Tuesday, December 11, 2012

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

1 comment:

  1. Cool! Does this analysis include the shoe and phone samples that Dan Smith collected at the UC Davis Citizen Science Microbiology meeting as well?

    see http://phylogenomics.blogspot.com/2012/01/notes-on-ucdavis-citizen-microbiology.html


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