Rob Dunn seeking community participation in suveying & analyzing Duke Forest warming chambers

Just got this email from Rob Dunn from NC State.  He said it was OK to post it … so I am .. (I note – I just completely love this idea).

Hi folks,

As you might (or might not) know, we have for five years now been running a large-scale warming experiment in which we have warmed twelve 5 meter diameter open-top chambers in forest understory at Duke Forest. We have warmed these chambers in a regression design with the warmest chambers as warm as temperatures are predicted to be in the region in 2100 and the coolest chambers at ambient temperatures (We also have no-chamber controls). These are small worlds each of which mimics aspects of futures we might face. This entire set-up is replicated at Harvard Forest. In these chambers we have been studying the response of insects (with a focus on ants) and plants  over the last five years. When we built them these chambers were the biggest warming experiment in a forest understory in the world. I don’t know if it is still true, but it probably is, if only because chambers of this size are so hard to keep going (especially in the early we felt like Fitzcarraldo dragging a ship through the rainforest) that most people have decided against repeating them elsewhere. 
Some basics on the chambers… http://robdunnlab.com/projects/warming-chambers/
I’m writing because on May 25th we are taking the chambers down and doing a final inventory of the response of everything–all the life we can possibly evaluate–to this warming. To varying extents we have considered the phenology of plants in the chambers, many things about ants in the chambers, shifts in composition of invertebrates in the chambers and simple responses of bacterial and fungal assemblages in the chambers. But, we have done all of this delicately, always mindful to not overly disturb the future world we are simulating. Now though that the chambers are coming down we can and will consider roots, plant biomass, the abundance of insect pests, fungal pathogens and much, much, more. 
As we do this intensive survey, we are hoping to train as many different eyes, lenses and perspectives on the chambers as possible. If you are potentially interested in studying some aspect of the response of understory forest life to warming, let us know. If you are interested in studying something that can be extracted from soil or litter samples, we may be able to send you material you can work on. If you have something grander in mind (and we love grand things), then we may need more help from you. If interested, send an email to me, copied to MJ Epps (Mj Epps <mycota@gmail.com>).  This collaboration might be in the form of bringing a new method to the chambers (looking at microbial processes, for instance) or considering a group of organisms we’ve somewhat ignored (e.g., fly larvae) or it might be something totally off the wall. Feel free to share this email with likable folks that might be interested. 
I’m also delighted to hear creative ideas about visualizing the differences that have emerged over the years of this experiment (hence the inclusion of several artists of various sorts on this email list, if you were wondering why you were copied). 
I hope this email finds you well. 
Best,
Rob

My microbiome talk at #FOGM15 – the perils (and fun I guess) of redoing one’s talk at the last minute

Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes.  My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology.  I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.

To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer.  And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes

 I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).

I got in pretty late and worked a little on my talk before going to bed.  I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did.  Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research.  I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture.  But once he suggested this notion my talk really congealed (in my head and on paper at least).  It is interesting to me how one simple suggestion from someone with vision and perspective can transform one’s thought process so much …

Anyway, the next day I headed over to the meeting venue (by the beach – life is rough in San Diego).  I got there in time to hear Francis Collins’ talk.  I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there.  More about this later I hope.  Anyway – that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more.  And eventually went to sleep.  Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it).  And voila – only 30 minutes before the PM session was to begin I finished the prep.  I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).

I note – I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome.  Anyway, I gave my talk, and recorded the slideshow with Camtasia.  Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk.
As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people’s pictures and names on all slides and references but I don’t always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on …

Here is a slideshow with Audio (which I recorded via Camtasia)

Here is the Slideshare posting of my slides

Thoughts on Citizen Microbiology and upcoming session at #ASM2013

I am sitting on a Southwest Airlines flight heading to Denver for the American Society for Microbiology 2013 meeting. At 3 PM today I am scheduled to co-chair (with David Coil from my lab) a session on “Citizen Microbiology” (well the full title is Citizen Microbiology: Enhancing Microbiology Education and Research with the Help of the Public). The schedule of the session is at the bottom of this post but it promises to be very interesting and exciting (no bias here at all).

As far as I know, this is the first session ever on “Citizen Microbiology” at a large meeting of any kind. We held a small workshop at UC Davis in January of 2012 on Citizen Microbiology but that was quite small. I note – I use a very broad definition for Citizen Microbiology including basically any project that engages the public in some way to participate in a research project relating to microbes. This is the perfect time to have such a session at a large meeting and the ASM General Meeting is an ideal setting. There are a series of converging forces that makes this timing ideal including:

There is a growing appreciation of microbes and the role they play on the planet. Some of this appreciation is broad – covering all microbes – all the time – everywhere. But much of it is due to a growing interest in the microbes closer to us – those that live in and on us (the human microbiome) – those that live in and on plants and animals and other organisms we care about – and those that live in the places where we spend much of our time (the microbes of the built environment). I mean – come on – everyone is talking about fecal transplants now in public – in cover stories of the NY Times Magazine and in Ted talks.

  • Technological and scientific advances have made it possible to better sample the microbes found in any particular location. Clearly, DNA sequencing technology and associated analytical tools are a central component of these advances, but other factors are important too. 
  • The world is becoming more and more digital which makes the sharing of information (which is key to Citizen Science) easier and better. And social media has made it easier to communicate and discuss actions like Citizen Microbiology. 
  • Citizen Science is growing by leaps and bounds in other areas (e.g., check out http://www.scistarter.com). 
  • Crowdsourcing (not the same thing as Citizen Science – more on this another time perhaps) is also growing in leaps and bounds. 
  • Crowdfunding is providing new ways to fund scientific activities. 
  • Sensors of all kinds are getting cheaper and easier to use and are being deployed widely. 
  • Many people are becoming more and more interesting in recording information about themselves and sharing it with others. 
  • The “open science” movement is making the literature, software, methods and data and more available to everyone with no or few restrictions thus allowing for more people in diverse environments to become engaged in research. 
  • Microbiology education and outreach is spreading with some great journalists and diverse other sources of information including hundreds of microbiology blogs and many other forms of social media being used. 

These are but a few of the reasons why I believe the time is right for Citizen Microbiology. But there are also what I would call somewhat negative reasons why the time is right too. These include 

  • Germophobia is rampant and fueled by media hype and marketing forces. 
  • We have done, and continue to do, serious harm to our microbial world. Antibiotics are overused. Antimicrobials are in everything. More and more children and missing out on vaginal birth. And so on 
  • Although our understanding of the importance of microbes is everywhere, there are also many who are overselling what we know – claiming that probiotics will cure all ailments for example. 
  • Some information about microbes that is out there on the web is, well, less that ideal 
  • The ethics of engaging the public in studies of microbes are not fully appreciated by some and not completely understood by most. 

So this is both an exciting and a critical time for microbes and microbiology. And I hope that this session will not only help launch the field of Citizen Microbiology, but will help get everyone to think about the bigger issues and how to move the field forward in the right directions. For there is so much we need to do and think about including

  • Ethics 
  • Funding 
  • Openness and sharing 
  • Visualization 
  • Analysis tools 
  • Communication 
  • Outreach 

And of course – the people at the session are not the only ones engaged in Citizen Microbiology or related activities (see a list we made a while back here). If you are doing a project please post something about it here. And if you are not doing a Citizen Microbiology project – well – why not? Get your act together.

Anyway – got to put away the computer as we land in Denver soon and I will rush off to the conference center, hopefully on time, to chair this exciting session. And I hope to see you there or have you follow online (check out the Twitter hash tag #ASM2013). And keep your eyes open for more excitement in this area.

————————-
Today’s session at ASM 2013:

(Division W Lecture) Authentic Research for Novice Scientists: Phage Discovery and Genomics by Undergraduate Students
Graham Hatfull;
Univ. of Pittsburgh, Pittsburgh, PA.

Understanding Human Influence on Microbial Distribution Patterns in the United States: A Citizen Science Approach
G. Barguil Colares1, J. Marcell1, D. Smith1,2, J. A. Eisen3, J. Gilbert1,2;
1Argonne Natl. Lab., Lemont, IL, 2Univ. of Chicago, IL, 3UC Davis, Davis, CA.

The Home MIcrobiome Project: Learning the Lessons of Citizen Science and Communication
J. A. Gilbert, D. Smith;
Argonne Natl. Lab., Lemont, IL.

The New National Lab: How Citizen Science is Transforming American Research
Darlene Cavalier;
Sci. Starter, Sci. Cheerleader, Philadelphia, PA.

Sequencing the Human Microbiome with Citizen Science
Z. Apte1, J. Richman2, W. Ludington3;
1uBiome, Inc, San Francisco, CA, 2Oxford Univ., Oxford, UNITED KINGDOM, 3Univ. of California, Berkeley, Berkeley, CA.

The American Gut Project: Challenges and opportunities for crowdsourcingmicrobial ecology
Antonio Gonzalez Peña;
Univ Colorado at Boulder, Boulder, CO.

Public Science in Private Places: A Study of the Microbial Ecology of One Thousand Houses in Fifty States and Five Countries
Rob Dunn;
NC State Univ., Raleigh, NC.


UPDATE: Notes from the Session Added 5/23

Here are some notes from the meeting:
Meeting Report: ASM 2013 in Denver, Day 1
ASM 2013, Day 1: From Oceans to Guts
Citizens doing Science, or Science on Citizens? (ASM 2013: Post 1)
Symbionticism: ASM 2013 LINKS
Storify by SPONCH

My storify embedded below

I love this … "Dr. Eleanor’s Book of Common Ants" based in part on citizen science data

This is really cool:  Dr. Eleanor’s Book of Common Ants.  Free to download.  With incredible pics from Alex Wild.  And based in part on data from the School of Ants citizen science project.  You can download the PDF or the iBook from iTunes.  From the folks at “Your Wild Life” including Holly Menninger and Rob Dunn and others.  Definitely worth checking out.

Sampling the Wild Microbial Life of My Home

Just finally got around to doing the sampling of my house for the Wild Life of Our Homes microbial sampling project.

I signed up online, got a kit, got a registration code, and did the sampling today.  I swabbed the exterior door frame, an interior door frame, the kitchen counter and my pillow case.  Plus as a bonus, my 7 year old daughter helped – learning a bit about microbial sampling and also taking pictures of me at work (and a few of herself).

https://picasaweb.google.com/s/c/bin/slideshow.swf

So many cool Citizen Microbiology projects going on now. Some information about them is here but I need to update the links there.

Guest post on "The phone microbiome" from Georgia Barguil in Jack Gilbert’s lab

From @Artologica on Etsy.  The Phonome. 

Today we have a very special guest post from Georgia Barguil in Jack Gilbert’s group at University of Chicago / Argonne National Lab.  Georgia has been coordinating analyses of microbial surveys that have been a collaboration between me and Jack (although really driven by Jack and his lab in most ways).  The study subject: cell phones and shoes.  The study locations: conferences and meetings in order to have participation in microbial surveys by “citizen” scientists of one kind or another.  We did this together at the AAAS meeting.  And then Gilbert’s lab did this at ThirstDC.  And then I did this at SciFoo at Google HQ.  We are working on a paper on this and wanted to get some results out to the community so Georgia wrote up this post.


Ever wanted to know what bacteria are on your shoes and phones? Of course you have! Here we explored the bacteria that call shoes and phones home; the shoes and phones belonged to employees at Google’s Headquarters, and to participants at the Thirst DC and AAAS annual meeting conferences over 2012 (Fig. 1). Altogether, 84 phones (34 from GoogleHQ, 23 from ThirstDC and 27 from AAAS) and 68 shoes (15 from SciFoo, 24 from ThirstDC and 29 from AAAS) were sampled. The DNA of these samples was extracted and the bacteria were identified by sequencing and subsequent computational analysis of a key gene (16SrRNA) found in all bacteria. Here we show some of the results.

Fig. 1: Map showing the 3 sampling locations: AAAS in Vancouver, SciFoo in California and ThirstDC in Washington

There are quite a lot of microorganisms found in these environments, as you can see in the graph below (Fig. 2), where each bar represents a sample and each color represents a group of bacteria. Also by looking at the chart you can see that the bacteria that live on phones and shoes are different, and found in different proportions. Actually, by comparing the bacterial profile from an unidentified sample with this collection, we could tell you whether that sample was from a phone or a shoe!

Fig. 2: Genus-level diversity and abundance of bacteria associated to phone and shoe samples.

In the shoe samples you can see a lot more colors, which implies that the shoes are home to more bacterial groups than the phones. Out of 560 groups of bacteria found, there were 90 that favored either shoes or phones; 70 of these groups favored the shoe environment while the other 20 favored the phone. Some of the groups that preferred the phones were:

  • Streptococcus (dark green)- many streptococcal species are nonpathogenic, and form part of the commensal human microbiome of the mouth, skin, intestine, and upper respiratory tract.
  • Staphylococcus (brown)- most species of this genus are harmless and reside normally on the skin and mucous membranes of humans and other organisms.
  • Rothia (gray)- is a common inhabitant of the human oral cavity and respiratory tract. Some species were identified as gluten-degrading natural colonizers of the upper gastro-intestinal tract.
  • Actinomyces (army green)- normally present in the gingival area, they are part of the commensal flora, and are the cause of most common infection in dental procedures and oral abscesses. Many Actinomyces species are opportunistic pathogens of humans and other mammals, particularly in the oral cavity. In rare cases, these bacteria can cause actinomycosis, a disease characterized by the formation of abscesses in the mouth, lungs, or the gastrointestinal tract.
  • Prevotella (red)- has been a problem for dentists for years. As a human pathogen known for creating periodontal and tooth problems, Prevotella has long been studied in order to counteract its pathogenesis.
  • Gemella (bright yellow)- group of bacteria primarily found in the mucous membranes of humans and other animals, particularly in the oral cavity and upper digestive tract
  • Micrococcus (pale green)- have been isolated from human skin.
  • Corynebacterium (yellow)- occurs commonly in nature in the soil, water, plants, and food products. The non-pathogenic Corynebacterium species can even be found in the mucosa and normal skin flora of humans and animals.
  • Propionibacterium (pale blue)- members of this group are primarily facultative parasites and commensals of humans and other animals, living in and around the sweat glands, sebaceous glands, and other areas of the skin. They are virtually ubiquitous and do not cause problems for most people, but some propionobacteria have been implicated in acne and other skin conditions.

It is evident that all of these groups are commonly found in the skin and mucous membranes of humans, so it is expected that these groups occur in phones due to the close contact with the hands, face, mouth and breath.

In the plot below (Fig. 3), phones (blue squares) and shoes (orange triangles) from all sampling locations were analyzed together and you can see that phones harbor a very different community to shoes (in fact this is a statistically significant difference) – but shoes all look quite similar while phone microbiome are actually quite variable. It may be possible that the microbiome of your phone is reasonably unique to you, and that we could tell whose phones was who’s by the microbes that lived on the phone.

Fig. 3: Principal coordinate analysis (PCoA) plot using the UniFrac distance obtained for all phone (blue squares) and shoe (orange triangles) samples.

When dividing the samples according to geographical location instead of phones/shoes (Fig. 4), the three sampling locations do not form discrete clusters, and are not statistically significantly different (p>0.05), which suggests that no matter the geographical location you sample, you will find similar bacterial communities.

Fig. 4:PCoA plot using the UniFrac distance obtained for both phone and shoe samples from the 3 sampling locations. The red squares represent AAAS samples, while the blue circles and orange triangles represent SciFoo and ThirstDC, respectively.

However, if we only consider the bacteria found on shoes (Fig. 5), then GoogleHQ (green circle) is statistically different from both AAAS (red square) and ThirstDC (blue triangle). This difference is mostly due to a higher abundance of Corynebacterium and Kocuria groups found in the GoogleHQ shoe samples.

Fig. 5: PCoA plot using the UniFrac distance obtained for all shoe samples from SciFoo (green circles), AAAS (red squares) and ThirstDC (blue triangles).

The microbiota found in phones was highly similar among the three sampling locations (Fig. 6), indicating that phones tend to harbor the same groups of microorganisms even in different locations, regardless of the phone model and owner microbiota. As it can be observed in the plot below, phone samples from AAAS (red squares), ThirstDC (orange triangles) and SciFoo (blue circles) are interspersed.

Fig. 6: PCoA plot using the UniFrac distance obtained for all phone samples in the 3 sampling locations. GoogleHQ is represented by the blue circles, while Thirst DC and AAAS are represented by orange triangles and red squares, respectively.

In conclusion, there were more biological differences between shoes and phones than between the three geographical locations. Phones and shoes harbored microbiomes representing the environments they most often came into contact with. Phones were closely related to the skin and upper respiratory tract, and shoes reflected the bacteria found in soil and the environment.

Although many of the groups found both in shoes and phones have pathogenic representatives, you should not be scared, as it does not mean that you are going to get sick. Most of the isolated, characterized and sequenced bacterial groups available in the sequence databases are the pathogenic ones, exactly because of their importance to human health by aiding in the diagnosing and treatment of diseases. Some of the “relatives” of these pathogenic bacteria are actually good-guys that are usually present in your normal microbiota and do not represent any risks, in fact they may actually be preventing the ‘bad-guys’ from growing on your phone!  On the other hand, it is always a good idea to clean your cell phone screen once in a while, just to be safe.


For some other reading about the phone sampling efforts see

Guest post: uBiome puts microbiome science in the hands of the people

It is a fascinating time to be doing microbiology. One of the latest occurrences is the spread of work on the human microbiome and even more recently the launching of several crowdfunding / citizen science efforts in this area. (Full disclosure – I am a collaborator on one of these efforts – the American Gut Project).  Another one of these efforts is a startup called uBiome. After seeing the announcement of their launch I asked Zac Apte, one of the founders, if he would be interested in writing a guest post for my blog on what they are doing. And, well, he agreed. And it is below (the post title “uBiome puts microbiome science in the hands of the people is from him too – I added the pic).


uBiome puts microbiome science in the hands of the people

Most people think “germs” is a dirty word. That’s what we’re taught since preschool. But the truth is that microbes aren’t just good or bad — it’s a lot more complicated than that. We are surrounded by microbes (on and inside of us) that form a complex ecosystem that supports and nourishes our health.

uBiome (www.indiegogo.com/ubiome) is a citizen science startup focused on allowing people direct access to this cutting ed research. By amassing a large set of microbiome samples along with health and lifestyle data, we will perform a microbiome-wide association study, examining specific traits as well as diseases such as diabetes, heart disease, hypertension, and depression in the context of the human microbiome.

We hope participants will join our community and track themselves in the long term — as you change your diet or exercise regime, begin taking a new medication, such as an antibiotic, or simply as you age. Now is a great time for a first data point.

Finally, we’re not just polling people for their poop. We’re also polling them for their creativity in scientific research. When our first dataset goes live, we’re going to ask our citizen scientists to form their own cohorts and we’ll empower them (statistically speaking) to test their own hypotheses. That’s our vision.

Our team has expertise in metagenomics as well as roots in population genetics, computer science, and network mathematics. We also have a team of scientific advisors which includes inventor and MacArthur Genius award winner Dr. Joseph DeRisi, biotechnology pioneer and inventor of the recombinant Hepatitis B vaccine Pablo Valenzuela, as well as doctors, bioinformaticians, and researchers.

We really appreciate Jonathan Eisen reaching out to give us this opportunity to say hello on the Tree of Life blog — and we look forward to engaging with you!

By Zac, Will and Jessica – the uBiome team

American Gut Project: Food, crowd sourcing, citizen science, open science, and MICROBES – what could be better?

A press release just came out announcing the American Gut Project: New public gut bacteria study expected to reach around world | University of Colorado Boulder.  From Rob Knight, Jeff Leach and others this project aims to engage the public in a large scale study of the connection between diet and the human gut microbiome.  Read more about it in the press release and I am sure more will come out soon.  Full disclosure – I have agreed to be a collaborator on the project – though as a fully open project I think pretty much anyone could be a collaborator.  Anyone this is definitely worth checking out.

As an aside – this is not the only crowd sourcing microbiome project out there.  I just became aware of another one called uBiome and I am working on getting a guest blog post from the organizers.  The American Gut project has got dozens of the major players in microbiome research involved.  And with Rob Knight being one of the key players one can expect it to big, cutting edge things.  Not sure about the scope / plans of uBiome but hopefully we will find out more soon.

Notes on #UCDavis Citizen Microbiology Meeting #UCDCitSci

We had a meeting at UC Davis on “Citizen Microbiology” from 1/23-1/24. It was a small meeting funded via my microBEnet project which itself is supported by a grant from the Alfred P. Sloan Fundation. The meeting was held at UC Davis – participants stayed at the new Hyatt on campus. We met in the new Conference Center. Participants at the meeting were me, David Coil (post doc in my lab), Paula Olsiewski (from the Sloan Foundation), Holly Bik (post doc in my lab), Darlene Cavalier (founder of ScienceForCitizens.Net), Dan Smith from Argonne National Lab, Denneal Jamison from UC Davis, Holly Menninger from NC State, Noah Feirer from CU Boulder, Josh Neufeld from Waterloo, Jason Bobe from The Personal Genome Project, Tom Bruns form UC Berkeley, Madhu Katti from Fresno State, Chris House from Penn. State, and Patrik D’haeseleer (from Lawrence Livermore National Lab).
Below is a “Storification” I made of the tweets and links from the meeting.

http://storify.com/phylogenomics/uc-davis-citizen-microbiology-meeting-ucdcitsci.js[&amp;lt;a href=”http://storify.com/phylogenomics/uc-davis-citizen-microbiology-meeting-ucdcitsci&#8221; target=”_blank”&amp;gt;View the story “UC Davis Citizen Microbiology meeting #UCDCitSci” on Storify&amp;lt;/a&amp;gt;]

Crosspost from http://microbe.net – fun stuff from Rob Dunn

I am cross-posting this from the microBEnet blog I co-write:
I am enjoying the posts to the Scientific American Blogs by Rob Dunn on his and other Citizen Science project(s) and I thought I would share here.
If you do not know about Rob Dunn’s projects, well, you should.  I am particularly fascinated by “The Wild Life of Your Homes” which relate to the above posts.  He does some other fascinating projects too like “School of Ants” and “Wild Life of Your Body“.  Completely brilliant stuff worth checking out.