Interesting Metagenomics

Extensive Academic Study shows CosmosID's “Best in Class Accuracy” and “Unrivaled Detection Resolution”

The fast-growing field of metagenomics enables rapid identification and unbiased characterization of the microbial communities associated with different biological specimens, based on high-throughput DNA sequencing coupled with robust bioinformatics. While all steps of this multistep process (sample collection to data analysis) are important in achieving high identification accuracy and maintaining the proper biological representativeness of the community, bioinformatic analysis of complex metagenomic datasets represents one of the most critical and challenging steps...

Chronic Fatigue and Intestinal Microbiomes

Chronic fatigue is a problem that affects a great number of people across the country and all around the world. This is an illness in which people tend to be extremely tired at all hours of the day, to an extent that it prevents them from participating in everyday activities. It is generally extremely difficult for those with chronic fatigue to feel well rested, even if they sleep significantly more than the average person.

This condition is being explored by scientists as having a possible correlation to imbalances and insufficiencies in the biota of the human digestive tract. Other such diseases include Multiple Sclerosis, Autism and Diabetes. These have all been seen to coincide in many instances with disruptions in the interior microbiomes of humans.

Stool Samples Give Insight into Possible Links

By studying the stool samples of healthy subjects versus those with intense chronic fatigue, researchers at Cornell University were able to determine that unhealthy subjects generally showed evidence of low levels of healthy bacteria in their gut. (Read more about this here). This adds to mounting evidence against the idea that chronic fatigue is a psychological or mental illness, and contributes to the belief that it is inherently a physical problem.

Further Research into Chronic Fatigue Stunted by Lack of Funding

Sadly, although increasing evidence points towards a link between chronic fatigue and disrupted bacterial cultures in the digestive tract, little money has gone into researching this connection, due to a general skepticism about the legitimacy of the problem in the public eye. Hopefully, this problem will be rectified in coming years with advances in microbiome study and technology.

Bacterial Gene Swaps and the Human Microbiome

A recent study done by scientist Ilana Brito highlights exactly how many complex factors go into human health and wellness—particularly as it relates to bacteria and the microbiomes living in and on humans.

This study was conducted using a combination of samples from Fijian village people and North American subjects. Bits of genetic material from microbes were taken from cheeks, spit samples, and fecal matter, and analyzed to identify exactly which genes were present, and which were active.

The results showed some surprising facts about the human microbiome, which has been proven to regulate a number of metabolic functions including digestion, as well as assist in immune system functions and overall health. One of these was the degree to which both diet and method of consuming food affects a person’s microbiome. For example, Fijians demonstrated on average a much higher level of starch-digesting microorganisms than the typical North American, as a result of their diet. Additionally, the lack of standardized sanitation, including increased personal contact and sharing of meals, may be the cause of a Fijian microbiome that is, on the whole, more diverse than that of North Americans.

Another interesting fact to note is that genes can often be swapped between bacteria and even entire microbiomes and also between species. The information that has been gleaned from this study may, as researcher Brito hopes, help make advancements in a number of realms of microbial study, including how hardy bacteria become resistant to even the strongest antibiotics. This could even help shed light on more complicated subjects such as allergies and asthma, problems that have been linked in other studies to the human microbiome and its interactions with the immune system.

This is just one of many fascinating studies being conducted on the human microbiome right now. For more information about related studies, check out CosmosID today!

Mapping the Microbiomes of Subway Systems

Recently, numerous scientific studies have been conducted on the topic of microbiomes that exist within and on the bodies of humans and other organisms. These are entire ecosystems of bacteria, viruses, and other microbes that live and grow on the skin, in the gut, and across other parts of living things, typically working in symbiosis and—rather than presenting a threat—actually improving our bodily functions such as digestion, by adding metabolic functions that we otherwise lack.

What many people do not know is that microbiomes do not only exist inside of people, animals, and plants. Microbiomes exist in nearly all isolated environments with features conducive to the growth of microbial life. One of these is the subway.

Recent studies done by an international group of scientists called MetaSub have revealed some interesting facts about the microbiomes of subways from major cities across the world including New York, Beijing, Rio de Janiero and many more.

To begin with, it should be known that in a typical subway, there are about 10 bacterial cells for every human cell. This is particularly striking considering the fact that a human body contains trillions of cells. Of these subway dwelling bacterial cells, scientists took samples from numerous surfaces including those often touched by humans and those infrequently touched.

Many of the results were surprising. For example, nearly half of the bacterial cells found belonged to no species yet discovered by science, highlighting our continuing need to explore the enormous and complicated world of bacteria.

On the other hand, many scientists working on the project were hopeful that the data collected in this project could be used in the future to help combat disease and improve general health and sanitation in the public.

At CosmosID we are thrilled to be involved in the in MetaSub project in helping identify and characterize the bacteria and other microbes that are in the subway samples. 

A New Antibiotic Resistance Gene in Bacteria Could Mean The End for Antibiotics

Since their discovery in the early 20th century, antibiotics have played a crucial role in fighting diseases and infections across the globe. Their ability to destroy pathogenic bacteria has saved millions of lives.. However, according to some scientists, the days of antibiotics are severely numbered. The overuse of antibiotics in both humans and livestock has led to a growth in the occurrence of antibiotic-resistant pathogens. Just recently, scientists in the United States discovered a bug in the urine of a Pennsylvania woman that is resistant to every type of antibiotic, even those reserved for the most serious illnesses.

The woman mentioned above carried inside of her a strain of E. Coli that was resistant to the antibiotic colistin. Colistin is an antibiotic that has, until now, been reserved as a last resort remedy for people carrying extremely harmful pathogens that can cause severe infections or kill their victims, such as CRE. While this is, for the moment, an isolated case, many scientists now worry that antibiotic resistant pathogens could become a serious health risk across the country and across the globe. Prior to this discovery, the same antibiotic resistant gene had already been found occasionally in bacteria in livestock and humans in China and Europe, but never before in the United States.

The inevitable decline in the usefulness of antibiotics that is likely to happen is the direct result of the overuse of antibiotics like colistin in livestock in countries like China, where regulation is lacking. The consequences could be dire. Many people who are infected with tough, antibiotic resistant bacteria in the future could be left entirely helpless and untreatable.

 So what can be done to prevent deadly outbreaks of super bacteria? Most scientists agree that the only way to stop epidemics of this sort from spreading is to detect them early by monitoring sick people and the genes of the bacteria within them. Last year, congress approved a bill that gave $150 million to the CDC to finance detection of antibiotic resistant bacteria at the state and local levels.

At CosmosID, we specialize in identifying microorganisms--thus helping to protect public health, and in identifying antibiotic resistance genes (including mcr-1, the colistin resistance gene, which we have in our database). Feel free to check out our website at in order to learn more.

How Walnuts May Improve Colon Health

Nuts have long been one of the most under-appreciated health foods. Despite being packed with protein, fiber, healthy unsaturated fats, and essential vitamins and minerals, nuts seem to suffer from a big PR problem. In fact, it is likely that it’s the fats and the calories (even though they are, in fact, healthy fats and calories) that scare off many people who would otherwise enjoy this healthy snack.

PR problem or not, scientific data continues rolling in--and virtually all of it points to the numerous health benefits of eating nuts. One recent study on the effects of walnuts on the microbiome underscores this point. Researchers at UConn Health and The Jackson Laboratory for Genomic Medicine found that eating regular walnuts could lead to a reduced risk for developing colon cancer.

This study, published this past May, showed that mice fed a diet rich in walnuts developed colon cancers at a much lower rate. Dr. Daniel W. Rosenberg of UConn Health, the principle investigator in this study, told an interviewer "There is accumulating evidence that eating walnuts may offer a variety of benefits related to health issues like cancer. This study shows that walnuts may also act as a probiotic to make the colon healthy, which in turn offers protection against colon tumors."

One of the most interesting aspects of this research--especially for us here at CosmosID--is exactly why and how walnuts improve colon health. As follow up research at the Jackson Laboratory for Genomic Medicine showed, the reason may have a lot to do with the bacteria that live in our guts. Walnuts may help promote a certain type of bacteria that digests fibers with anti-inflammatory properties--therefore protecting against the formation of tumors.

Though further studies will be necessary in order to confirm that walnuts do indeed have cancer-preventing properties, this study offers yet another reminder that our diets--as well as the microbes in our digestive system--have an enormous impact on our overall health and wellbeing.

For more exciting news about microbiome research, visit CosmosID online!

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

One More Reason to Quit Smoking: The Oral Microbiome

Times have certainly changed since the 1960s back when doctors would endorse cigarette brands on TV advertisements! Over the course of the past half-century, there has been a near-constant stream of new research that has shown us exactly how bad smoking is for the human body. From causing various forms of cancer to increasing the risk of chronic diseases to simply causing wrinkles--there is no denying that smoking is incredibly damaging. Despite this fact, over a billion people around the world still smoke. For this reason, new information continues to pour in. If you needed one more reason to get motivated to quit smoking, the New York University School of Medicine might have it for you: smoking alters the microbial makeup of the bacterial ecosystem in our mouths--and that’s bad news!

As you may already know, there are hundreds of species of bacteria living in the human digestive system, and those bacteria have a monumental effect on our overall health and wellbeing. Thanks to a plethora of new research regarding the digestive microbiome, public awareness of its importance has skyrocketed--thus contributing to modern health trends such as the pursuit of a diet rich in antioxidants and probiotics.

It is also known that an important microbial ecosystem also inhabits the mouth. Though this microbiome has yet to be studied as carefully as the digestive ecosystem, there is no doubt that it plays an important role in our health. In fact, researchers surmise that the changes provoked by smoking could be at least partially responsible for weakening the body’s defenses against cancer-causing chemicals.

There is good news too, however. The same study that revealed smoking’s effects on the oral microbiome also noted that, with time, these effects are reversible--as long as the smoker changes his or her habits and stops smoking! If you want more information on quitting, visit the American Cancer Society’s quit smoking guide. If you would like more information on promoting healthy bacterial ecosystems in the body, visit CosmosID online!

Drugs for Your Bugs?

In recent years, a great deal of research has come out indicating that the bacteria inside of our guts have an enormous influence on our health. In fact, this influence extends beyond the digestive system and includes other health systems--the health of the microbial ecosystem in your stomach could influence your cardiovascular health, your weight, and even your mental and emotional well-being. As the link between gut bacteria and overall health is strengthened, scientists have begun studying the causes behind our bacterial makeup--why is it that some people have healthy microbiomes, and other people don’t?

The answers to that question have been many. Our diet plays a big role, but so do our physical activity levels and our genes. Moreover, the drugs we take can also have an effect on our microbiome--usually in the form of antibiotics, which kill millions of good bacteria and have an overall negative effect on our gut health. This fact, however, begs an interesting question: what if we could design drugs to improve the health of the human microbiome.

Until now, most efforts to improve the microbiome have been natural and slow moving. “Eat healthier, and consume probiotics,” says conventional wisdom. Recently, however, this approach has begun to change. In 2010, for example, Matthew Redinbo (a biochemist at the University of North Carolina,) began researching drugs to treat the microbiomes of chemotherapy patients. His hope was that, by using such an approach, he could combat the side effects of a necessary treatment. The idea took off, and Redinbo continues researching direct treatment of the microbiome to this day.

In the near future, we may be able to treat a variety of health problems by regulating the microbial imbalances that cause them in the first place. This is exciting news--and here at CosmosID we are proud partner with leaders in this field. Visit our website to learn more about the work we do.


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