Who’s really riding the subway with you? Characterization of the microbial communities on Boston transport

(Figure modified from Hsu et al., 2016, Boston transport map and wikicommons image of Boston)

Understanding the microbes around us is an important challenge to take on. There have been articles covering changes in microbial communities among rural and more urbanized environments and there’s a whole blog dedicated to microbes and the built environment. An interesting model system for studying the relationship between microbes that inhabit the built environment and humans include transit systems, some of the largest of which shuttle around more than 1 million passengers daily. Clarifying microbial community dynamics in transportation systems has implications related to human health and disease.

Figure 1. Hsu et al., 2016.

Figure 1. Hsu et al., 2016.

Sometimes progress related to understanding microbes in the built environment is accompanied by two steps back. Last year, a study on New York subways (which are part of the largest public transport system in the US) stated that the NY subway system harbored the bugs responsible for the plague (Yersinia pestis) and anthrax (Bacillus anthracis) (Afshinekoo et al., 2015). However, not long after the publication of this study, other authors demonstrated that the data was not actually properly analyzed (Ackelsberg et al., 2015).

Figure 2. Hsu et al., 2016.

Figure 2. Hsu et al., 2016.

Considering how integral public transport is to everyday life for so many people, it’s a bit surprising that there are very few studies focused on understanding the microbes associated with these systems. Just this week, the first attempt at obtaining a comprehensive microbial metagenomic profile was published by Hsu and colleagues this week.

Figure 3. Hsu et al., 2016.

Figure 3. Hsu et al., 2016.

Researchers sampled everything from seats to hanging grips across three subway lines, as well as the touchscreens of the ticketing machines at five subway stations. They obtained a total of 73 samples and using a combination of 16S amplicon and metagenomic sequencing allowed for the characterization of microbial community composition. They found that the type of surface sampled was more influential on taxonomic composition, in comparison to the material itself, or differences in train line or geographic location. You can take a sigh of relief, not many antibiotic resistance genes or virulence factors were identified. The authors suggest that this study as well as future similar attempts might indeed improve future transit system design.

Figure 4. Hsu et al., 2016.

Figure 4. Hsu et al., 2016.

Touchscreen microbial communities were more similar to other touchscreen samples, and train line didn’t seem to really influence community structure. The authors reported that location of ticketing machines (either indoor / outdoor or underground) did have some influence on community diversity, and specifically, indoor or outdoor exposure markedly influences its composition. Essentially, microbial communities in subways originate from human skin and the bacterial side of things was mainly made up of members from the Firmicutes, Proteobacteria, and Actinobacteria while the yeast Malassezia globosa, as well as Propionibacteriam phages accounted for the majority of the nonbacterial representatives. Interestingly, this study demonstrated that with the use of the appropriate methods, no pathogens were detected.

Figure 5. Hsu et al., 2016.

Figure 5. Hsu et al., 2016.

With the mountains of sequence data available, it’s essential that methods developed for analysis are able to accurately identify the presence of pathogens. This is essential in not only places like hospitals, but also on fresh produce and in public transportation systems. Previous instances where data was incorrectly assessed highlight the danger of not appropriately utilizing available methods for data analysis.

References

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. Tiffany Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M. Hartmann, Afrah Shafquat, CaseyDuLong, Catherine Baranowski, Dirk Gevers, Jessica L. Green, Xochitl C. Morgan, John D. Spengler, and Curtis Huttenhower. 

Avoiding Pandemic Fears in the Subway and Conquering the Platypus. A. Gonzalez, Y. Vázquez-Baeza, J. B. Pettengill, A. Ottesen, D. McDonald, and R. Knight. 

Lack of Evidence for Plague or Anthrax on the New York City Subway. Joel Ackelsberg, Jennifer Rakeman, Scott Hughes, Jeannine Petersen, Paul Mead, Martin Schriefer, Luke Kingry, Alex Hoffmaster, Jay E. Gee. DOI: 10.1016/j.cels.2015.07.008

Modern methods for delineating metagenomic complexity. Afshinnekoo, Ebrahim, et al. Cell systems 1.1 (2015): 6-7. DOI: 10.1016/j.cels.2015.07.007

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About Kelle Freel

I'm currently a postdoc working at the Hawai'i Institute of Marine Biology with Dr. Mike Rappé. I'm interested in the biogeography and ecology of microbes, especially of the marine variety. After studying a unique genus of marine bacteria at Scripps Oceanography in grad school, I moved to France, where I worked with a group studying yeast population genomics. In my free time, I like to do outdoorsy stuff, travel, and cook.
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