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

Microbes, art and a bit of satire all in one place – Design Interactions at the RCA

Got pointed to an interesting site recently – “Design Interactions at the RCA”  This is a program (or as they call it – a programme) at the Royal College of Art in London.  One of the current students – Lana Porter – contacted me about a possible project she was working on involving microbes.  She also pointed me to some past projects connected to microbes from the program.  The two she pointed to are:

  • Viruses, close enemies or distant cousins? | Design Interactions at the RCA. From Mikael Metthey.  It appears to be from a few years ago but I am not sure.  Regardless, it is pretty humorous.  It is basically a description of an attempt to create “more intimate ways to approach the process of vaccination” by having poxteddy bears and cowpox rides and vaccination playgrounds.
  • The Race.  From Michael Burton.  Also from a few years ago. This one is about antibiotics and microbial evolution and the hygiene hypothesis.  

And then browsing around the site led to some other interesting concepts:

Seems like a fun programme (or program) …

Headline says it all "Opera singer grows algae on her face by feeding it w/ her breath & then the audience eats it"

Wow.  I am always on the lookout for microbe-themed art.  In most cases, when I see such art, I think “wow – that is an interesting way of embedding microbes into a traditional form of art”.  You know – painting with microbes or art with microbes in it or such.  Well, in this new case I can say this is the most unusual and most creative use of microbes in art I have ever seen: Opera singer grows algae on her face by feeding it with her breath and then the audience eats it

You see, an opera singer work a “head-mounted, face-clinging device” which contained within in some algae in water.  And then the algae was fed by the opera singer’s breath.  This is part of something called the “Algae Opera“.  The most amazing part of this is described in the io9 article

“Because the algae’s growth is dependant on the amount of CO2 it receives, the singer controlled her pitch and volume to alter various characteristics of the algae, including taste (what they called “sonic enhancement”). Depending on the way she sang, the different pitches and frequencies could make the food taste either bitter or sweet”

And then at the end of the performances the audience was invited to sample some of the algae. Yum.  Certainly a bit weird.  But kudos on the creativity index.

What to do – what to do – cool microbial art w/ a #badomics word — must resist purchasing — must resist …

OK – thanks to Dan Smith for pointing me to: Phonome original watercolor painting bacteria by artologica

This was inspired in part by phone sampling I helped Dan and Jack Gilbert do at the AAAS meeting.  And Michelle Banks (i.e., @artologica) has not only made microbial art out of it but has coined a new OME word.  I think she is aiming directly at me here … must resist.  Must resist.

This is both crazy and completely brilliant: The Microbial Academy Of Sciences

Oh My God.  This is so wild and crazy I can’t just write OMG – I have to write the whole thing out: The Microbial Academy Of Sciences: What Bacteria Can Discover That We Can’t | Co.Exist: World changing ideas and innovation

The article describes an art exhibition in San Francisco in which one part involves giving microbial cultures access to images from space.  The reason for this is possibly captured in this quote

“Because cyanobacteria can perform photosynthesis,” Keats says, “they’ll be able to detect patterns of starlight just as human scientists do with their eyes. The difference will not be in their methodology, but rather in the conclusions they reach.”

and even better

But in all those eons, bacteria have never been given observatory access, to study the cosmos for themselves. … My observatory is built to address that unfortunate oversight, providing the resources for colonies of bacteria to research a theory of everything, reconciling cosmic and quantum observations in their own bacterial way.”

I know some hard core scientists may object to this and some of the other lines by the artist but I personally think this is brilliant (in a devious way but brilliant nevertheless).   Everyone out there should read this article by Morgan Clendaniel.  And I for one and going to try to go to the exhibit ASAP.  I personally cannot believe I have not heard of this yet since it seems to have opened in January …

Germophobia: wanna get people in the mood for "Contagion" movie about killer virus – grow harmless microbes in public #microbialart

Well, this story is pretty cool in many ways. David Coil, who works on my “microBEnet” project posted an entry on our blog: Microbial art in the built environment: bacterial billboard goes viral which called my attention to the story.

Seems that the folks promoting the microbe-focused movie “Contagion” came up with a fun marketing idea. They created a living billboard with microbes on it

It is pretty cool. Just watch how the letters come out and the billboard becomes 3D. It would be fun to do this with some event at UC Davis .. will have to think about it. But overall, I think this idea is really cool and very very well executed.

However, I do want to note some of the reporting on it has gotten a few details a bit off. For example, in the Washington Post: ‘Contagion’ bacteria billboard is exactly what it sounds like (Video) – Celebritology 2.0 – The Washington Post they write

“A YouTube video shows the process in which “two large Petri dishes were inoculated with live bacteria including penicillin, mold and pigmented bacteria.” The result is the most amazing, creepy and literal viral marketing campaign in recent history”

Well, not exactly. Penicillin and mold are not live bacteria. Penicillin is alas, not even alive but I think they are referring to organisms that make the antibiotic, not the antibiotic itself. And this is certainly a great viral marketing campaign, but it is not “literally” viral marketing as these are not viruses in the billboard.
The Montreal Gazette has a better story on the campaign: Bacterial billboard brings ‘culture’ to Hollywood marketing. In the article they describe in more detail the ideas and some of the challenges behind the living billboard. Most interesting to me:
“We wanted to create an organic execution that people could fall in love with,” said Anthony Ganjou, founder of U.K.-based CURB media, an agency specializing in natural and sustainable media whose previous creations include billboards made out of grass plants and light installations made out of glow-in-the-dark bacteria.
Using 35 different strains of bacteria and fungi — including penicillin, mould and pigmented bacteria — CURB’s team of 25 microbiologists and immunologists tested different strains of bacteria to see which would work best at creating a message that would slowly grow into letters making up the film’s name.
So I guess they too called the mold penicillin not Penicillium … may be more common than I thought. But also worth noting is this is a agency that specializes in living billboards and this is not the first time they have done something with microbes. In fact they have done some pretty cool living/outdoor ads including using compost, crop circles, mowing patterns, and even, yes, bioluminescence: Bioluminescence – CURB, sustainable advertising, natural media
Going back to the accuracy of the reporting issue. I note there are others out there who have flagged the story and the concept due to the fact that the movie is about a killer virus and the billboard is of course using bacteria and fungi. For example see Katherine Hobson’s post at the Wall Street Journal Blog: Studio Promotes Killer-Virus Movie … With Bacterial Billboard. In it she says
We at the Health Blog are very sensitive to mixing up viruses and bacteria, probably because we’ve made that error ourselves before.
So on one hand, we think the promotion Warner Bros. Canada dreamed up for Steven Soderbergh’s “Contagion,” which opens today, is clever …..
But then she goes on to critique it

On the other hand, the movie is about a virus — the fictional MEV-1. People are already confused about the differences between viral and bacterial ailments, to the point where they will demand antibiotics for problems that likely have a viral cause, like upper respiratory infections.

Personally I think this may be a bit too curmudgeony. The campaign clearly had the desired effect by showing, well, that microbes can grow fast. So the microbes they used were not viruses. And so the ones they used were not harmful. It still is creepy in a way. It is a fine balance of course. We (the royal we here) want to promote microbes as being fun. And we also want to promote them as not always being dangerous. But microbes also do kill a lot of people. And this billboard will probably do more to get people talking and thinking about bacteria and mold than any other movie promotion in recent memory.
In the end microbes I guess creep people out much of the time. And we microbe fans just need to work on that to find ways such that microbes are not always viewed as icky.  So – sure this is capitalizing on a general feeling of germophobia.  But hey – that is pervasive and not the fault of the movie marketers (NOTE – ORIGINAL VERSION OF POST LEFT OUT THE “NOT” HERE – OOPS).
Just a last little note here – though some of the reporting has implied otherwise, there are lots of examples of microbes being used in art or related enterprises. See for example Microbial Art as well as the “Growing Impressions” work of Baldwin and Gulden and the work of Hunter Cole.  Lots of other living art out there including microbes – if anyone knows other examples please post.