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The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities

BACKGROUND: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we...

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Autores principales: Gohli, Jostein, Bøifot, Kari Oline, Moen, Line Victoria, Pastuszek, Paulina, Skogan, Gunnar, Udekwu, Klas I., Dybwad, Marius
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924074/
https://www.ncbi.nlm.nih.gov/pubmed/31856911
http://dx.doi.org/10.1186/s40168-019-0772-9
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author Gohli, Jostein
Bøifot, Kari Oline
Moen, Line Victoria
Pastuszek, Paulina
Skogan, Gunnar
Udekwu, Klas I.
Dybwad, Marius
author_facet Gohli, Jostein
Bøifot, Kari Oline
Moen, Line Victoria
Pastuszek, Paulina
Skogan, Gunnar
Udekwu, Klas I.
Dybwad, Marius
author_sort Gohli, Jostein
collection PubMed
description BACKGROUND: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. METHODS: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. RESULTS: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer. Temperature had a strong effect on diversity in air but not on surface diversity. Among-sample diversity was also significantly associated with air/surface, season, and temperature. CONCLUSIONS: The results presented here provide the first direct comparison of air and surface bacterial microbiomes, and the first assessment of seasonal variation in subways using culture-independent methods. While there were strong similarities between air and surface and across seasons, we found both diversity and the abundances of certain taxa to differ. This constitutes a significant step towards understanding the composition and dynamics of bacterial communities in subways, a highly important environment in our increasingly urbanized and interconnect world.
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spelling pubmed-69240742019-12-30 The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities Gohli, Jostein Bøifot, Kari Oline Moen, Line Victoria Pastuszek, Paulina Skogan, Gunnar Udekwu, Klas I. Dybwad, Marius Microbiome Research BACKGROUND: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. METHODS: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. RESULTS: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer. Temperature had a strong effect on diversity in air but not on surface diversity. Among-sample diversity was also significantly associated with air/surface, season, and temperature. CONCLUSIONS: The results presented here provide the first direct comparison of air and surface bacterial microbiomes, and the first assessment of seasonal variation in subways using culture-independent methods. While there were strong similarities between air and surface and across seasons, we found both diversity and the abundances of certain taxa to differ. This constitutes a significant step towards understanding the composition and dynamics of bacterial communities in subways, a highly important environment in our increasingly urbanized and interconnect world. BioMed Central 2019-12-19 /pmc/articles/PMC6924074/ /pubmed/31856911 http://dx.doi.org/10.1186/s40168-019-0772-9 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Gohli, Jostein
Bøifot, Kari Oline
Moen, Line Victoria
Pastuszek, Paulina
Skogan, Gunnar
Udekwu, Klas I.
Dybwad, Marius
The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
title The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
title_full The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
title_fullStr The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
title_full_unstemmed The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
title_short The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
title_sort subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924074/
https://www.ncbi.nlm.nih.gov/pubmed/31856911
http://dx.doi.org/10.1186/s40168-019-0772-9
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