AMERICAN SOCIETY FOR MICROBIOLOGY
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
By Tiffany Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M. Hartmann, Afrah Shafquat, Casey DuLong, Catherine Baranowski, Dirk Gevers, Jessica L. Green, Xochitl C. Morgan, John D. Spengler, Curtis Huttenhower
Abstract
Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional pro- filing showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures.
Importance
Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs.
Mass transit systems host large volumes of passengers and facilitate a constant stream of human/human and human/built environment microbial transmission. The largest urban mass transit system in the United States (that in New York) facilitates an average of 11 million trips per weekday. The next four largest systems (those in Washington, DC; Chicago; Boston; and San Francisco) transport just over 1 million passengers per weekday (1), and yet little is known about the mass transit system microbial reservoir. Understanding the associated dynamics of microbial transmission between humans and the built environment and those of microbial occupation and persistence on different surfaces can inform decisions regarding public health and safety.
Microbial DNA sequencing-based studies have revealed that microbial communities of the built environment are greatly influenced by their human occupants. Communities within homes showed high similarity to those of their inhabitants (2), and specific surfaces frequently contacted by human skin, such as keyboards or mobile phones, had microbial communities that reflected those of skin (3, 4). In restrooms and classrooms, variation in microbial community composition across surface types was associated with variations in human contact with those surfaces: desks contained human skin and oral microbes, while chairs contained intestinally and urogenitally derived microbes (5, 6). However, a limitation of most built environment microbiome research is that human contact, surface type, and material composition are frequently confounded. For example, in the classroom study described above, different forms of human contact were associated with distinct microbial community profiles; however, the desks and chairs were also constructed from different materials.
Previously observed subway microbial communities comprised microbes from both humans and the environment. Air samples from within the New York and Hong Kong subway systems included microbes originating from soil and environmental water in addition to human skin (7, 8). A recent metagenomic study of New York subway stations (9) has been widely criticized (10) and left unanswered many questions regarding detailed analysis of the transit microbiome, but it has provided an initial reference data set for further analysis of subway microbiome diversity. In addition, while that study collected information regarding surface types, it did not standardize their characterization or, as a result, investigate surface-specific enrichments for microbial taxa. Understanding the separate influences of human contact, surface type, and surface material would help identify mechanisms through which microbial communities form and persist on surfaces within built environments.
In the present report, we provide the first comprehensive metagenomic profile of microbial communities across multiple surface types and materials in a high-volume public transportation system. Samples were collected from seats, seat backs, walls, vertical and horizontal poles, and hanging grips inside train cars in three subway lines, as well as from touchscreens and walls of ticketing machines inside five subway stations. Using a combination of 16S amplicon and shotgun metagenomic sequencing, we characterized the microbial community composition, functional capacity, and pathogenic potential of the Boston mass transit system. In agreement with previous studies, we observed combinations of human-, soil-, and air-derived microbial communities across the system. Taxonomic differences were most strongly associated with surface type, in contrast to geographic, train line, and material differences, in a multivariate analysis. The distribution of metabolic functions was dominated by Propionibacterium acnes bacteria, which made up a majority of the community. Minimal antibiotic resistance genes and virulence factors were detected across transit system surfaces. In addition to identifying the most important factors determining microbial colonization, our results may serve as a baseline description of microbes on public transportation surfaces, which will be relevant for future design of healthy transit environments. 
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Discussion
Here, we report on the microbial profile of the Boston metropolitan transit system. Previous studies have characterized the Hong Kong and New York subway aerosol communities (7, 8), as well as surfaces in the New York subway (9), but we believe this to be the first study to have determined how space utilization by passengers, surface type, and material composition individually affect microbial ecology. We further describe the microbial community metabolic potential across surface types and metagenomically assess the absence of pathogenic potential. The former primarily reflected P. acnes pathways on holds and aerobic respiration on seats and touchscreens; resistance and virulence factors among the latter were depleted relative to environments such as the human microbiome.
The surface type was the major driver of variation in composition, lending support to three potential hypotheses positing that differences may be driven by (i) human body interactions (6); (ii) the material composition of these surfaces, which may enhance microbial adherence and growth; or (iii) a combination of the two factors. Our data support the third hypothesis. First, we observed a significant enrichment of oral microbes on horizontal poles and grips, which may be higher up and closer to the face of each rider or may reflect transfer through skin-mediated contact (Fig. 1C). Second, both 16S data and shotgun data showed enrichment of vaginal commensals on seat surfaces, which may be transmitted through clothing. Third, we found that seats were enriched in vaginal and oral taxa relative to seat backs and that outdoor touchscreens were enriched in alphaproteobacteria relative to indoor touchscreens. If surface material were the only driver of microbial composition, seats versus seat backs and indoor versus outdoor touchscreens should have similar taxonomic profiles. The surface material certainly plays at least a partial role, however, as we observed decreased levels of Corynebacterium spp. in vinyl seats compared to polyester seats. Overall, our observations indicate that both human body interactions and surface material shape community composition, with the former being the stronger driver.
Previous studies of the transit microbiome, particularly those performed in New York (9) and Hong Kong (8), have also shown environmental exposure to be an additional driver of its microbial community composition. Afshinnekoo et al., for example, found that the human DNA in samples reflected census demographics for the surrounding region (9), although we saw no differentiation at the microbial level among Boston train lines serving suburbs with different ethnodemographics. We primarily observed the impact of environmental exposure on outdoor touchscreens, in agreement with the higher alpha diversities for outdoor stations in Hong Kong reported by Leung et al. The surfaces that we investigated are nearly uniformly exposed to a high volume and diversity of rider interactions. This frequent human contact could homogenize many potential influences on microbial populations, such as demographics or weather. Since the body sites used for contact, indoor/outdoor location, and material composition remain consistent, these exposures would thus shape the taxonomic differences we observed across the Boston subway.
There are few nonopportunistic pathogens in the built environment outside hospitals (43). None were reported for restrooms (5), classrooms (6), or Hong Kong subway aerosols (8), possibly due to lack of phylogenetic resolution with 16S sequencing. During partial assembly of home (2) and rest room (44) surface metagenomes, shotgun sequencing facilitated identification of opportunists with pathogenic potential, but even with the increased resolution, outright virulence factors were rare. Robertson et al. detected no human pathogens in New York subway aerosols by the use of Sanger sequencing and pyrosequencing (7). Furthermore, although Afshinnekoo et al. reported that 12% of the taxa detected represented known pathogens in the National Select Agent Registry and PATRIC database, that database uses an extremely broad definition of “pathogen,” and these results were later refuted (10). Our study assessed whether typical subway microbial communities were unusual in their carriage or transfer of antibiotic resistance genes and virulence factors. We detected low numbers of these genes, and they were present in amounts that were drastically smaller than those observed in the human gut.
One goal of studying the microbiology of the built environment is to establish a baseline to which deviations can be compared to detect potential public health threats. As with the human microbiome, however, intersubject variability appears to be quite high in built environments (e.g., buildings) and in transit systems, and both greater cross-sectional breadth and greater longitudinal depth are still necessary. All subway microbiome papers published to date have reported a high level of skin-associated genera. In addition to this work, Leung et al. (who studied Hong Kong subway aerosols) reported results that included species of Micrococcus (4.9%), Enhydrobacter (3.1%), Propionibacterium (2.9%), Staphylococcus, and Corynebacterium (1.5%), while Robertson et al. detected high levels of members of the families Staphylococcaceae , Moraxellaceae , Micrococcaceae , Enterobacteriaceae, and Corynebacteriaceae. The report of Afshinnekoo et al. from their study of the New York subway is the only major exception, with the most abundant organisms instead found to be Pseudomonas stutzeri , Acinetobacter, and Stenotrophomonas. If microbes shed from skin (or still resident on shed skin cells) do dominate mass transit environments, it must be determined whether these microbes are deposited, dormant, or actively growing or whether they can be stably transferred from one individual to another.
Like those in built environments, however, human-associated microbes are by no means the only apparently functional community residents even when abundant. Notably, our samples from walls, which are not consistently touched but are in the presence of high human density, had biomass lower than and microbial compositions different from samples from other train surfaces. Establishing a “typical” microbial baseline for mass transit environments will require thoughtful sample design that controls for local space properties, short- and long-term temporal variation (e.g., time of day and season), and cross-sectional differences within and between cities. It may also prove useful to monitor for a combination of innocuous versus undesirable organisms and metabolic or functional profiles, as the results have been observed to indicate greater stability than those seen with analyses of taxonomy in the human microbiome (45). In some cases, specific pathogens may be easier to detect; in others (e.g., when individual pathogens may be extremely low density), structural, functional, or metabolic shifts may be better indicators of changing transit profiles and, consequently, of health hazards. In all such cases, future studies should incorporate expertise from architecture, engineering, public health, microbiology, and ecology, thus allowing both confident and interdisciplinary analyses as well as institutional changes in response to scientific findings.
In conjunction with other published investigations, this work helps to characterize the “urban microbiome” and, in doing so, adds to our understanding of how these microbial communities are formed, maintained, and transferred. Such studies fall in a critical space between the categories of environmental and human-associated microbial ecology and as such must address the challenges of both. Improved approaches to such studies should include designing studies with rich metadata, including architectural features, human contact, environmental exposure, surface type, and surface material; accounting for a wide range of potential biochemical environments, contaminants, and biomass levels; and involving institutional review boards, city officials, and engineers as appropriate. Future work will help to determine which urban microbes are viable and resident (as opposed to transient), as well as to identify the mechanisms utilized by the microbes to persist in the built environment. It will also be important to identify microbes that can be transferred between people via specific fomites, since this has the potential especially to inform public health and policy (by monitoring organisms or gene content or both). A greater understanding of these processes may thus eventually lead to construction of built environments that enhance and maintain human health.
About the American Society of Microbiology
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The American Society for Microbiology is the largest single life science society, composed of over 47,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences. ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.
Tags: Afrah Shafquat, ASM, Boston, Boston MTA, Casey DuLong, Catherine Baranowski, Curtis Huttenhower, Dirk Gevers, Erica M. Hartmann, Galeb Abu-Ali, Germs, Jessica L. Green, John D. Spengler, Jose Vallarino, MA, Mass Transit, Massachusetts, Microbiology, Pathogens, Public Health, Regina Joice, Subway, Tiffany Hsu, Xochitl C. Morgan
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