Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

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 metro...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	built environment microbiome subway transit Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/57aa6941e596451ca65c18ea3f592984
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spelling	oai:doaj.org-article:57aa6941e596451ca65c18ea3f5929842021-12-02T18:39:34ZUrban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment10.1128/mSystems.00018-162379-5077https://doaj.org/article/57aa6941e596451ca65c18ea3f5929842016-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00018-16https://doaj.org/toc/2379-5077ABSTRACT 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 profiling 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. Author Video: An author video summary of this article is available.Tiffany HsuRegina JoiceJose VallarinoGaleb Abu-AliErica M. HartmannAfrah ShafquatCasey DuLongCatherine BaranowskiDirk GeversJessica L. GreenXochitl C. MorganJohn D. SpenglerCurtis HuttenhowerAmerican Society for Microbiologyarticlebuilt environmentmicrobiomesubwaytransitMicrobiologyQR1-502ENmSystems, Vol 1, Iss 3 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	built environment microbiome subway transit Microbiology QR1-502
spellingShingle	built environment microbiome subway transit Microbiology QR1-502 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 Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
description	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 profiling 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. Author Video: An author video summary of this article is available.
format	article
author	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
author_facet	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
author_sort	Tiffany Hsu
title	Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
title_short	Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
title_full	Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
title_fullStr	Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
title_full_unstemmed	Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
title_sort	urban transit system microbial communities differ by surface type and interaction with humans and the environment
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/57aa6941e596451ca65c18ea3f592984
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Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

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