GI Tract Bacteria Helps Decrease Stroke


Certain types of bacteria in the gut can leverage the immune system to decrease the severity of stroke, according to new research from Weill Cornell Medicine. This finding can help mitigate stroke — which is the second leading cause of death worldwide.

In the study, published March 28 in Nature Medicine, mice received a combination of antibiotics. Two weeks later, the researcher team — which included collaborators at Memorial Sloan Kettering Cancer Center — induced the most common type of stroke, called ischemic stroke, in which an obstructed blood vessel prevents blood from reaching the brain. Mice treated with antibiotics experienced a stroke that was about 60 percent smaller than rodents that did not receive the medication. The microbial environment in the gut directed the immune cells there to protect the brain, the investigators said, shielding it from the stroke's full force.

"Our experiment shows a new relationship between the brain and the intestine," said Dr. Josef Anrather, the Finbar and Marianne Kenny Research Scholar in Neurology and an associate professor of neuroscience in the Feil Family Brain and Mind Research Institute at Weill Cornell Medicine. "The intestinal microbiota shape stroke outcome, which will impact how the medical community views stroke and defines stroke risk."

The findings suggest that modifying the microbiotic makeup of the gut can become an innovative method to prevent stroke. This could be especially useful to high-risk patients, like those undergoing cardiac surgery or those who have multiple obstructed blood vessels in the brain.

Further investigation is needed to understand exactly which bacterial components elicited their protective message. However, the researchers do know that the bacteria did not interact with the brain chemically, but rather influenced neural survival by modifying the behavior of immune cells. Immune cells from the gut made their way to the outer coverings of the brain, called the meninges, where they organized and directed a response to the stroke.

"One of the most surprising findings was that the immune system made strokes smaller by orchestrating the response from outside the brain, like a conductor who doesn't play an instrument himself but instructs the others, which ultimately creates music," said Dr. Costantino Iadecola, director of the Feil Family Brain and Mind Research Institute and the Anne Parrish Titzell Professor of Neurology at Weill Cornell Medicine.

The newfound connection between the gut and the brain holds promising implications for preventing stroke in the future, which the investigators say might be achieved by changing dietary habits in patients or "at risk" individuals.

"Dietary intervention is much easier to accomplish than drug use, and it could reach a broad base," Dr. Anrather said. "This is a little far off from the current study — it's music of the future. But diet has the biggest effect of composition of microbiota, and once beneficial and deleterious species are identified, we can address them with dietary intervention."

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Bacteria in Immune Cells May Protect Against Chronic Inflammation

A population of bacteria inhabits human and mouse immune cells and appears to protect the body from inflammation and illness, Weill Cornell Medicine scientists discovered in a new study. The findings challenge conventional wisdom about the relationship between bacteria and the human body — and about how the microbes influence health and disease.

The study, published March 15 in Immunity, focused on "good" or "commensal" bacteria that live in the human intestine and are essential for digestion and proper immune function. The majority of these commensal bacteria are found in the tube-like inner core of the intestine, called the lumen. The intestine itself acts as a barrier, keeping the bacteria inside the lumen and ensuring that they do not enter the rest of the body. Many reports have demonstrated that if commensal bacteria managed to escape the lumen, they would activate the immune system and cause disease.

But in their study, Weill Cornell Medicine investigators identified a group of commensal bacteria residing in close contact with immune cells outside of the intestinal lumen that defy this thinking. The discovery may alter the way scientists understand diseases like HIV, inflammatory bowel disease, some cancers, and cardiovascular disease.

Sonnenberg Laboratory. Front center, Dr. Gregory Sonnenberg. Back (from left, clockwise): Dr. Jeremy Goc, Thomas Fung, Xinxin Wang, Dr. Nicholas Bessman and Stephane Pourpe Photo credit: Roger Tully

"For a long time, the assumption was that the human body is essentially sterile and that a physical separation between the immune system and our commensal bacteria was necessary to prevent chronic inflammation," said lead author Dr. Gregory Sonnenberg, an assistant professor of microbiology and immunology in medicine and a member of the Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine. "While this is certainly true for most types of commensal bacteria, our new data demonstrate a special class of commensal bacteria that can closely associate with immune cells in a way that is mutually beneficial for both mammals and the microbes."

To learn more about this population of microbes, the researchers studied "germ-free" mice — rodents that are bred to have no bacteria in their bodies and have no contact with outside bacteria. They added this newly identified class of bacteria, called lymphoid tissue-resident commensal bacteria (LRC), to the mice.

The LRC colonized lymphoid tissues — specifically cells in the immune system — located outside of the intestinal lumen. When Dr. Sonnenberg and his colleagues investigated what the bacteria were doing, they found that they did not cause inflammation as expected. Rather, they did exactly the opposite — they limited the inflammatory response in the immune tissue.

The researchers then tried to experimentally induce intestinal tissue damage and inflammation in the rodents. They found that the mice that had LRC in their lymphoid tissue were protected.

"So it seems that these bacteria residing in lymphoid tissue are actually protecting the mice, rather than driving disease as would be expected," said lead author Thomas Fung, a graduate student in Dr. Sonnenberg's lab. "We further found that the immune responses induced by these bacteria are mutually beneficial; they not only protected mice from experimental tissue damage, but they also facilitated bacteria colonization of lymphoid tissues."

These are early findings, but the implications for human health are important to consider, Dr. Sonnenberg added. For example, the prevailing view is that in people with inflammatory bowel disease, colorectal cancer or HIV infection, commensal bacteria disseminate from the lumen of the intestine into the periphery of the body and promote inflammation.

"Our new data indicate that some unique bacteria residing in lymphoid tissues could instead promote tissue protection and limit inflammation," he said, "and our research highlights that it will be important to consider changes in lymphoid tissue-resident microbes during human health and disease."

The Sonnenberg Laboratory is also investigating whether LRCs can be developed as an innovative therapeutic approach to limit chronic inflammation and promote tissue repair in diseases such as inflammatory bowel disease.

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New Desktop-Sterilization Device Disinfects Cell Phones in Just 10 Minutes


Cell phones treated for just 10 minutes in a new desktop-sterilization device were fully rid of germs, including those that may be responsible for common skin infections, Weill Cornell Medicine researchers found in a new study. The findings, published Feb. 11 in the journal Plasma Medicine, suggest a quicker, easier, cheaper and more thorough way to clean common electronic devices, and may offer a new strategy to disinfect biomedical equipment and other objects used in healthcare settings.

"The reality is, stuff is growing on cell phones all the time. Now we have a device that uses this cool plasma technology to get rid of it with speed and ease," said principal investigator Dr. Jason A. Spector, a professor of surgery and of plastic surgery in otolaryngology at Weill Cornell Medicine and a plastic surgeon at NewYork-Presbyterian/Weill Cornell Medical Center. "This is something that's innately relevant to all of our lives. I could imagine having one of these sterilization devices throughout every hospital or any patient care facility for that matter for treating electronic devices and biomedical equipment at the end of every day."

Medical equipment is typically sterilized by either using toxic gas on delicate items or high-pressured steam on metal equipment. Because both of these methods would harm electronic devices typically used in the hospital setting, there's no quick and thorough way to rid them of bacteria. This new portable device, developed by the company Sterifre, Inc., uses a "cold" plasma system (actually room temperature) that doesn't harm electronics and only requires air, industrial-grade hydrogen peroxide, and a power source to run.

Invented by Dr. Czeslaw Golkowski, a Cornell University alum and a former research associate there, the device, called the Sterifre Countertop Sterlizer, came to Ithaca as part of the Kevin M. McGovern Family Center for Venture Development in the Life Sciences, which was established to assist high-potential, early-stage life science spin-off companies at the university.

"This research is an excellent example of inter-campus collaboration," said Dr. Spector, who is also an adjunct professor in the Nancy E. and Peter C. Meinig School of Biomedical Engineering at Cornell University and director of the Laboratory of Bioregenerative Medicine and Surgery at Weill Cornell Medicine. "Here at Weill Cornell Medicine, we're able to take cutting edge technologies developed by our engineering colleagues and help come up with real-life applications."

To demonstrate, Dr. Spector and investigators on his team used the sterilizer on 51 cell phones — including Apple iPhones, Blackberry devices and the Samsung Galaxy S4 — from lab staff and other volunteers. The investigators swabbed the phones for bacteria that accumulated after every day, normal use, then placed them in the device. They treated half of the phones for five minutes and the other half for 10. The investigators then swabbed the phones again after cold plasma treatment and cultured all swabs for 24 hours.

The phones treated for five minutes had a 93 percent reduction in bacteria, but for every device in the 10-minute group nothing grew — demonstrating that they were completely disinfected and bacteria free. All of the cell phones emerged working normally with no damage or change in appearance. Although the investigators only looked at the efficacy of killing bacteria in this study, the technology used in this device should be equally effective in killing fungi, spores and viruses, Dr. Spector said.

Because many of the delicate components in cell phones are also found in other electronics, including tablets, laptops and medical monitors, investigators believe that the sterilizer will work on them, too. They are in the planning stages to test that hypothesis.

The technology's usefulness may extend beyond cleaning medical equipment. Dr. Spector is also testing how well it disinfects wounds in animal models. Early data is promising, he said, as it appears to both non-invasively sterilize wounds and help in wound healing. "There's the potential for this device to have a huge impact in the biomedical field at large."

The device is already commercially available on a limited basis, and efforts are underway to get it approved by the U.S. Food and Drug Association.

"I can imagine these things populating hospitals, clinics, schools. You could even have one at home if you wanted to disinfect your baby's bottle," said Dr. Spector, who also tested the device on less delicate equipment, including his 10-year-old son's fragrant sneakers, which came out smelling fresh again. "That's the beauty of this device — you can put anything that you can think of in there."

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Symbiotic Relationship


Researchers Explore the Microbiome, Medicine's Newest Frontier

By Amy Crawford

Portraits by John Abbott

intestinal epithelium lining mouse's gastro-intestinal tract

A color-enhanced image of the intestinal epithelium that lines the gastro-intestinal tract of a mouse. Scientific images: Drs. Gregory Sonnenberg and David Artis

The most exciting discoveries can begin with the humblest material — and for researchers in the lab of immunologist Dr. David Artis, that often means mouse droppings. Once an obliging rodent provides a stool sample, a technician uses a chemical buffer to break down bacterial cell walls, unleashing the coils of DNA within. After further chemical preparation to enrich the genetic information, the sample is fed into an Illumina MiSeq, a desktop machine half the size of an office photocopier that, over the course of about 48 hours, sequences billions of base pairs to reveal a catalog of hundreds of types of bacteria: the mouse's microbiome. "After painstaking collection and preparation, you load your samples and allow the machine to run overnight," explains post-doctoral researcher Dr. Lisa Osborne, who has analyzed her share of murine fecal bacteria in the name of better understanding how the microbiome works in humans. "A lot of sophisticated magic happens inside that box."

The technology may not look flashy, but it's enabling a revolution in how scientists think about the bacteria that share our bodies — no longer as mere pathogens, but as members of a tiny ecosystem that coevolved with us, and on which our health depends. Dr. Artis and his colleagues hope these communities of microbes can offer insight into one of the most confounding problems in modern medicine: the set of painful chronic conditions known as inflammatory bowel disease (IBD). But IBD is not the only reason scientists at Weill Cornell and elsewhere are increasingly interested in microbiota. It turns out that the human microbiome may have far-reaching impact throughout the body, influencing how our immune systems develop, how our food is metabolized — and even, perhaps, the peculiarities of our personalities. New knowledge about the complex web of relationships between humans and the microbes that live within us is calling into question not only our understanding of disease, but of what it means to be human. "This is one of the major topics in contemporary biomedicine, and it's profoundly reshaping the way we think about health and disease and individuality," says Dr. Carl Nathan, the R. A. Rees Pritchett Professor of Microbiology and chairman of microbiology and immunology. "I grew up thinking that a given person has one genome, one set of genes that you inherit from your two parents. That's much too simple."

intestinal tissue of healthy mouse

A stained histologic section of intestinal tissue isolated from healthy mouse.

Medical training taught Dr. Nathan that the hereditary genome he learned about in school was not the only one that makes us who and what we are. There's also the somatic genome — the accumulated mutations and re-arrangements that some cells undergo, either as part of an abnormal process that can lead to cancer or as part of a healthy immune system, which adapts to recognize the myriad pathogens a person encounters throughout life. Another code is found within mitochondria, organelles that power our cells and, scientists believe, evolved in multicellular organisms like humans from symbiotic bacteria. "Then there's the fourth genome," Dr. Nathan says. "That's the collective complement of genes of all the bacteria that normally reside in us. And the ways that this impacts medicine are almost countless."

In a suite of gleaming new labs on the fifth floor of the Belfer Research Building, some 20 people are working to unravel the mysteries of the microbiome. Some are hunched over laptops, while others collect data from a machine called a flow cytometer set up in a corner. In a culture room, several sit at biosafety cabinets, manipulating cells collected from mice or human patients.

The team is led by Dr. Artis, who was recruited as the Michael Kors Professor in Immunology. Widely considered a world leader in his field, he has recently been involved in studies that uncovered links between the immune system's response to gut bacteria and systemic allergies, as well as how the immune system keeps gut bacteria where they belong. Last year, Dr. Artis, along with some of his longtime collaborators, was lured away from the University of Pennsylvania to head Weill Cornell's new Jill Roberts Institute for Research in Inflammatory Bowel Disease.

When Dr. Artis, who grew up in Scotland, was an undergraduate in the early '90s, he took a course on evolution and became fascinated by how the mammalian immune system had evolved in conjunction with the pathogens that infect us. After earning a Ph.D. in immunology at the University of Manchester, he crossed the Atlantic to do postdoctoral work at Penn, where he would later join the faculty. Some of his early research there centered on the immune system's interaction with helminths, tiny worms that can make their home in human intestines, into which they find their way via under-cooked meat or contaminated water. Broader interest in the human microbiome as anything but pathogenic had yet to take hold, but Dr. Artis and other researchers were beginning to recognize something that ran counter to our previous understanding of these parasites as little more than uninvited passengers that make us sick. "We were interested in the pathogens that infect us, and one class of pathogens is worms," Dr. Artis explains. "The interesting thing is that to eradicate worms, the body mounts the Type 2 inflammatory response. It's the same type of response in allergies, only there it's reacting to innocuous antigens in peanuts and milk products and so forth."

healthy mouse tissue with normal microflora

A color-enhanced tissue section from a healthy mouse showing the presence of normal microflora.

Over most of human history, the Type 2 response was an effective way to combat common parasites, and it's still called into action in much of the world, where helminths remain a problem. But in the United States and other industrialized countries, sanitation and medicine have virtually eliminated intestinal worms, leaving the Type 2 response a weapon without a proper target. That mismatch may contribute to the startling increase in allergic disease, asthma and other immune disorders, including certain forms of IBD.

As Dr. Artis' research looked at the ways in which immunity in the presence or absence of parasites could be involved with allergic reactions and chronic inflammation, a great shift was taking place in how researchers, doctors and even the general public think about other organisms that live in our bodies. It was a shift that paralleled the discovery of microorganisms themselves in the late 17th century, when the Dutch scientist Antonie van Leeuwenhoek trained his homemade microscopes on droplets of rainwater. "Like most discoveries in science," Dr. Artis says, "these quantum leaps are triggered by new technologies that allow us to see differently." A decade ago, studying the organisms living in someone's colon would have required culturing them in a petri dish, a time-consuming technique that could only begin to reveal the multitudes of bacteria that make up a complete human microbiome. That has changed, largely thanks to an international science project that some have compared to the 1969 moon landing in both its historical importance and its legacy of innovation.

In 2000, President Bill Clinton and British Prime Minister Tony Blair appeared on television to announce that an international team of scientists had completed a rough draft of the human genome, some 3 billion base pairs that make up roughly 20,500 genes. The project had been a massive undertaking, involving researchers in six countries working for more than a decade. In addition to the invaluable information about our own DNA that the project provided, it also spurred the development of new technology that would enable further discoveries. Today, commercially available genetic sequencing platforms like the Illumina MiSeq are considered de rigueur for any well-stocked research institution — Weill Cornell's Genomics Resources Core Facility has several — and what took the Human Genome Project years to accomplish can be done overnight. Now, researchers are using that technology to read and understand that fourth human genome, that of the bacteria that make their homes in our bodies. "Sequencing technology allows us to identify the microbiota at a level that we would never have been able to understand before," Dr. Artis says. "That technology has really accelerated our ability to profile the organisms in this complex ecosystem, and it also allows us to report how their composition changes in the context of disease."

Much as the sequencing of the human genome inspired the popular imagination a decade ago, today studies of the human microbiome have filtered from scientific journals and into the popular press. Breathless newspaper articles have told us how gut bacteria influence the workings of the mind, and that they might determine why some of us get fat while others stay slim on the same diet. In a 2013 New York Times Magazine cover story, the writer Michael Pollan recounted how sequencing the genes of the 100 trillion bacteria in his own body led him to think of himself "in the first-person plural — as a superorganism, that is, rather than a plain old individual human being."

Dr. Greg Sonnenberg, an assistant professor of microbiology and immunology in medicine, sees this as an asset to science. "The current level of excitement is fantastic," says Dr. Sonnenberg, who has collaborated on seminal studies with Dr. Artis and who was also recruited to lead a lab at the Roberts Institute. "The more you learn about the microbiome, the more it just touches upon everything; it is involved in probably every human disease out there. It's like the rainforest, where you can go through and find different bugs that may have the ability to provide therapeutic benefit in many diseases. And that's where the field is today. Now we need to get down to the nitty gritty in determining which species are important, which species are doing what and how are they interacting with each other. It's an extremely complex system."

Dr. Sonnenberg cautions that many recent papers based on sequencing data have likely uncovered mere correlations. While some members of the microbiome are clearly associated with certain medical conditions, he explains, that doesn't mean the bacteria caused the conditions. Much more work must be done to understand the functions of the bacteria that make up the human microbiome, and how the chemical signals and byproducts they produce affect us and each other. "Hopefully," he says, "that's going to translate to more research being done that advances us to the point where it will benefit patients more directly."

There is already one way in which doctors are using knowledge of the microbiome to benefit patients. Clostridium difficile (C. diff.) is a highly antibiotic-resistant bacterium that causes severe diarrhea and kills some 14,000 Americans each year. Patients most at risk are those in whom antibiotics have wiped out beneficial gut bacteria, leaving the coast clear for C. diff. to grow unimpeded. So far the most successful treatment involves replacing those good bugs with a fecal transplant — that is, inserting the stool of a healthy volunteer into the colon of a C. diff. sufferer — and restoring the normal, healthy balance of gut bacteria. "The concept is both intriguing and somewhat repulsive," admits Dr. Charlie Buffie, who will finish his medical degree at Weill Cornell in 2016, having completed his doctoral work at Sloan Kettering through the Tri-Institutional M.D.-Ph.D. program. "But the efficacy of a fecal transplant has been strikingly high under the right circumstances." Fecal transplant cures about 90 percent of C. diff. patients, but doctors aren't sure exactly why. And because the treatment by its very nature is impossible to standardize, government regulators are uneasy and doctors are reluctant to use it in immunocompromised patients. Dr. Buffie, however, may have found a partial answer to those quandaries.

Dr. Charlie Buffie

The components of a fecal transplant are as numerous as those of the human microbiome itself. But one that seems to be especially effective in controlling a C. diff. infection is a related species called Clostridium scindens. In a study published last year in Nature, Dr. Buffie and colleagues in the Sloan Kettering lab of immunologist Dr. Eric Pamer used C. scindens to defeat C. diff. in mice whose normal microbiomes had been disrupted with antibiotics. In the future, Dr. Buffie says, patients with C. diff. might be given precisely calibrated mixtures of beneficial bacteria or drugs that mimic the metabolic products of C. scindens that seem to prevent C. diff. from propagating. That would allow patients to avoid the potential safety risks — not to mention the ick factor — of a fecal transplant. Says Dr. Buffie: "Being able to isolate, define and construct compositions of bacteria that we know have positive effects and that do not have negative effects — that's definitely an attractive solution."

This line of research also holds promise for IBD patients, says Dr. Randy Longman '07, an assistant professor of medicine in gastroenterology and alumnus of the Tri-Institutional M.D.-Ph.D. Program who joined the Jill Roberts Center for Inflammatory Bowel Disease in 2013. Preliminary evidence suggests that fecal transplantation could help those with a form of IBD called ulcerative colitis, and Dr. Longman and his colleagues are working to figure out why. "The idea is to be able to get specific about the microbes," he says. "If we isolate some of these bugs from patient samples and then put them into gnotobiotic mice we may be able to understand how these microbes interact with the immune system within the intestine."

Although Dr. Longman's primary occupation is research, he spends one day a week in clinical practice, working to help patients manage their illness. "Inflammatory bowel disease, epidemiologically, affects people in the prime of life," Dr. Longman notes. "So many of the patients that I'm seeing for initial diagnoses are young people with so much of their lives in front of them. There is a tremendous need for new medicines and new therapeutic strategies." Like his colleagues, Dr. Longman is optimistic that cracking the secrets of the microbiome will lead to better treatments, and his patients will one day get relief from the stress of living with a chronic condition. "Right now, treating IBD is a management thing," he says. "We don't cure it right now. But we do hope for that."

Today, fecal transplantation remains the best microbiome-based treatment available. But as research points to gut bacteria's involvement with a variety of other ailments, scientists are hoping that future patients could be helped by targeted probiotics or drugs modeled after the chemical signaling of good bacteria. "There may be a point where it isn't necessary to cultivate certain bacteria in your body," Dr. Nathan says, "but rather to take a pill that provides the compounds those bacteria are making — to do the job they do, but in a more orderly, defined, predictable, consistent, safe way." In the future, such treatments might be used not only for C. diff. and IBD, but eventually for metabolic disorders, obesity and even neurological problems. "Whether the food you eat influences a predisposition to atherosclerosis — that's controlled by the bacteria in the body," Dr. Nathan says. "There are influences on behavior, on weight gain, probably on asthma. There's a connection to autism that's recently been reported." The microbiome may have an impact on every system in the human body, he stresses, and its importance is inestimable.

Dr. Artis echoes Dr. Nathan's enthusiasm, and notes that most breakthroughs are yet to come. He draws an analogy to the years after van Leeuwenhoek's microscope first revealed the hidden world in a water droplet. "The pace of discovery is so rapid; this field has really exploded," he says. "But in terms of understanding the complexities of microbiota in the body, we're in our infancy."

Living Underground

The New York Subway System Hosts a Complex Bacterial Ecosystem, Too

Infographic of DNA in New York subway forming bacteria in human body

Infographic showing the relative amount of DNA found in the New York subway system form bacteria associated with the human body. Click to enlarge.

Just as each human body holds a complex ecosystem of bacteria in the gut, every major metropolis is home to a medley of bacteria and pathogens, coexisting with that city's residents. Until recently, little was known about these native microbial communities, which surround us in streets, buildings and public transit areas.

Using the subway system as their testing ground, Weill Cornell investigators fanned out beginning in June 2013 and collected samples of hundreds of DNA from bacterial, viral, fungal, and animal species — like insects and domestic pets — in the underbelly of New York City. They then compiled the data and turned it into an interactive pathogen map, dubbed PathoMap, and recently published their findings in Cell Systems.

While most of the collected microbes are harmless, some are not — including live, antibiotic- resistant bacteria, which were found in 27 percent of the samples. Two samples included DNA fragments of anthrax, and three carried a plasmid associated with Bubonic plague. Reassuringly, those five were discovered at very low levels and showed no evidence of being alive. Other DNA — half of what was collected, in fact — could not be identified as any known organism, because the databases against which they are compared are still incomplete.

While this might sound troubling, there's no need to worry right now, says the study's senior investigator, Dr. Christopher Mason, the WorldQuant Foundation Research Scholar and an associate professor in Weill Cornell's Department of Physiology and Biophysics and in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine. These apparently virulent organisms are not linked to widespread sickness or disease in this environment, Dr. Mason says. "They are instead likely just the co-habitants of any shared urban infrastructure and city," he says, "but additional testing is needed to confirm this."

The knowledge that these bacteria are present and having no obvious negative effect on the 5.5 million daily subway riders demonstrates that most of them are neutral to human health, he adds. They may even be helpful, as they can out-compete dangerous bacteria. "The presence of these microbes and the lack of reported medical cases is truly a testament to our body's immune system," Dr. Mason says, "and our innate ability to continuously adapt to our environment." Would these pathogens be typical for other cities? With the aim of answering that question, collaborators are collecting samples from airports, taxis and public parks in 15 other cities around the world under a recent grant from the Sloan Foundation.

The PathoMap project involved investigators from Weill Cornell, five additional New York City medical centers and more than a dozen national and international institutions. Over the course of 17 months, medical students and other volunteers used nylon swabs to collect DNA from turnstiles, benches, railings, trashcans and kiosks in all operating subway stations across the five boroughs. The team also collected samples from inside trains, swabbing seats, doors, poles and handrails. They time-stamped each sample and tagged it using a GPS system, later sequencing about 1,500 samples (out of more than 4,200 collected) and analyzing those results. "PathoMap establishes the first baseline data for an entire city," Dr. Mason says, "revealing that 'molecular echoes' of commuters appear on all surfaces — from the bacteria on their skin to the food they eat, and even from the human DNA left behind, which matched U.S. Census data."

The data on New York City's ecosystem — an ingredient in building a smart city — already has potential real-world applications. Researchers could monitor the system for changes that would signal disease or a potential threat, or someday create a live model tracking real-time changes to this urban microbiome. The PathoMap, Dr. Mason says, is just the beginning.

— Anne Machalinski

This story first appeared in Weill Cornell Medicine, Vol. 14, No. 1.

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In the lab: Dr. David Artis with postdoc Dr. Anne-Laure Flamar
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NIH Awards Seven-Year Grant to Weill Cornell Medical College to Tackle Global Tuberculosis Epidemic


Memorial Sloan Kettering Cancer Center and Weill Cornell to Co-Lead Tuberculosis Research Unit

Effort Will Seek Improved Treatments and Enhanced Understanding of Deadly Infection

NEW YORK (February 18, 2015) — In an effort to stop tuberculosis (TB) from becoming progressively less treatable worldwide, the National Institutes of Health has awarded Weill Cornell Medical College more than $6.2 million in first-year funding to support a research collaboration among six institutions in close alliance with voluntary pharmaceutical partners. The total funding, provided by the National Institute of Allergy and Infectious Diseases, could be up to $45.7 million over seven years.

The bacteria that causes tuberculosis infecting macrophages

The bacteria that causes tuberculosis is infecting macrophages, the host cell that plays a key role in defense against the bacteria. Photo credit: Ruojun Wang

TB-causing bacteria are increasingly becoming resistant to the most commonly used treatments, presenting a growing problem in a globalized world, says TB Research Unit principal investigator Dr. Carl Nathan, chair of the Department of Microbiology and Immunology at Weill Cornell. For patients who don't respond to those drugs, the infection can require more than two years of therapy with multiple, toxic and expensive alternatives, which often fail. When TB, which is spread through the air, is not effectively treated, it is usually lethal.

"Neither academia nor pharma can solve this problem working alone. We have to work together to improve treatment of tuberculosis, or it will continue to spread and become even more resistant to treatment than it is today," says Dr. Nathan, who is also director of the Abby and Howard P. Milstein Program in Translational Medicine.

Dr. Michael Glickman, an infectious disease specialist and Alfred Sloan Chair at Memorial Sloan Kettering Cancer Center, serves as the TB Research Unit's co-principal investigator. He notes that TB is the single leading cause of death from a bacterial infection, and the second leading cause of death from any pathogen. One in three people globally is infected with the bacteria that cause TB. Of those people, between 5 and 10 percent eventually develop the active disease. Each person with an active case of untreated TB may go on to infect 10 or 20 additional people. There are millions of infections and deaths each year from TB — in 2013, an estimated 9 million new cases were reported and 1.5 million people died, according to the World Health Organization.

"The incredible concentration of TB expertise in the Tri-Institutional community, which includes investigators studying human genetics of TB susceptibility, microbiology, and immunology, constitutes a formidable research team to contribute to tackling these problems," Dr. Glickman says.

Two parallel research tracks

The TB Research Unit is designed to help address significant gaps in understanding how TB bacteria establish and maintain infection in the human body as well as how agents might attack vulnerabilities in the bacteria.

The most common form of TB is distinctive in that humans are its only natural host. Because the TB bacterium has co-evolved with humans for tens of thousands of years, it "has learned enough about our immune systems to survive our efforts to eliminate it," Dr. Nathan says. Two issues have plagued those efforts: persistence, the ability of TB bacteria to enter a drug-tolerant state, and latency, the capacity of the bacteria to hide within a person for decades before resuming growth and causing disease.

Current TB drugs take months to treat latent and persistent disease, Dr. Nathan says. The drug isoniazid was first tested in the United States in 1952 by a Cornell physician and remains a mainstay, he says. "Most of today's TB drugs are old and would likely not pass federal approval if introduced today," Dr. Nathan says.

The Tuberculosis Research Unit involves two parallel tracks. The first, overseen by Dr. Glickman, addresses TB infection biology in patients, and the center of this work shifts to Haiti, where TB, including drug-resistant TB, is a major health problem.

Dr. Michael Glickman

With the help of patients at Weill Cornell's GHESKIO clinic in Haiti, overseen by Weill Cornell physicians Drs. Jean Pape and Daniel Fitzgerald, researchers will investigate biological factors that affect the course of TB infection — and likely treatment. For example, a participating group of researchers from Rockefeller University led by Drs. Jean-Laurent Casanova and Laurent Abel have found a gene that appears to control susceptibility to reactivation of TB infection in young adults. They will search for other such genes to help explain why only a minority of individuals with latent infection develop clinical disease, while the majority remain disease-free. Dr. Glickman's group will study the expression of genes by blood cells that may provide markers of resistance to initial infection and an early indication of treatment response. He will also investigate the effect of special types of lymphocytes and the role of composition of the intestinal bacteria in resistance to infection and response to therapy. Dr. Nathan's group, working with Dr. Fitzgerald, will study a subset of TB bacteria in patients' sputum that is undetected by standard techniques but may be largely responsible for persistence.

The hope is that these studies will identify compounds, biomarkers and genetic susceptibilities, to be tested in future clinical trials, which can shorten treatment, eliminate latency and overcome persistence. "Only in this way will we finally turn the tide of tuberculosis," Dr. Nathan says.

The second, parallel track of the grant, led by Dr. Nathan, continues and expands ongoing efforts by investigators at Weill Cornell and other institutions who have been working with the Bill & Melinda Gates Foundation's TB Drug Accelerator. In that program, pharmaceutical companies provide chemical compounds that academic labs test in diverse ways, seeking compounds with new mechanisms of action. The active compounds, called "hits," must pass through a gauntlet of increasingly stringent tests, often undergoing extensive chemical modifications, before they qualify as "leads" that can be considered for later stages of drug development.

In this "hit-to-lead" work, researchers seek the active compounds that are most potent and least toxic, try to identify their molecular targets, and test whether their properties can be improved. In particular, Dr. Nathan's lab tests if the compounds can kill persistent TB bacteria. These tests were developed in response to ongoing studies of TB's biology, including its genetics and the genetics of the host response, Dr. Nathan says.

Through the Drug Accelerator program and related collaborations, multiple drug companies have allowed Dr. Nathan's team to screen more than 1.3 million compounds. Such open access to company compound collections "is almost unheard of," says Dr. Nathan, "particularly when access is granted to the same academics by several companies at once.

"This is door-opening for university researchers, who would not otherwise have access to compounds of this quality. Equally important is the side-by-side partnership with the companies' scientists, who provide specialized knowledge about working with, analyzing, and improving the compounds," he said.

Collaborators at the University of Kansas will produce new versions of some of the most promising compounds. Researchers at Rutgers New Jersey Medical School will study the pharmacologic behavior of the compounds in mice. Dr. Glickman is contributing a family of promising antimicrobial chemicals that he discovered in his own research. Dr. Nathan's colleagues at Weill Cornell, Drs. Dirk Schnappinger, Sabine Ehrt and Kyu Rhee, are focusing their efforts on identifying molecular targets that the compounds could most profitably attack and those that the most advanced compounds inhibit.

The TB Research Unit is funded by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (U19 AI 111143).

Weill Cornell Medical College

Weill Cornell Medical College, Cornell University's medical school located in New York City, is committed to excellence in research, teaching, patient care and the advancement of the art and science of medicine, locally, nationally and globally. Physicians and scientists of Weill Cornell Medical College are engaged in cutting-edge research from bench to bedside aimed at unlocking mysteries of the human body in health and sickness and toward developing new treatments and prevention strategies. In its commitment to global health and education, Weill Cornell has a strong presence in places such as Qatar, Tanzania, Haiti, Brazil, Austria and Turkey. Through the historic Weill Cornell Medical College in Qatar, Cornell University is the first in the U.S. to offer a M.D. degree overseas. Weill Cornell is the birthplace of many medical advances — including the development of the Pap test for cervical cancer, the synthesis of penicillin, the first successful embryo-biopsy pregnancy and birth in the U.S., the first clinical trial of gene therapy for Parkinson's disease, and most recently, the world's first successful use of deep brain stimulation to treat a minimally conscious brain-injured patient. Weill Cornell Medical College is affiliated with NewYork-Presbyterian Hospital, where its faculty provides comprehensive patient care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center. The Medical College is also affiliated with Houston Methodist. For more information, visit

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Center for Global Health Office of International Affairs

Researchers Produce First Map of New York City Subway System Microbes


Most Identifiable Bacteria are Harmless, but a Few are Linked to Disease or are Treatment-Resistant

Paints a Molecular Portrait of New York City's Balanced Microbial Ecosystem

Monday, Aug. 3, 2015 — The authors of this study have posted updated information based on new analysis. Please see the amended study here: Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

NEW YORK (February 5, 2015) — The microbes that call the New York City subway system home are mostly harmless, but include samples of disease-causing bacteria that are resistant to drugs — and even DNA fragments associated with anthrax and Bubonic plague — according to a citywide microbiome map published today by Weill Cornell Medical College investigators.

Infographic: DNA found in New York subway form human body bacteria

Infographic showing the relative amount of DNA found in the New York subway system form bacteria associated with the human body. Click to enlarge.

The study, published in Cell Systems, demonstrates that it is possible and useful to develop a "pathogen map" — dubbed a "PathoMap" — of a city, with the heavily traveled subway a proxy for New York's population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study's senior investigator, Dr. Christopher E. Mason, an assistant professor in Weill Cornell's Department of Physiology and Biophysics and in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine (ICB).

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.

Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists' fingertips.

"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract," Dr. Mason says. "These bacteria may even be helpful, since they can out-compete any dangerous bacteria."

Heatmap of the Pseudomonas genus, the most abundant genus found across the city. Hotspots are found in areas of high station density and traffic (i.e. lower Manhattan and parts of Brooklyn).

Heatmap of the Pseudomonas genus, the most abundant genus found across the city. Hotspots are found in areas of high station density and traffic (i.e. lower Manhattan and parts of Brooklyn). Photo Credit: Ebrahim Afshinnekoo

But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.

Yet these apparently virulent organisms are not linked to widespread sickness or disease, Dr. Mason says. "They are instead likely just the co-habitants of any shared urban infrastructure and city, but wider testing is needed to confirm this."

For example, there has not been a single reported case of the plague in New York City since the PathoMap project began in June 2013.

"Despite finding traces of pathogenic microbes, their presence isn't substantial enough to pose a threat to human health," Dr. Mason says. "The presence of these microbes and the lack of reported medical cases is truly a testament to our body's immune system, and our innate ability to continuously adapt to our environment.

"PathoMap also establishes the first baseline data for an entire city, revealing that low-levels of pathogens are typical of this environment," he adds. "While this is expected in rural environments, we've never seen these levels before in cities. We can now monitor for changes and potential threats to this balanced microbial ecosystem."

"Jumping into the Unknown"

Scientists now believe that the diversity of microorganisms that are present in, on and around humans comprise a significant component of overall health. In the average human, there are 10 times as many microbes as human cells, and products processed by these microbes comprise more than one-third of the active, small molecules in the bloodstream. This collective microbiome is seen to impact health by exacerbating or resisting infectious diseases, controlling obesity risk, and regulating metabolic rates. Yet there is very little known about the native microbial communities that surround people in streets, buildings or public transit areas.

In the study, the research team — which includes investigators from five other New York City medical centers and others from around the country and internationally — sought to define the microbiome in New York City's subway system, which in 2013 was used by an average of 5.5 million people per day, according to the city's Metropolitan Transportation Authority. Over the past 17 months, the team — many of them student volunteers, medical students and graduate students — used nylon swabs to collect, in triplicate, DNA from turnstiles, wooden and metal benches, stairway hand railings, trashcans, and kiosks in all open subway stations in 24 subway lines in five boroughs. The team also collected samples from the inside of trains, including seats, doors, poles and handrails. Investigators are currently analyzing additional samples collected during all four seasons to study the temporal dynamics of the microbiome.

The sample collectors were equipped with a mobile app built by the researchers, which allowed them to time stamp each of the samples, tag it using a global positioning system and log the data in real time. DNA from the microbes was sequenced using the most advanced research technology at the Weill Cornell Epigenomics Facility and the HudsonAlpha Institute for Biotechnology. They sequenced 1,457 samples out of more than 4,200 collected, and the results were analyzed in the ICB.

"We had our hypothesis about what's on the surfaces of the subway, which reflects a massive, diverse, busy metropolis, but we really had no idea what we would find," says co-lead author Ebrahim Afshinnekoo, a senior at Macaulay Honors College -Queens who starting working on the project as a Tri-Institutional Computational Biology and Medicine Summer Student in 2013.

Staphylococcus aureus

Staphylococcus aureus is frequently found in the human respiratory tract and on skin. It is an opportunistic bacteria that is always associated with disease, though some strains are found to cause skin infections, respiratory disease and food poisoning. Treating antibiotic resistant strains of S. aureus (methicillin resistant staphylococcus aureus or MRSA) is a worldwide problem in clinical medicine. Photo Credit: Janice Haney Carr/CDC

The majority of the DNA from all the samples, 48.3 percent, did not match any known organism, "which underscores the vast wealth of unknown species that are ubiquitous in urban areas," Afshinnekoo says.

The most commonly found organism (46.9 percent) was bacteria. Despite some riders' fears of catching cold or flu from fellow straphangers, viruses were rare — they made up .032 percent of the samples. However, some seasonal viruses are RNA viruses, not DNA viruses, and they would not be identified with the collection methods used in the study.

Of the known bacteria, the majority (57 percent) found on the surfaces of the subway have never been associated with human disease, whereas about 31 percent represented opportunistic bacteria that might pose health risks for immune-compromised, injured or disease-susceptible populations, researchers report. The remaining 12 percent have some evidence of pathogenicity.

They found that dozens of microbial species were unique to each area of the train, and that there is a significant range of microbial diversity across different subway lines. The Bronx was found to be the most diverse with the most number of species found, followed by Brooklyn, Manhattan and Queens. Staten Island was the least diverse.

"We built maps that detail what organisms are present in each area of the city, creating a molecular portrait of the metropolis," says co-lead author Dr. Cem Meydan, a postdoctoral associate at Weill Cornell Medical College.

Despite sampling surfaces of areas of high human traffic and contact, the researchers found that only an average of 0.2 percent of reads uniquely mapped to the human genome. Using tools like AncestryMapper and ADMIXTURE, the investigators took human alleles and recreated census data of a particular subway station or neighborhood. Their results showed that the trace levels of human DNA left of the surface of the subway can recapitulate the U.S. Census data. For example, a Hispanic area near Chinatown in Manhattan appeared to hold a strong mixture of Asian and Hispanic human genes. An area of North Harlem showed African and Hispanic genes, and an area of Brooklyn with a predominantly white population was predicted to be Finnish, British and Tuscan.

"This provides a forensic ability to learn about the ancestry of the people who transit a station," Dr. Mason says, "and it means the DNA people leave behind can reveal a clue as to the area's demographics."

The researchers also compared their microbial data with U.S. census data, as well as average ridership data from the MTA. They found a slightly positive correlation between these two variables and the population density of microbes on the subway, suggesting that the more people in an area, the more diverse the types of bacteria.

Efforts like PathoMap in New York can readily be applied to other cities to provide a new tool for disease and threat surveillance, Dr. Mason says. "With the further development of sequencing technologies, I believe having a live model tracking the levels of potential pathogens could be possible," he says. "I envision PathoMap to be the first step in that model."

Projects are already underway that build upon PathoMap's initial data and further the researchers' goal of investigating the microbiome of large, complex cities. Collaborators across the country have collected samples from airports, subways, transit hubs, taxis and public parks located in 14 states — including New Jersey, Massachusetts, Maryland, Florida, Illinois, Texas and California. By sequencing the DNA of these samples, Dr. Mason hopes to create the first ever comparison of major cities in the nation that contextualizes urban and rural, high density and low density environments.

The Impact of Superstorm Sandy

The researchers also worked with the MTA to gain access to the South Ferry station that was completed submerged by Superstorm Sandy in 2012, and which was still closed during sampling. (The station reopened in April 2013.) Dr. Mason's team sampled the walls and floors of the station, and found 10 species of bacteria present that were found nowhere else in the system. Notably, all of the species are normally found in marine or aquatic environments.

Dr. Christopher E. Mason

"The walls of the subway still carry the echo of the hurricane, and you can see it in the microbiome," Dr. Mason noted. "The big questions are — how long will it stay? How does this impact health and the design of the built environment of the subway? This is why we have kept sampling and swabbing since we started. The temporal dynamics are key."

The study was supported by the National Institutes of Health (F31GM111053), the Weill Cornell Clinical and Translational Science Center, the Pinkerton Foundation, the Vallee Foundation, the WorldQuant Foundation, the Epigenomics Core Facility at Weill Cornell, the HudsonAlpha Institute for Biotechnology, Illumina, Qiagen, and Indiegogo (for crowdfunding and crowdsourcing support).

Study co-authors include, from Weill Cornell Medical College, Shanin Chowdhury, Cem Meydan, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Nell Kirchberger, Isaac Garcia, David Gandara, Amber Simmons, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth M. Hénaff, Paul Zumbo; Timothy Nessel, Bharathi Sundaresh, and Elizabeth Pereira from Cornell University; Sergios-Orestis Kolokotronis from Fordham University; Sean Dhanraj, Tanzina Nawrin, Theodore Muth, Elizabeth Alter and Gregory O'Mullan from City University of New York; Ellen Jorgensen from Genspace Community Laboratory; Julia Maritz, Katie Schneider, and Jane Carlton from New York University; Michael Walsh from the State University of New York, Downstate; Scott Tighe from the University of Vermont; Joel T. Dudley and Eric E. Schadt from the Icahn School of Medicine at Mount Sinai; Anya Dunaif and Jeanne Garbarino from Rockefeller University; Sean Ennis, Eoghan Ohalloran and Tiago R Magalhaes from the University of Ireland; Braden Boone, Angela L. Jones, and Shawn Levy from HudsonAlpha Institute for Biotechnology; and Robert J. Prill from the IBM Almaden Research Center.

Weill Cornell Medical College

Weill Cornell Medical College, Cornell University's medical school located in New York City, is committed to excellence in research, teaching, patient care and the advancement of the art and science of medicine, locally, nationally and globally. Physicians and scientists of Weill Cornell Medical College are engaged in cutting-edge research from bench to bedside aimed at unlocking mysteries of the human body in health and sickness and toward developing new treatments and prevention strategies. In its commitment to global health and education, Weill Cornell has a strong presence in places such as Qatar, Tanzania, Haiti, Brazil, Austria and Turkey. Through the historic Weill Cornell Medical College in Qatar, Cornell University is the first in the U.S. to offer a M.D. degree overseas. Weill Cornell is the birthplace of many medical advances — including the development of the Pap test for cervical cancer, the synthesis of penicillin, the first successful embryo-biopsy pregnancy and birth in the U.S., the first clinical trial of gene therapy for Parkinson's disease, and most recently, the world's first successful use of deep brain stimulation to treat a minimally conscious brain-injured patient. Weill Cornell Medical College is affiliated with NewYork-Presbyterian Hospital, where its faculty provides comprehensive patient care at NewYork-Presbyterian Hospital/Weill Cornell Medical Center. The Medical College is also affiliated with Houston Methodist. For more information, visit

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Outsmarting Bacteria


An Inside Story Behind the Global Battle With Pathogenic Microbes

"Most of the bacteria in our bodies live in a friendly consortium with us. In fact, we need them," says Dr. Carl Nathan, the R.A. Rees Pritchett Professor of Microbiology and director of the Abby and Howard P. Milstein Program in the Chemical Biology of Infectious Disease.

"But a few aggressive species learned the trick of 'keeping their heads down' and surviving long before we were walking the earth. They are smart. They are very good at evolving resistance to antibiotics used to fight worldwide killers like TB and malaria — as well as infections we are more familiar with in this country such as pneumonia and sepsis.

"We assume there is a pill for these more familiar infections, and up to now there has been. But it's increasingly becoming the case that there is no treatment. We are emptying our medicine chest of effective drugs to use against them," says Dr. Nathan, who is also chair of the Department of Microbiology and Immunology.

Glimmer of Good News

At Weill Cornell, thanks to a Gates Foundation grant, Dr. Nathan and his associates are screening hundreds of thousands of compounds for new drugs. "One that we found is an anti-inflammatory that has been used for aches and pains by hundreds of thousands of people for many years and, it turns out, is also effective in killing TB bacteria. It could be a fast track to a new TB drug. Our goal is to share our findings with any scientists who are interested to speed up discoveries for life-saving treatments."

Dr. Nathan was recently inducted into the National Academy of Sciences in recognition of his research that has led to new understanding of how the immune system defends the host against infection. His lab at Weill Cornell is screening drugs long-approved for a variety of treatments that might also be used as weapons against bacteria, as well as diverse chemical compounds whose potential anti-infectious activities have not yet been characterized.

The Research Leads to Cures Initiative

With these efforts, Dr. Nathan and other Weill Cornell scientists are hoping to contribute to the development of effective, safe treatments for infectious diseases around the world. These researchers are the heart of the Research Leads to Cures Initiative — a new and critical phase of the Discoveries that Make a Difference Campaign.

Learn more about the people leading these efforts in translational research and patient care, and find out how you can help fulfill the promise of the many medical discoveries that are under way here at Weill Cornell.

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