MetaSUB: First International Summit of Metagenomics & Metadesign of Subways and Urban Biomes

Get ready for a microbiome and metagenome festival in NYC!

We are excited to announce the first international summit on metagenomics and metadesign of subways and urban biomes (MetaSUB), held in New York City (NYC) on June 20, 2015, at the New York Genome Center (NYGC). This will be held right after a related meeting at the New York Academy of Sciences (NYAS) on June 19, 2015, called “Microbes in the City.”  Registration for both meetings are here:

“Microbes in the City” on June  19, 2015

“MetaSUB” on June 20, 2015.

Why?  We recently created the first surface-based, city-scale, microbiome and metagenome profile for New York City. Our paper highlighted preliminary findings from a 2013-2014 dataset of over 1,450 samples from surfaces of the New York City (NYC) subway system, the Gowanus Canal, and some parks. However, our profile of the NYC subway system was just the beginning of discovering the richness of the metagenome and microbiome of the built environmnent (MoBE), subways, and urban biomes (SUB). Indeed, when looking at annual ridership, NYC only ranks 7th on the list of the world’s busiest subways. And so we began to draft a plan for a much larger expansion of the NYC study, a project we are calling MetaSUB, the Metagenomics and Metadesign of Subways and Urban Biomes.

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 world-wide, 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. For a full list of members and collaborators look here. 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 a 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.

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 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.

For more details on the both meetings in NYC, please see the links above, and register for the events there. We will feature a great line-up of speakers, break-out meetings, free child care for all attendees who need it (8AM-5PM, in  a cool genomics room at NYGC), and also a trip to the NY Transit Museum, to get a sense of how the subways have changed over the years.

Also you can check out our website and follow us on twitter (@MetaSUB, or @mason_lab) to stay updated on the status of our study.

Finally, please save the date for the next two international meetings for the MetaSUB Consortium:
2016: June 29-30 in Shanghai, China.
2017: June 29-30, in São Paolo, Brazil.

We hope to see you in NYC this summer!

On behalf of The MetaSUB Consortium,

Christopher Mason, Ph.D.

Weill Cornell Medical College

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Christopher Mason

Christopher Mason is an associate professor at Weill Cornell Medical College.