Mapping a hidden world
Dr. Chris Mason taking a swab sample in the New York City subway system
Microbiome
Mapping a hidden world

Scientists around the globe have embarked on an ambitious project to chart and better understand the microbiome, pushing the frontiers of life sciences.

For the average New Yorker, the local subway station is a waypoint to quickly get to work. For Dr. Chris Mason, however, it’s the gateway to the hidden world of the microbiome. When the Associate Professor of Physiology and Biophysics and of Computational Biomedicine at Weill Cornell Medicine in Manhattan entered the 68th Street stop for the number 6 train on a recent morning, he whipped out a handful of nylon swabs to run over the handrails, turnstiles, benches and even electronic info boards above the platform to collect samples. Back in his lab, he ran the samples through assays to identify the genetic material collected in the urban wild.

New York is but one of 72 large cities around the world where scientists like Dr. Mason are chasing insights into the microbiome. They’ve come together under the roof of the MetaSUB International Consortium to map and better understand the interactions between microbes that permeate virtually every aspect of human life.

HUMANS: HOME
TO 100 TRILLION MICROBIAL CELLS

“Every time we touch an object or breathe, we make contact with millions of microscopic organisms such as bacteria, viruses, fungi, protozoa and even algae that have colonized every surface on Earth and made a home inside our bodies,” says Dr. Mason. Experts estimate that every human holds a total of 100 trillion microbial cells, which likely outnumber the number of cells in the human body.

The microbiome has a far-reaching impact on life. On the one hand, it’s responsible for infectious diseases such as cholera or the avian flu. On the other hand, microorganisms act as a live shield to protect humans from pathogens, aid with digestion, process drugs, and promote overall health and well-being. Understanding the myriad of interactions is therefore considered one of the most exciting and dynamic new frontiers of life science. It promises to bolster public health defenses, develop new therapeutic applications and even improve disciplines such as forensics, city planning and architecture.

So far, humans have not fully grasped the size and diversity of this parallel world. In 2013, Dr. Mason started a project called PathoMap that collected samples from the New York City subway yielding the first detailed metagenomic profile of a large metropolis in 2015.

MetaSub takes research to
global scale

MetaSUB will take this microbial sleuthing to the global scale. In June 2016, Weill Cornell Medicine led a myriad of other scientists, researchers and trained citizen scientists who started to collect and analyze samples of DNA and RNA in high-traffic areas of several dozen large cities around the world. The Meta SUB project, headed by Dr. Mason as principal investigator, will run for five years. “Our goal is to drill into longitudinal profiles of the world’s major cities and study how their genetic makeup, pathogen load and even antimicrobial resistance change over time”, explains Dr. Mason.

Getting to know the hidden world around us promises big pay-offs. Researchers hope to better understand the relationship between bacteria that colonize our bodies and conditions like obesity, metabolic syndrome or even mental conditions such as anxiety and attention deficit hyperactivity disorder (ADHD).


This work requires a standardized protocol and platform to make sure the results can be reliably gathered, interpreted and then compared. QIAGEN therefore provides the consortium with its DNeasy PowerSoil as well as QIAseq FX DNA kits to process genomic materials for analysis and preparing the sequencing libraries. “Understanding the various microbiomes and their impact on human health and environment is a key area of interest for our company,” says Michael Kazinski, QIAGEN’s Senior Director Molecular Preanalytic Technologies. “We want to support basic research and medical development with technology that a researcher can use who’s neither an expert in bioinformatics or genetics.”

New insights for public health

With technological advances and rapidly emerging knowledge on the microbiome, researchers increasingly generate insights that are applicable to public and environmental health. For Dr. Mason, the microbiome could even propel the idea of personalized medicine forward. He considers the rich microbial world around us a “phalanx of friends” that should be harnessed to design an individual, “geospatially-informed treatment” plan. In the not-too distant future, a physician could use it to check on any past antimicrobial resistance and implement the best antibiotic for an infection.

It’s a vision worthy of scouring the entire world.

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