Metagenomics in the News

Why Too Much Sanitation Can Be a Bad Thing

Throughout the past couple of centuries, many parts of the world have seen a drastic increase in sanitation. Developed countries have seen a decrease in the prevalence of disease and an increase in average lifespan, due at least in part to medical advances such as the development of antibiotics and antibacterial medicine, widespread access to clean running water, and efforts to educate people on cleanliness. However, recent studies are showing that this type of hyper-sanitation may actually be unhealthy.

A correlation has been discovered in both developed and developing countries between increases in sanitation and the prevalence of serious auto-immune problems, such as type one diabetes. Countries with advanced sewer systems, better access to medicine, and widespread hygiene programs have actually seen a much sharper increase in the incidence of illnesses of this type in the past half century than less developed countries. The key to understanding this trend may lie in our evolutionary history, and in both the good and bad bacteria that live inside of us.

One possible reason that autoimmune diseases are less prevalent in less-developed countries is because, as infants and children, the people of these countries are exposed to more bacteria and challenges to their immune system than in more-developed countries. Their bodies build up better immunity to pathogens while they are still young. If breastfeeding, they also are protected by the antibodies they receive from their mothers’ milk and these diseases do far less damage to them than they would if they weren’t exposed to them until they were adults. Chicken pox and polio are just two common examples of this type of disease. Another possible reason for the decrease in autoimmune disease in developing countries is that having a more challenged immune system early in life changes how people respond to infections later in life. And yet another possible explanation is that different microbiomes respond differently to the same virus.

Why are our bodies like this? For millions of years, as we evolved into humans, we were forced to live in harsh and unsanitary conditions. Our bodies became used to frequent contact with pathogens and have an expectation of being challenged. Ultimately, it seems, allowing our bodies to process diseases naturally and “educating” our internal biome of microorganisms is the more healthy thing to do.

Studying Violent Expiratory Events (aka Sneezes)

One of the most important tools in the fight against the spread of infectious disease is understanding how germs are spread from person to person. That’s why Lydia Bourouiba, a researcher at the Massachusetts Institute of Technology (MIT) in Cambridge dedicates a great deal of her time and work to mapping out the dynamics of the sneeze. With the help of a sophisticated video camera that records over a thousand frames per second, Dr. Bourouiba and a team of researchers carefully analyzed the trajectory of all that saliva and mucus that we expel when we let out a big sneeze. The results are gross, surprising, and quite insightful. As it turns out, all those germ-filled particles travel quite a bit further than you might think.

Violent expiratory events

Studying coughing and sneezing is especially important when it comes to understanding the spread of infection because the two bodily functions are, as Bourouiba puts it, violent expiratory events. In other words, the two send germs propelling through the air in a manner that facilitates the airborne spread of disease. Apart from these two events, the options that germs have for traveling from person to person are much more limited—they would basically necessitate direct contact.

So just how far can airborne germs travel?

The traditional line of thought assumed that a sneeze would propel airborne germs one—maybe two—meters. As the video studies mentioned above ultimately proved, however, the true reach of a sneeze is much greater. The truth of the matter is that sneezes can propel droplets of mucus and saliva up to eight meters—and the moisture from these “expiratory events” can remain suspended in the air for over ten minutes! This has serious ramifications for the ways that healthcare workers will think about protecting themselves and their patients from infected individuals.

For more information on what bacteria and viruses might be in your sneezes, simply visit our blog at CosmosID—what you learn may surprise you!

CosmosID and MetaSUB Consortium Announce Global Collaboration for Studying Anti-Microbial Resistance and Urban Metagenomics Across 54 Cities

June 21, 2016. Rockville, Maryland and New York City, New York

Today, CosmosID announced a collaboration with Weill Cornell Medicine to support a global study involved in exploration of the microbial community diversity, characterization of  anti-microbial resistance (AMR) genes and the discovery of new biosynthetic gene clusters (BGCs) from cities around the world. CosmosID’s computational tools and curated genome databases will be used for accurate and precise identification of microbial community composition and AMR markers.  CosmosID has analyzed over 20,000 biological samples from various sources that range from human, animal, plant, water, and soil using their database comprising more than 65,000 microbial genomes, including bacteria, viruses, fungi, parasites, and antibiotic resistance and pathogenicity markers.

The global study is a Grand Challenges Explorations winner, an initiative of the Bill & Melinda Gates Foundation that seeks to foster innovation to solve key global health and development problems.  The International MetaSUB Consortium (Metagenomics and Metadesign of Subways and Urban Biomes) will map the unseen genomes and epigenomes of 54 of the world’s cities beginning on June 21, 2016, in what has been called Global City Sampling Day (CSD).  This coordinated sampling day and data collection is also synchronized with the Global Ocean Sampling Day (OSD) Project, thus providing a “genetic snapshot” of the world’s cities and oceans at the same time. 

The MetaSUB Consortium plans a five-year, 54-city study, coordinated across six continents and 32 countries, with planned sampling of high-traffic areas across city subway systems, buses, and parks. Current cities include Buenos Aires, Sydney, Vienna, Ribeirão Preto, Rio Da Janeiro, São Paulo, Santiago, Beijing, Guangzhou, Hong Kong, Shanghai, Bogota, Zagreb, Cairo, Marseille, Paris, Berlin, Hyderabad, New Delhi, Tehran, Rome, Sendai, Tokyo, Mexico City, Auckland City, Ilorin, Lagos, Oslo, Lisbon, Porto, Doha, Moscow, Singapore, Johannesburg, Seoul, Barcelona, Stockholm, Zurich, Izmir, Sheffield, Montevideo, Baltimore, Boston, Chicago, Denver, Fairbanks, New York City, Sacramento, San Francisco, Seattle, Washington DC, Sheffield, and London.

The 2016 Olympics in Rio de Janeiro will also feature a measurement of the city’s metagenome response to the “natural experiment” of a global human migration event, when an estimated 1 million people attend the Olympics.  Sampling will occur before, during, and after the 2016 Olympics, and collections for RNA and DNA will be prepared to look also for the presence of any RNA viruses (e.g. Influenza and Zika). In some cities (e.g. NYC, Boston, Montevideo) orthogonal data will be generated from sewer systems and beaches, and also compared to the OSD data. These data, methods, techniques, and analysis results will all be made open to the public and free for all to use.

Participating funding agencies and Foundations include the Alfred P. Sloan Foundation (2015-13964) for the meetings, and for the sample collections the Clinical and Translational Science Center (CTSC), the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the WorldQuant Foundation, the Bert L and N Kuggie Vallee Foundation, and support from the National Institutes of Health (F31GM111053, R01NS076465, and R25EB020393). Industry partners in the project include CosmosID, GISCloud, QIAGEN, Illumina, Promega, and Copan.  The Phase I, GCE Grant entitled “Global Distribution and Epigenetic Stratification of Anti-Microbial Resistance (AMR)”was awarded to Weill Cornell Medicine and Principal Investigator (PI) Christopher Mason, Ph.D.; Co-Investigators in New York City include Eric Schadt, Ph.D. from the Icahn School of Medicine at Mount Sinai and Martin Blaser, M.D., of New York University (NYU), as well as principal investigators around the world. . For more information, please visit or

Chocolate, Wine, and the Digestive Microbiome

If you enjoy wine or chocolate, (and let's be honest--who doesn't enjoy at least one of those treats,) then you will love the recent news out of Belgium! According to recent research, both wine and dark chocolate could potentially have beneficial effects on the digestive microbiome. Before you get too excited, remember the old adage “everything in moderation” still applies! However, as long as you don’t overdo it, you can rest easy knowing that you might be doing your belly a favor whenever you sip back a glass of malbec or savor a delicious bar of dark chocolate.
Scientists at the Flemish Gut Flora Project have been studying the way that the food we eat influences the bacterial makeup of the microbial ecosystem in the human digestive system. In general, their findings have supported the notion that we do, in fact, have a great deal of control over our digestive microbiomes.

Even though no change is going to occur overnight, this comes as very good news: as multiple other studies have shown, the makeup of our internal microbial ecosystem can have an enormous impact on our overall health and well-being. Certain types of bacteria, when they exist in over-abundance, can create a disposition toward weight gain, high blood pressure, digestive issues, and even cognitive problems--just to name a few examples! Other types of bacteria, when present in the right of amounts, might predispose our bodies towards healthier patterns.

Though the exact ramifications of different combinations and ratios of internal bacteria are still being studied, the general rule that research seems to point toward is that bacterial diversity is the “golden standard” that we should strive for. This is exactly why chocolate and wine might be so healthy. As these recent studies have shown, both wine and dark chocolate encourage microbial diversity. This is most likely due to the antioxidants that both of these treats contain.

So here’s to the health of our digestive microbiomes! Have a relaxing glass of wine or a delicious bar of chocolate, and feel good about yourself! To learn more about how research is changing our understanding of health and nutrition, visit CosmosID online today!w


Stroke Severity May Be Influenced By Intestinal Bacteria

Stroke severity is caused by a complex convergence of many factors. Because the varying severity of strokes means the difference between death, disability, and a speedy recovery, scientists are obviously very interested in examining every possible detail that could determine the severity of a stroke. A recent study published in Nature Medicine suggests that one important factor may come from an unexpected origin: the bacteria living in the human gut.

In recent years, the intestinal microbiome has been identified as a possible factor in a number of other neurological disorders--from depression to anxiety to alzheimer's and more. The implication, though seemingly far-fetched, has held true throughout numerous studies: a healthy, well-balanced microbiome in the stomach can lead to healthier outcomes for the rest of the mind and body.

Fortunately, it is possible to influence the intestinal microbiome. Nobody is “stuck” with the microbiome given to them by their childhood diets and antibiotic use: we can all cultivate healthier microbiomes through special diets and, in some cases, through supplements.

That is exactly what scientists in the aforementioned study aimed to achieve. By altering the composition of the microbiomes of lab mice, they hoped to increase the amount of beneficial regulatory T cells while decreasing the amount of gamma delta T cells. Not only did they achieve this goal, but when strokes were later induced in the lab mice, those who had received an increase in regulatory T cells experienced, in general, much better outcomes than those mice which had not.

Researchers hope that future investigations will be able to build on this knowledge and work towards a future where we will be able to cultivate healthier microbiomes in order to lessen the threat posed by strokes. Here at CosmosID, we offer the tools and the expertise to help make such research as effective as possible. Visit our website to learn more.

CosmosID partners in new Center of Excellence for Sustainable Water Reuse, Food & Health, with a 10M$ Award by the USDA to the UMD School of Public Health

Rockville, MD – April 6, 2016 - In today’s world of severe droughts and dramatic changes in climate, the shortage of clean water has become a major challenge. To support the improvement of community water sources, the USDA Water for Agriculture Challenge program has awarded a $10M four year grant to the University of Maryland, College Park, School of Public Health and its collaborating partners, one of which is CosmosID, to launch a new Center named CONSERVE: A Center of Excellence at the Nexus of Sustainable Water Reuse, Food and Health. Agriculture Secretary Tom Vilsack, said “the grants we are announcing today are the latest of many steps USDA has taken to help communities who are struggling with water quality”.

The multidisciplinary team, led by Dr. Amy R. Sapkota at the University of Maryland, College Park, School of Public Health, will dedicate its efforts to developing innovative, safe, and sustainable ways to irrigate food crops in variable climates. “We are running out of water in our key food production regions,” Dr. Sapkota, an environmental microbiologist, said. “We need to act now to figure out how to shift water usage patterns and successfully reuse water to sustainably and safely grow our food.”

The University of Maryland, College Park, School of Public Health selected CosmosID to join their team based on the capability of CosmosID to provide a rapid, accurate, and actionable platform for metagenomic microbial identification and characterization. CosmosID Founder and Chief Scientific Officer, Dr. Rita Colwell, is a world leader in water-related research and a distinguished microbiologist. Dr. Colwell was awarded the 2010 Stockholm Water Prize by the King of Sweden for outstanding water-related achievements. “The University of Maryland has a long history of excellent work in water research,” said Dr. Colwell. “CosmosID has partnered with the Orange County, CA, Water District and organizations in Europe and the Middle East to develop methods for water reuse. Therefore, it’s exciting to be part of this effort developed by the University of Maryland because water reuse is a major challenge globally. This award by the USDA to the University of Maryland, College Park, School of Public Health is recognition of the strength of the formidable team clearly highly qualified to meet this challenge headed by Dr. Sapkota, an outstanding scientist.”

Jon Ryan, 703-995-9879


About CosmosID:

CosmosID is a genomic big data company focused on rapid identification of microorganisms for infectious disease diagnostics, public health surveillance, food safety monitoring, pharmaceutical discovery, and microbiome analysis for health and wellness. Using patented methods and curated databases of more than 65,000 microbial genomes, including bacteria, viruses, fungi, parasites, and antibiotic resistance and pathogenicity markers, CosmosID provides ultra fast identification of pathogens and commensal flora to sub-species or strain level, comprehensive profiles of microbial community resistance and virulence, and highly sensitive relative abundance predictions for all microorganisms in a sample.

Antibiotic Use in Children May Have Long-Lasting Impact the Microbiome

For many years, doctors have been warning about the risks posed by the unnecessary use of antibiotics. Not only are antibiotics completely ineffective against many common viral infections that cause sore throats, colds, and earaches--they can also cause unwanted side effects and lead to antibiotic-resistant “superbugs.”  Earlier this year, a group of Finnish researchers published a study suggesting one more reason to be wary of unnecessary antibiotics: the use of antibiotics in children might be associated with the disruption of the development of a healthy gut microbiome.

A healthy human digestive system contains thousands upon thousands of different species of good bacteria that help regulate important bodily functions.  When this delicate ecosystem is disrupted, it can have detrimental effects on health.  It is especially important to cultivate a healthy, balanced microbiome in children because they are in a critical stage of development.  Unfortunately, this study suggests that the use of antibiotics can affect the makeup of the microbiome for years to come.

Macrolide antibiotics appear to be the most detrimental in terms of their effect upon the microbiome.  For example, researchers found that Bifidobacterium and Bacteroides levels didn’t normalize for a full year after the use of macrolides; and Collinsella and Anaerostipes levels didn’t normalize for two full years. Penicillin didn’t seem to cause such dramatic changes.

Why are these changes such a cause for concern?  The same study cited earlier also found correlations between changes in the microbiome and frequent use of macrolides which may increase the risk of health conditions such as obesity and asthma. This is because the bacteria affected by the use of antibiotics help regulate both metabolism and the immune system.

To learn more about recent developments in the study of the human microbiome, be sure to check out our blog here at CosmosID.  As a genomic big data company specializing in the research and identification of microorganisms, we take a special interest in these developments--and encourage you to do the same.