Distribution of Microbial Communities and Antimicrobial Resistances in Urban Environments and on the ISS Space Station.

The majority of the world's population lives in cities, yet our understanding of the dynamics and distribution of bacteria, viruses, and antimicrobial resistance (AMR) genes in urban built environments is limited. Cities and urban transport hubs like metro stations and airports represent the sites of highest human population density, and are thus hotspot areas for microbial and genetic exchange in both developing and developed countries. Moreover, most inhabitants, visitors and passenger carry a mobile phone, which serves as a molecular echo of the travel history of a person as well as a representation of his or her personal microbiome. Through leveraging next-generation sequencing (NGS) and metagenome sequencing methods, combined with rapid computational analysis, we can reveal the microbial and genetic profiles, AMR gene content, localization, and movement patterns imprinted on phones and city surfaces, as readily as for clinical samples. International Consortium for Metagenomics of Subways and Urban Biomes (MetaSUB) at Weill Cornell Medicine, which is funded by the NIH, WorldQuant, and the Bill and Melinda Gates Foundation. We are currently analyzing >5.000 whole-genome shotgun metagenomes using samples collected in the subways (15000 samples total of more than 85 cities in 21 different countries). In parallel we analyzed for interrogating microbiomes obtained from > 2000 mobile phone surfaces, which we showcased during several international conferences. To our knowledge this is the first study investigating a comprehensive and worldwide view of urban microbiomes and AMR exchange. To complement our knowledge, we are comparing the generated metagenomes with data collected by the Extreme Microbiome Project and microbial isolates collected at the ISS by NASA during the last 11 years. Furthermore, to evaluate our findings and improve the accuracy of microbiome analyses, we developed novel protocols for metagenomic linked-DNA genomic sequencing (using 10X Genomics Chromium) and long-read sequencing (using Oxford Nanopore MinION and PromethION sequencers).