A new #citizenmicrobiology project from @YourWild_Life looking for gutter samples #GutterCheck

Here is a great chance to participate in a microbiology of the built environment citizen science project on gutters.

“Examining this water…I found floating therein divers earthy particles, and some green streaks, spirally wound serpent-wise…and I judge that some of these little creatures were above a thousand times smaller than the smallest ones I have ever yet seen, upon the rind of cheese, in wheaten flour, mould, and the like.”Antonie van LeeuwenhoekAs a rule

Source: The Wild Lives of Gutters – Your Wild Life

If you happen to be in the Raleigh area, you should sign up.

And if you are not in the Raleigh area but are driving through there, they state:

As of right now we are focused on gutters either in Raleigh, North Carolina and surrounds. Though if you happen to be driving through, we’d never turn down a sample of gutter muck.

I recommend they call this project “Gutter Check”.

 

Participatory metagenomics

First of all, a big thanks to Jonathan Eisen for reaching out to us. We are grateful for the invitation to introduce our project to the microBEnet community. And we’d love to talk if you are doing citizen science work using metagenomic tools.

good-germs-bad-germs-filmCitizen science comes in many different shapes and sizes. It can be led by academic researchers, enrolling people in collective experiments. But it can also be led by everyday folk, utilising the tools of science to ask their own questions. In the science of the microbiome, the complexity and expense of metagenomic sequencing has tended to favour the former, laboratory-led approach. Sometimes the aim of such lab-led citizen science is public engagement – to get people excited about the science. Sometimes it is a useful method to collect big datasets about real world situations. Often, it is both of these things together. But usually the role of the participant is limited to swabbing a pre-defined area of their home (or person). Rarely have the participants been able to shape the experimental design.

Our aim is to try and let people design their own experiments, in and on their own homes, utilising metagenomic tools. We are a team of interdisciplinary researchers (scientists and social scientists) based at Oxford University in the UK. We have been inspired by ground-breaking citizen-science microbiology projects in the US and elsewhere – particularly those utilising metagenomic methods to explore the built environment. Indeed, many of those inspirational projects have featured on this blog. Our own focus is on the microbial ecologies of kitchens. But as an interdisciplinary team, we are interested in both the bacteria and the people in kitchens – and particularly in what the people think about the bacteria!

We are working with a small group of households (14) in Oxford, UK. Every few months, our group gets together to discuss the results of their previous experiment, and to design a new one. So far, the group has conducted a ‘microbial safari’ of various common sites in their kitchens (re-enacting well known experiments like those published by Rob Dunn et al and Gilberto Flores et al). They’ve also explored how the bacteria on their chopping boards change over time, and how different cleaning products and techniques affect bacterial ecologies. They are currently trying to find out how bringing home the groceries can change the microbial ecology of their refridgerators. And each time they design an experiment, we get to discuss why they are asking particular questions, and what they think about the results.

Our social science team are also interested in the broader field of citizen science microbiology – what people are up to, what is working well, how different research teams are facilitating deeper engagement with interested publics. If you’re working on a citizen science project using metagenomics, we’d love to talk!

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You can find out more about our project here or follow us @goodgerms.

Jamie Lorimer, Rich Grenyer, Beth Greenhough and Timothy Hodgetts

 

Good germs. Bad germs. An interesting new citizen microbiology project.

This is definitely worth checking out – a Citizen Microbiology project on the Built Environment

From the Good Germs project.

More on the project:

There is a growing popular and policy interest in the microbiome, and the possibilities of more nuanced or ‘probiotic’ ways of living with germs. To date however there has been limited public engagement with the science and technology of metagenomics. The project engages with the growing scientific, popular and policy interest in the microbiome: the microbial life in, on and around us.

They have been posting some of their results to their blog too.

The Wild Life of Showerheads: Another great #CitizenMicrobiology project from ‏@RobRDunn - 

Rob Dunn is one of the true pioneers of Citizen Science and in Citizen Science projects involving microbes.  And here is another fascinating project from Dunn and colleagues.

The Wild Life of Showerheads Photo by Lea Shell- Rob Dunn Lab When Anton Von Leeuwenhoek, the first microbiologist, began to study microscopic life, he did so with a sense of stupefied awe. He

Source: Showerheads

You can sign up to possibly be a participant in the project and join Dunn and colleagues in learning about the microbes lurking in showerheads.

For a  related post see

The squeaky wheel gets the open access

cc.logo.largeThis is a story of my first involvement pushing a publication that wanted to be University owned “all rights reserved” to becoming one released under a Creative Commons license.  I’m not sure that the arcane details will be of interest to many people, but I think there’s an important lesson here about sticking to your guns if you support open access.

A couple of years ago, I was asked to write a chapter on Citizen Microbiology for a book on Citizen Science that would be published by Arizona State University (ASU) press as part of a series they were doing.   Flattered, I of course accepted… I am really passionate about citizen science was happy to contribute anything I could.

Then I mentioned it to Jonathan Eisen, my supervisor and the first question he asked was “what will be the licensing on the book?”.   I thought to myself “Who cares?  I get to write a book chapter!”.  But I passed on the question and got a response to the effect that it would be published under a standard ASU “all rights reserved” copyright sort of arrangement.  And even though I’m a big proponent of open-access, for example I will only publish scientific research in open-access journals, I didn’t think much about the book copyright.  Until Jonathan pointed out to me that not only had all of my citizen science work been funded by the Alfred P. Sloan Foundation (which supports open access)… but that it was a bit ironic to have a book about citizen science be closed access!

So I asked about the possibility of the book being Creative Commons, and got a fairly lukewarm reception and the suggestion that they might allow authors to post chapters, but that third parties wouldn’t be allowed to use any of the text.  At which point Jonathan suggested that I pull my chapter from the volume.  I waited for the formal agreement, but it looked both restrictive and complicated.  I again asked about using Creative Commons and said I wouldn’t publish otherwise.

The counter-offer this time was pretty interesting.  Basically I would release my chapter on microBEnet under a Creative Commons license, and the ASU would “re-print” my chapter in their book.   That seemed like a bit of a kludge but workable so I agreed.  But the contract they sent me contained phrases like “I agree to assign and do hereby assign fully to ASU all intellectual property and other rights in the Publication.”   That didn’t seem right, so I re-wrote the contract in my own words (never a good idea when lawyers are involved).  And then I realized that I shouldn’t have to sign a contract at all… since I was going to publish the work and they would just use it.   The next version they sent contained even more scary sounding language that didn’t seem at all compatible with a Creative Commons license.   Again, I didn’t sign it and asked if they could just use the chapter.

I think at this point the editors of the book began to push the lawyers for the whole volume to just be under a Creative Commons license and be done with the thing.  Many e-mails, phone calls, and discussions ensued.  Lawyers talked to publishers who talked to editors etc.  Insane hypothetical scenarios involved Nazis were brought up (I’m not kidding).  In the end, both ends of the spectrum gave way.  I would have preferred the entire book be released under a CC-by license and they (initially) would have preferred to retain all copyright control.

So the compromise was a CC-NC-ND license with an author agreement that allowed ASU to sell the book.  I’m not sure what happened with the other chapters but mine is here on microBEnet.

Thanks to Jonathan for pushing me to do the right thing and thanks to the folks at ASU who made this all come together in the end.

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.

#TakeASample for National Citizen Science Day

I always looks forward to spending a chunk of my Friday listening to Science Friday. This segment is too good not to share… Science Club is back! Ariel Zych and Charles Bergquist, the awesome Science Club hosts, are celebrating National Citizen Science Day (April 16) with a new Science Club they are calling #TakeASample.

This is awesome challenge you can take on with your kids, a classroom, a lab, or yourself. They want to hear from scientists too! Ongoing citizen science projects are also featured on their website with a great representation from the microbes (Including American Gut and Drug Discovery From Your Soil).

Have a listen and have fun!

Journal Club: Crowdfunding Science

What is better than Open Access?! Citizen Science AND Open Access! The March issue of JMBE was all that. You have probably already heard of Kittybiome and/or The Koala Project, 2 ongoing projects in the Eisen Lab. Both projects were featured in the paper, “Crowdfunding Campaigns Help Researchers Launch Projects and Generate Outreach”, published in the current issue of JMBE.

The paper hardly seems to cover all that we learned as we took on the task of making our first crowdfunding campaigns. There were some things that seemed really important at the beginning, such as which platform to use. It turns out that the platform really doesn’t matter unless you’re after certain bells and whistles. Then there were other things that we didn’t think were that important, but ended up being the main reason our campaigns were successful. Having friends and family contribute gave the campaigns the momentum and attention they needed to reach their goals. Soliciting is always uncomfortable, even with your own mother, but well worth it in the end.

After the campaign has ended, the perks have been sent out, and the money has arrived in it’s own grant account, the work has only begun. Since we wrote this paper, we realized that there is nothing we could have done to prepare for all of the hiccups we encountered as we started the actual science part of this journey.

My experience was my project had to be revised numerous times. Politics at the wildlife hospital, time restrictions, and ethics approval meant I wouldn’t be able to get enough mother/joey pairs to do my original project. I changed my focus to how the antibiotic treatments were changing the gut microbiome of individual koalas instead. My project still ended up smaller than I expected because koalas kept dying before I was done sampling from them. I also encountered a lot of failed experiments in the lab; it turns out koala poo is so full of inhibitors that it is really hard to work with. Holly had the opposite problem; her project ended up bigger than she expected. There was no way she could keep up with sending kits out, processing samples that came in, and the data communication. Luckily Holly was able to form a mini-science army to help with lab work and the web app design. Everyday it seems there is a new challenge that arises.

If I had the chance to revise any part of the paper, I would change the section of “Setting a Funding Goal”. The truth is that money doesn’t go very far in science. After a few DNA extraction kits and a sequencing run, there isn’t too much left over for the little reagents and supplies that we underestimated when setting our funding goals. Because Holly and I didn’t want to cut corners, we ended up having to spend our own money and seek additional support from other grants at times.

Kudos to Marc Edwards, selected as one of Fortune’s World’s Greatest Leaders

This really made my day / week / month.  Marc Edwards has been selected as one of Fortune Magazine’s “World’s Greatest Leaders”.

Source: Marc Edwards

Here’s what they wrote about him

Edwards, a MacArthur “genius” grant recipient, is one of the nation’s top experts on water contamination–and nowhere has his impact been bigger than in Flint, Mich. In August, Edwards and a team of researchers made the 11-hour bus ride from Virginia to Flint. There, the group acted as scientists, journalists, and advocates, collecting hundreds of water samples, filing Freedom of Information Act requests, and updating the public through a blog. Edwards’s team proved that Flint’s water supply was poisoning its residents­–triggering state and federal intervention and a nationwide debate over water safety.

A true inspiration who shows the power of persistence, science, engineering, and public engagement, and much more.  Kudos to Marc and the team of people who have worked with him over the years to make the world a better place.