What Lies Beneath - Probing New York’s Microbial Underbelly

Tue, 10 February 15 09:56

A group of international researchers, including scientists from UCD Academic Centre on Rare Diseases, have completed a fascinating study of the genomic flora contained within the New York subway system. The study, published in Cell Systems, a new high profile scientific journal, reveals a complex ecosystem which, while including many harmless organisms, also included drug resistant disease-causing bacteria and even DNA fragments associated with anthrax and bubonic plague.  The citywide microbiome ‘PathoMap’ shows that it is possible and useful to develop a pathogen map of a city with the main transit system acting as a proxy for its population.

While the PathoMap demonstrates a generally reassuring profile of non-pathogenic bacteria, viruses, fungi and animal species, approximately one half of the DNA sequences collected could not be matched to any  known organism, mainly because we do not yet have genomic information on several organisms e.g. cockroaches. The study also revealed DNA fragments of Bacillus anthracis (anthrax) and a plasmid associated with Yersinia pestis (bubonic plague) albeit at very low levels and not in a live format.

Irish scientists participated in the study bringing advanced informatics analysis to bear on the data set collected by the team led by Dr Chris Mason  at Weil Cornell Medical College.  Dr Sean Ennis, Eoghan O’Halloran and Dr Tiago Magalhães from the UCD Academic Centre on Rare Diseases provided their innovative Ancestry Mapper and used admixture techniques to study the human DNA collected from across the subway which is used by 5.5 million people on average every day.  

Despite sampling an area with high human contact, the researchers found that only an average of 0.2 percent of sequenced material uniquely mapped to the human genome.  Nevertheless, the UCD Researchers were able to provide population analysis which correlates with the US Census records.  For example, a Hispanic area near Manhattan’s Chinatown appeared to comprise a definite mix of Asian and Hispanic human genes.  Similarly, an area of North Harlem showed African and Hispanic genes while an area of Brooklyn with a predominantly white population was predicted to be close to Finnish, British and Tuscan in origin, which could possibly be Irish, but because no high definition genome of the Irish population currently exists this could not be seen.

This study confirms the previous demonstration by the UCD group that population subtypes can be identified from complex genomic data which reveal the relationships between local and global populations.  As the authors of the New York PathoMap study note, this provided a forensic ability to learn about the ancestry of the people who use the Metropolitan Area Transit System.

Speaking about the project, Dr Sean Ennis, Director, UCD Academic Centre on Rare Diseases (ACoRD) said

We are very excited about this project and our collaboration with the group led by Dr Chris Mason at Cornell. PathoMap is an ongoing project, whose next step will involve the study of subway systems in other cities such as Dublin, London, Paris, Mexico City and São Paulo. As part of the next stage of PathoMap we plan to provide information about microbial systems of Luas and Dart.

Dr Tiago Magalhães said

The technologies used to produce in PathoMap are very powerful with applications in forensics, anthropology, identification of differences between different human populations, and also in identifying genetic causes of rare diseases, work that our group at ACoRD/UCD has been producing for the past few years.

With similar studies underway across the globe, efforts like the New York microbiome map can provide new insights into disease surveillance and indicate changes to the balanced microbial ecosystem and risks to inherent disease protection.