Co-occurrence patterns of bacteria within microbiome of Moscow subway

Natalia S Klimenko; Alexander V Tyakht; Stepan V Toshchakov; Margarita A Shevchenko; Aleksei A Korzhenkov; Ebrahim Afshinnekoo; Christopher E Mason; Dmitry G Alexeev

doi:10.1016/j.csbj.2020.01.007

Co-occurrence patterns of bacteria within microbiome of Moscow subway

Comput Struct Biotechnol J. 2020 Feb 1:18:314-322. doi: 10.1016/j.csbj.2020.01.007. eCollection 2020.

Authors

Natalia S Klimenko^{1

2}, Alexander V Tyakht^{1

2}, Stepan V Toshchakov³, Margarita A Shevchenko⁴, Aleksei A Korzhenkov³, Ebrahim Afshinnekoo^{5

6

7}, Christopher E Mason^{5

6

7

8}, Dmitry G Alexeev^{1

9

10

11}

Affiliations

¹ Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar Str., Building 42, Premise 1, Room 1639, Moscow 143026, Russia.
² Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia.
³ National Research Center "Kurchatov Institute", Akademika Kurchatova Sq., 1, Moscow 123182, Russia.
⁴ Immanuel Kant Baltic Federal University, Universitetskaya Str., 2, Room 106, Kaliningrad 236040, Russia.
⁵ Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
⁶ The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
⁷ The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
⁸ The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
⁹ ITMO University, Kronverkskiy Pr., 49, St. Petersburg 197101, Russia.
¹⁰ Novosibirsk State University, Pirogova Str., 1, Novosibirsk 630073, Russia.
¹¹ Atlas Biomed Group, 92 Albert Embankment, Lambeth, London SE1 7TT, UK.

Abstract

Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.

Keywords: 16S rRNA; Biosurveillance; Built environments; Co-occurrence patterns; Subway; Urban microbiome.