Pathologists and clinical laboratory managers can expect environmental microbiome detection and monitoring to play an increasingly important role in disease diagnosis, treatment and prevention

For decades, microbiologists and clinical laboratory professionals have prowled the corridors of hospitals to swab physicians’ neckties, the hands of nurses and staff, and various surfaces. These swabs were then cultured to demonstrate how easily infectious microbes can be transmitted in everyday activities.

Now researchers, including microbiologists, are combing the New York City subway system to swab surfaces, collect specimens, and create a map of the urban microbiome. Researchers at Weill Cornell Medical College in New York City want to use the microbiome to pioneer a new method for city-level pathogen monitoring.

Involving Medical Laboratories in Public Pathogen Monitoring

The approach involves rapid, continual sampling and analysis of microbiomes in public places to detect changes that could signal a microbial threat due to bioterrorism or emergent disease. The project could serve as a model for detection, rapid-response, and containment of bioterrorism and other microbial dangers and may eventually involve medical laboratories.

Pictured above is Christopher E. Mason, Ph.D., an Assistant Professor in the Department of Physics and Biophysics at Weill Cornell University in New York City. He is leading an unusual project to study the microbiome in New York City’s subways and other public places. (Photo copyright by PathoMap.)

Pictured above is Christopher E. Mason, Ph.D., an Assistant Professor in the Department of Physics and Biophysics at Weill Cornell University in New York City. He is leading an unusual project to study the microbiome in New York City’s subways and other public places. (Photo copyright by PathoMap.)


“[T]here is no establishment or understanding of the baseline microbiome of public surfaces,” observed Christopher E. Mason, Ph.D., Assistant Professor at Weill Cornell’s Department of Physics and Biophysics. “[T]here is almost zero data,” stated Mason, who heads the project and was quoted in a story published by

Microbiome Map Project Uses Next-generation Sequencing

The student-driven project is called PathoMap. It seeks to study the microbiome at the city level. Volunteers from colleges across NYC are assisting in the sample collection process. They collected 1,404 surface samples from 468 NYC subway stations, the GenomeWeb story reported.

The students also collected sporadic swabs from other public places. These included airplanes, taxis, boats, a petting zoo, and park benches. Air samples were also collected, according to a story published at

PathoMap Uses Next-Generation Gene Sequencing

Next, the research team analyzes the samples using next-generation gene sequencing systems from Illumina [NASDAQ: ILMN] that perform paired-end shotgun sequencing. “PathoMap seeks to use new DNA sequencing methods to monitor pathogens and dangerous organisms in real time as they emerge within a country or city,” the researchers stated on the project’s website.

PathoMap from PathoMap on Vimeo.

Here is a video about the PathoMap project underway at Cornell Weill University in New York City. The goal is to study the microbiome found in the city’s subway system and other public places. Researchers have found the following: Chryseobacterium gleum (a source of hospital-acquired infections); Shigella boydii (can cause dysentery in humans through fecal-oral contamination); and Lysinibacillus sphaericus (produces a toxin that can control mosquito populations). (Video copyright PathoMap.)

PathoMap uses a mobile software application from GIS Cloud to record and analyze samples over time. GIS Cloud is a next-generation platform for apps that manage location information.

New York University Center for Genomics and Systems Biology and Mount Sinai School of Medicine are collaborating on the study. Estimated costs for the project—including sample prep, sequencing, data analysis, and data storage—will run around $1 million.

Pilot Study Will Establish Initial City-level Microbiome Database

Mason’s team is in the process of sequencing the microbial samples and analyzing the data, according to the GenomeWeb story. The initial samples will establish a baseline of microbes present in the NYC subway system. The researchers will expand this initial database by collecting additional samples from the same sites during different seasons of the year. In this way, PathoMap will increasingly generate information on urban microbiomes as more data is collected and processed.

Biomap Applications Extend Beyond Detecting Bioterrorism

Events in recent years have made public health officials acutely aware of the importance to rapidly and accurately detect acts of bioterrorism. That’s according to the National Institutes of Health website. “Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health,” NIH officials stated.

But bioterrorism detection isn’t the only focus of the PathoMap project. A microbial map could have many potential uses, according to a story. The approach could also help to detect and respond to other microbial dangers, such as identifying emerging diseases.

In addition to enhancing rapid response to biothreat situations, the scientists seek to promote awareness of microorganisms present on common surfaces in the environment. The hope is that eventually the entire urban microbiome will be sequenced and analyzed to provide useful information to the public.

Related Projects Include the Human Microbiome Project

PathoMap joins the ranks of a number of initiatives whose aim is to expand understanding of the relationship between microbiomes and health. One such program is the Human Microbiome Project (HMP). The HMP seeks to study complex microbial communities from various areas of the human body. HMP publications have demonstrated that the microbiome is a major genetic signal in humans and contributes key properties essential to human function. One primary goal of the project is to explore the relationship between disease and changes in the human microbiome, according to Wikipedia.

“The recent emergence of faster and cost-effective sequencing technologies promises to provide an unprecedented amount of information about these microbial communities,” observed Anthony S. Fauci, M.D., co-chair of the Human Microbiome Project’s Implementation Group and Director of the National Institute of Allergy and Infectious Diseases. “[This] in turn will bolster the development and refinement of analytical tools and strategies.”

Dr. Fauci’s comment appeared in a National Institutes of Health press release.

For pathologists and clinical laboratory managers, the growing number of human and environmental microbiome-focused studies means a growing body of clinically relevant information, as this knowledge is translated into innovative strategies for the diagnosis, treatment and prevention of disease.

—Pamela Scherer McLeod

Related Information

What Microbes Live in YOUR Subway Station?

Mapping New York City’s Microbiome, One Subway Station at a Time

Pathomap Mapping NYC’s Microscopic Residents

Pathomap: a big task regarding small things: a microbial map of New York City

Mapping the Microbiome

Boston to Test Bioterror Sensors

Current and Developing Technologies for Monitoring Agents of Bioterrorism and Biowarfare