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

Abstract

Figure 3B has been corrected to show the general coverage of the Yersinia pestis pMT1 plasmid, but not the murine toxin gene (yMT). The initial claim of ''.consistent 203 coverage across the murine toxin gene.'' was erroneously based on looking at gene annotation coordinates from different reference sequences. No reads mapped to the yMT gene when updated annotations were used. The Summary, Results, and Discussion sections have been revised to remove and clarify misleading and speculative text about pathogenic organisms. We now state that although all our metagenomic analysis tools identified reads with similarity to B. anthracis and Y. pestis sequences, there is minimal coverage to the backbone genome of these organisms, and there is no strong evidence to suggest these organisms are in fact present, and no evidence of pathogenicity. The figure and the text have been corrected online and in the print version.

Urban stress is associated with variation in microbial species composition—but not richness—in Manhattan

“…Medians (and, in our data set, parks) are unlike indoor environments, which are dominated by human-associated microbes (Lax et al, 2014). This is true even though the medians are, in many cases, just feet above the subway system in which human-associated microbes are most abundant (Afshinnekoo et al, 2015).…”

The ecology of environmental DNA and implications for conservation genetics

“…We are aware of only two population genetic analyses of macrobial eDNA, and both targeted humans. 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. These studies have demonstrated that macrobial eDNA can provide data from rapidly evolving loci, in both organellar and nuclear genomes, which coarsely describe geographic patterns of population genetic diversity.…”

Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers

“…Environmental surveys of the New York City (NYC) subway system microbiome and airborne microbes found that metagenomic analysis tools were unable to find a match to any reference genome for about half of input reads, demonstrating the complexity of the data and limitations of current methods and databases [16,17]. Environmental studies also highlight the importance of reliable species identification when determining pathogenicity.…”