Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

By Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, D. Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, D. Reeves, J. Gandara, S. Chhangawala and 36 more. 2015

287 citations recorded by the source corpus.

SUMMARY The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

Subfields: Molecular Biology, Public Health, Environmental and Occupational Health

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In Molecular Biology

1. M. Barnes
2. C. Turner
3. P. Simner
4. K. Carroll
5. Elizabeth A. Archie
6. Steve Miller
7. Jenny Tung

Citations in the corpus

• Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases (2017, methodology): “of approaches, such as the use of k-mer, marker and alignments, are required to analyze the data to ensure the highest sensitivity and specificity for taxonomic classification [9, 39].”
• Social behavior and the microbiome (2015, background): “Such studies have identified both disease-causing microbes and antimicrobial-resistance genes among the taxa and sequences shared through social contact [15 ,32].”
• The ecology of environmental DNA and implications for conservation genetics (2016, methodology): “Kapoor et al. (2014) applied Ion Torrent sequencing to human mtDNA control region amplicons from urban Cincinnati, USA streams, and Afshinnekoo et al. (2015a) applied Illumina shotgun sequencing to eDNA from object surfaces in the New York City, USA subway system.”