphs (with dozens of
Latin species names) that are hard to make sense of. Finding ways to display
this complex data in a way that is meaningful to the public is, to my mind, one
of the great remaining challenges in citizen microbiology.

Citizen Microbiology in Action

Most current citizen microbiology projects are focused on low-cost DNA sequencing
to ask questions about what microbes are living where, and they collect data
in collaboration with the public. For example, the Wildlife of Our Homes project
examines what microbes (and other organisms) are present in the homes of
volunteers. The Home Microbiome Project went even further and found people
who were about to changes houses, sampling both houses before and after–as
well as the participants themselves–in order to understand the relationship of
the human microbiome and the home microbiome. People are often very excited
to participate in this kind of project, as they not only have the opportunity to
learn more about microbiology in general, but also to learn what lives in their
own home. Who isn’t curious about that?

However, the closer a project gets to the participant (e.g. a local beach, versus
your home, versus you) the more potential legal, ethical, privacy, and biosafety
complications arise. Entering this realm are projects where members of the
public can collect personal samples from themselves (skin, saliva, feces, etc.) and
have the microbiomes of those samples analyzed. Two example projects in this
area are the publicly funded American Gut Project and the privately funded
uBiome Project. These projects, along with conventional microbiology research
(e.g. the Human Microbiome Project) are already sparking a paradigm shift in
our understanding of human health and disease and our interdependence with
our microbes. This is a case where public participation can generate critical
scientific data, as well as be directly relevant to the participant. As discussed
above, this presents a number of opportunities as well as challenges.
I have experienced many of these opportunities and challenges though my involvement
in helping to organize a nationwide citizen microbiology project called
Project MERCCURI. MERCCURI is a tortured acronym for Microbial Ecology
Research Combining Citizen and University Researchers on ISS (International
Space Station). This project had several interrelated goals:

– To conduct a large nationwide survey of microbes found on shoes and cell
phones.

– To collect microbial samples from the International Space Station.

– To observe the growth of a number of “nonpathogenic” (non diseasecausing)
microbes in microgravity on the ISS and compare this to growth
on earth.

– To use these three scientific goals to engage the public in thinking about
microbiology, and to a lesser extent, doing science in space.

This project was conceived by and co-organized with Science Cheerleader, a
nationwide organization of professional cheerleaders pursuing science careers.
Through this project, we organized a number of events at various venues, usually
sporting events or museums. At these events, members of the public volunteered
to swab their cell phones and shoes for microbes. These swabs were later analyzed
to determine which bacteria were present there and for comparison to similar
swabs on the ISS. Also at these events, different swabs were taken from surfaces
like doors, handrails, etc. Bacteria from these surface swabs were cultured, and
a candidate species was chosen from each event to fly to the International Space
Station for the growth experiment.

Over the course of the project we experienced many of the challenges and
opportunities common to large citizen science projects. A number of additional
challenges and opportunities arose because of the microbial component. We
present here a brief summary of our experiences in the hope that it is helpful to
anyone participating in, organizing, or simply interested in citizen microbiology.
For Project MERCCURI, we dealt with the biosafety consideration by only
having members of the public collect swabs, but not be involved in growing the
organisms (all of which took place in a microbiology laboratory at the University
of California Davis). Swabbing a doorknob probably presents less risk than
touching it normally! We dealt with some regulatory issues by limiting the
project to the United States. Most importantly, this meant that samples couldn’t
get stuck in customs for days, killing the microbes or confounding the results.
To address privacy concerns, all participants signed a detailed consent form.
We also had a separate photography consent form, particularly if minors were
involved. Privacy was addressed through barcoding the samples and keeping
participant information separate from the samples themselves. We also agreed
to pool the data from each event, and not track individual participants for this
reason. Because of the pooling, and the fact that we didn’t collect samples from
people directly, we were able to get approval for a waiver from an Institutional
Review Board (IRB). If, for example, we had given each participant data about
their own microbes (as with uBiome and American Gut), this could have become
much more complicated. IRB approval is normally required for any human
subject research at any publicly funded institution.

Sample preservation was addressed through the use of dry swabs (freezing not
required) and giving event coordinators a FedEx account number so that all
samples could be shipped overnight to the lab at UC Davis. This neatly avoided
the biosafety issue of growing microbes on site, but did require that participants
were on the ball. In one unfortunate case a group of volunteers lost the sterile
swabs we mailed and bought cotton swabs at a local drugstore, which turned out
to be heavily contaminated with fungal spores. In several cases, swabs were left
in hot car trunks for a couple of days and didn’t produce any living microbes by
the time they got to California.

Logistical and organizational constraints aside, our biggest challenges related to
communication about the project. First, even explaining the project to people
was challenging, given the many moving parts and the non-obvious relationship
of cheerleaders, microbes, and space. Second was the major hurdle of the reaction
of many participants along the lines of “germs are gross” or “I’ll bet you’ll find
a lot of nasty stuff on my cell phone.” Part of how we dealt with these two
challenges was through providing access to relevant information, including a
website with information about the project and information fliers distributed
to everyone we talked to about the project. Once the candidate species were
selected for flight into space we created “baseball cards” of each microbe that
emphasized the beneficial (or at least not harmful) nature of all the bacteria we
chose.

But anecdotally, our biggest success with regard to public education was simply
through talking to hundreds and hundreds of people at these events. The very
nature of the project drew people to our tables and attracted volunteers who
might not otherwise have given microbiology a second thought. People were
excited to participate in a nationwide survey of microbes and many were thrilled
at the chance to be involved with something associated with space. Through
these “hooks” we were able to convey our core messages about the ubiquity and
benefits of microbes.

Conclusion

As discussed in previous chapters, citizen science is an incredibly powerful tool
from both the perspectives of scientists and the public. Scientists gain the
benefits of additional data and samples, as well as the opportunity to educate
people about their work. Participants gain a chance to contribute to the process
of science and to learn and become excited about a particular area of science.
Citizen microbiology shares much with other kinds of citizen science projects, but
brings some unique challenges and opportunities. Challenges include negative
associations with microbes, logistical issues, privacy concerns, and problems with
both interpretation of data and communication of the results. The opportunities
include the ease of many experiments, the potential value of the data, and
getting people excited about the microbes that affect the world around us and
our own health. Because of the existing preconceptions about microbes (both
good and bad), and the possible human health implications, citizen microbiology
has incredible potential on both the scientific and educational sides of the coin.

Further Reading

Project MERCCURI: http://spacemicrobes.org

State of the Oyster: https://wsg.washington.edu/state-of-the-oyster-study-testing-shellfish-for-health-and-safety-

Phage Hunters: http://phagesdb.org/phagehunters

Wildlife of Our Homes: http://homes.yourwildlife.org

Home Microbiome Project: http://homemicrobiome.com

American Gut: http://humanfoodproject.com/americangut

uBiome: http://ubiome.com

David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at the University
of California Davis. His background is in microbiology and his current research
interests focus on bacterial genomics and microbial ecology. He loves teaching,
mentoring, citizen science, and other forms of science communication, including
designing an educational board game called Gut Check: The Microbiome Game.