MetaSUB 2015 Conference Introduction

With a generous grant from the Alfred P. Sloan Foundation, we are launching the project this year. The MetaSUB project expands on the NYC study to create a worldwide, longitudinal metagenomic profile of subways and urban biomes. There are 16 confirmed sites (with more in discussion), spanning 5 continents and many environments, which will help create the first ever comparative metagenomic study of cities. These mass-transit systems represent unique urban biomes, microbiomes, and metagenomes and thus could become comparative portraits of dynamic biological and genetic aspects of the built environment. Moreover, interactions between passengers and the subway surfaces define perhaps one of the world’s largest, high-traffic, and universal built environments for dense urban areas. Also, these subway surfaces define the daily commute for millions of people every single day and billions of people each year, and yet there is very little known about the impact of surface type, season, commuter type, or subway design.


In order to successfully launch such a massive study we have created a MetaSUB Consortium with experts from around the world in the fields metagenomics, bioinformatics, molecular biology, and microbiology, as well as engineers, designers, artists, citizen scientists, material scientists, and architects. This interdisciplinary consortium was designed to achieve all of MetaSUB’s five aims including:


  1. Establish a methodology for sample (air and surface-based) collection across the 16 cities, including an expansive focus on detailed and rich metadata (as Paula Olsiewski says, ”one person’s metadata is another person’s data.”).
  2. Develop bioinformatics pipelines that integrate taxa classification, functional and phylogenetic analysis, biosynthetic gene clusters, potential pathogenicity, and human ancestry and forensics.
  3. Design of the transit systems. This will involve annotation and testing of the variety of types of surfaces of cities, subway design styles, community use (e.g. food or animal presence), air flow, air measures, and surface material (e.g. glass, plastic, metal, ceramic). One great example of these types of integrated sensors is the “Array of Things”. We aim to use these data to create smarter urban and transit ecosystems.
  4. Establish and test several tools for metagenomic profiling to improve taxa classification and enable built-in standards for metagenomics work, in collaboration with Marc Salit at the National Institute of Standards and Technology (NIST), the Extreme Microbiome Project (XMP), and the Metagenomics Research Group (MGRG) of the Association of Biomolecular Resource Facilities (ABRF), and coordinate with the MicroBiome Quality Control (MBQC) project.
  5. Create educational materials and templates for high school, college, and graduate students to learn about metagenomics methods and techniques, as we have done in collaboration with Jeanne Garbarino at Rockefeller University in the after school Learning at the Bench (LAB) Program.

The ultimate goal of MetaSUB is to shift the current paradigm in city-planning and urban design. Just as there is a standard and measurement of temperature, air pressure, wind currents– all of which is considered in the design of the built environment– we propose that the microbial ecosystem is just as dynamic and just as integral to the built environment as these other standards, and should be considered in our designs. Thus, we hope to build a “metagenometer” or “bio-barometer,” a system that can track the molecular echoes, microbiome auras, and metagenomic signatures left behind by this phalanx of microbial friends, and allow us to design “smart cities” with them in mind.
On behalf of The MetaSUB International Consortium,


Christopher E. Mason, Ph.D.
Weill Cornell Medicine