Each city has its own exclusive microbiome, finds study

A new study performed by an international consortium of researchers including a team of researchers from the University of Maryland School of Medicine (UMSOM) reports that each city has its own exclusive microbiome or a “fingerprint” of bacteria and viruses that uniquely identify it.

City. Image Credit: Sean Pavone/Shutterstock.com

As part of the international project, samples gathered from hospitals and public transit systems in 60 cities across the world were sequenced and analyzed, and the results were recently published in the journal Cell.

The study is regarded as the largest-ever global metagenomic study of urban microbiomes, covering both the air and the surfaces of various cities. It involved an extensive analysis of all the microbial species identified—including thousands of bacteria and viruses and two newly identified single-cell organisms that are not included in reference databases.

Lynn Schriml, Ph.D., co-author of the study and Associate Professor in the Department of Epidemiology & Public Health, Institute for Genome Sciences (IGS), at UMSOM, headed the sampling efforts for the study at Baltimore’s transit systems.

Baltimore’s distinct microbial signature reveals a unique, fascinating, and diverse world, providing insights into geographical variation and previously unknown microbial genomes.”

Lynn Schriml, Associate Professor, Department of Epidemiology & Public Health, Institute for Genome Sciences, University of Maryland School of Medicine

According to Christopher Mason, Ph.D., senior author of the study, a professor at Weill Cornell Medicine, and the director of the WorldQuant Initiative for Quantitative Prediction, “Every city has its own ‘molecular echo’ of the microbes that define it. If you gave me your shoe, I could tell you with about 90 percent accuracy the city in the world from which you came.”

The research was performed prior to the COVID-19 pandemic shut down cities across the world. Therefore, the researchers are now analyzing how the pandemic impacted the microbiome fingerprint of each city. “It’s a good question,” Schriml added, “and we are address this in follow-up research.”

In 2020, the consortium initiated the MetaCOV project to study the change in urban metagenomes and isolate the occurrence of the SARS-CoV-2 virus (the virus responsible for COVID-19) in urban environments (for example, wastewater, ATM machines, transit systems, and hospitals).

Results of the latest study are based on the analysis of 4,728 samples collected from cities on six continents over a period of three years and denote the first systematic worldwide catalog of the urban microbial ecosystem. Apart from distinct microbial signatures in different cities, the analysis unraveled a core set of 31 species found in 97% of samples across the sampled urban areas.

The team identified 4,246 known species of urban microorganisms while also finding that any subsequent sampling will still possibly continue to identify species that have never been observed before. This highlights the raw potential for discoveries associated with microbial diversity and biological functions awaited in urban environments.

Going forward, the study results also have several prospective practical applications such as finding potential new compounds that can be used as antibiotics and small molecules annotated from biosynthetic gene clusters (BGCs) that have the potential for drug development.