Molecular echos: traces of the microbiome left behind by millions

Chris Mason, PhD, Associate Professor of Physiology and Biophysics and of Computational Biomedicine at Weill Cornell Medicine in Manhattan, offers a unique perspective on New York's subway system.  

On a typical morning at the 68th Street station for the number 6 train, he can be found meticulously swabbing various surfaces like handrails, turnstiles, benches, and even the electronic information boards above the platform. His goal is to gather samples of the myriad of microorganisms that thrive in these heavily frequented public spaces.  

These samples are then taken back to his lab, where they undergo assays to decode the genetic material present, providing insights into the diverse microbial life that coexists with urban dwellers. This research not only highlights the complexity of urban ecosystems but also underscores the often unseen and unappreciated biodiversity in our daily environments. 

“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 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.

A global microbiome network

New York is just one among 72 major cities worldwide where scientists, following the lead of Dr. Mason, are delving into the mysteries of the microbiome. These scientists have united under the MetaSUB International Consortium, aiming to map and understand the complex interactions of microbes, which play a crucial role in various aspects of human life. 

In June 2016, Weill Cornell Medicine spearheaded the MetaSUB project, collaborating with a diverse group of scientists, researchers, and trained citizen scientists. This global initiative involves collecting and analyzing DNA and RNA samples from high-traffic areas in numerous large cities.  

Mason, the principal investigator of MetaSUB, envisions a five-year project focused on creating longitudinal profiles of major cities to examine changes in their genetic makeup, pathogen load, and antimicrobial resistance over time.  

“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. 

The microbiome has a profound and wide-ranging impact. It's a double-edged sword: on one side, it's responsible for infectious diseases like cholera and avian flu; on the other, it acts as a protective shield, aiding in digestion, processing drugs, and promoting overall health. Consequently, understanding these complex interactions is seen as a thrilling and dynamic new frontier in life sciences, with potential benefits for public health, therapeutic developments, and even in fields like forensics, city planning, and architecture. 

Standardizing Research for Consistent Results

Researchers engaged in the study of the microbiome are on a mission to uncover the influence of bodily bacteria on various health conditions, such as obesity, metabolic syndrome, and mental health issues including anxiety and ADHD. This exploration holds the potential to revolutionize our understanding and treatment of a wide range of health issues, offering substantial benefits to medical science. 

To ensure that research results are consistent, reliable, and comparable, a standardized protocol and platform are essential. This is where QIAGEN steps in, equipping the consortium with vital tools. They provide DNeasy PowerSoil and QIAseq FX DNA kits, which are instrumental in processing genomic materials for analysis and preparing sequencing libraries. These tools are crucial for the accurate and efficient analysis of microbial DNA. 

Michael Kazinski, Senior Director of Molecular Preanalytic Technologies at QIAGEN, emphasizes the company's dedication to this field. "Understanding the various microbiomes and their impact on human health and environment is a key area of interest for our company,” he states. QIAGEN is committed to supporting both basic research and medical development by offering technology accessible to researchers who may not be experts in bioinformatics or genetics.  

This commitment from QIAGEN underscores the importance of collaborative efforts between technology providers and researchers in advancing our understanding of the microbiome and its vast implications for human health. 

Advancements in technology, coupled with the expanding knowledge of the microbiome, are enabling researchers to glean insights with significant implications for public and environmental health. This burgeoning field is increasingly contributing to practical applications that can enhance health and wellbeing on a broad scale. 

A Vision for Personalized Medicine

For Mason, the microbiome is not just a scientific curiosity; it's a key to unlocking the future of personalized medicine. He views the rich microbial ecosystem surrounding us as a "phalanx of friends" – allies that can be leveraged to develop tailored, "geospatially-informed treatment" plans for individuals. This approach goes beyond the one-size-fits-all methodology, offering a more nuanced and effective way of addressing health issues. 

In the foreseeable future, Mason envisions a healthcare scenario where a physician could utilize an individual's microbiome profile to assess past antimicrobial resistance. This information could then guide the selection of the most effective antibiotic for treating an infection. Such a strategy represents a significant leap in medical practice, potentially reducing the trial-and-error approach often associated with antibiotic prescriptions and enhancing treatment outcomes. 

This vision of harnessing the microbiome for personalized medicine is a compelling one, making the extensive global research efforts, like those led by Mason and his colleagues, not just scientifically intriguing but also vitally important. The pursuit of understanding the complex interplay of microbes within our environment and bodies holds the promise of transforming healthcare, making it a mission worthy of exploration on a global scale.