Interesting Metagenomics

Contacts and the Ocular Microbiome

If you read our blog here at CosmosID, you’re already well aware that significant amounts of research have come out over the past couple years regarding the microbial ecosystem that lives within each and every human being. And, as you surely know, one reason scientists are suddenly so intent on learning more about the intestinal microbiome is because it appears that the bacteria inside of us have far-reaching effects on our overall wellbeing.

Recently, in late March of 2016, a new study came out regarding eye microbiota associated with wearing contact lenses.

As reported by Time Magazine, a group of researchers from the New York University School of Medicine examined the microbial ecosystems living on the eyes of 58 different subjects. The variable? Some of these subjects used contact lenses, whereas others did not.

The results revealed a starker difference than one might expect. First of all, the ocular microbiomes of the subjects who wore contacts did indeed show substantive differences in terms of what species were most prominent. Additionally, the make-up of the contact-wearers’ ocular microbiomes were more diverse and quite similar to the microbiome of the skin (which makes sense if you think about placing contacts in your eyes every day).

Unfortunately, no study has yet answered the question of whether this might have a positive or negative effect on human health. Some research has previously indicated that those who wear contacts are more prone to certain eye conditions; however, it is unclear if the makeup of the ocular microbiome is the culprit. It could just as well be that our eyes get infected in spite of this adjustment in bacterial makeup--not because of.

As science continues to search for answers to complex questions such as this one, CosmosID will continue helping to provide answers by helping to identify microorganisms for researchers across all disciplines. Visit our website for more information!

Research Of Mosquito Microbiome Raises Interesting Questions

A large portion of the research being published on the human microbiome can be generalized into two categories: scientists study lab mice in order to extrapolate conclusions about the human microbiome, or else scientists take direct samples from humans. Though this is obviously an oversimplification, it is worth noting because such a perception can lead to a very narrow concep of microbiome research and its possible implications. A new study published in the British interdisciplinary scientific journal Nature should help challenge those stereotypes.

The study examined a very specific aspect of the mosquito microbiome: namely, C-type lectins (CTLs.) CTLs are a diverse family of proteins that bind onto different types of carbohydrates on the outside of cells. Many lectins are involved in immunity and scientists believe that lectins might be important in determining the bacterial makeup of the mosquito gut.

In mammals, it has been documented that CTLs help target and destroy many forms of bacteria. That is why the results of this study were a bit surprising: researchers discovered that, in the mosquitos being studied, the CTLs were actually helping defend certain bacteria from antimicrobial peptides, which are used to destroy harmful bacteria. It appears that CTLs may be a bit more “intelligent” than once thought: perhaps they help select the best microbial makeup possible in order to build a healthy microbiome.

There are two possible implications for this work. There is, of course, a “conventional” purpose for this researcher: scientists now know a bit more about the way CTLs work in general, and may be able to learn more about how the human body chooses its own microbiome in some capacity. Additionally, however, Kevin Bonham of Scientific American believes that this research may also be aimed in a different (though equally ambitious) direction: altering mosquito behavior in order to prevent the spread of mosquito born illness.

Whether you need to explore microbiomes of mosquitos, ants, mice, or humans, we are ready to help here at CosmosID. Just reach out for more information.

Mental Health and the Microbiome

It’s no secret that bacteria have pulled a complete one-eighty when it comes to public relations. Not long ago, the word “bacteria” was pretty much universally feared. Of course, we still have a modern understanding of the existence of good and bad microbes and we all know that it is important to be clean and careful. However, “bacteria” is no longer a dirty word the way it used to be.

In fact, there are now an enormous number of yogurts, kefirs, cheeses, and other foods whose makers actively boast about their probiotic content. How did bacteria suddenly become so hip? Simple: an evolution in our understanding of how bacteria affect the body. That understanding continues evolving to this day, and it appears that the impact of the bacteria inside of us is perhaps even more far-reaching than previously imagined. Recent research has even found a compelling possible link between the microbiome and mental health.

For example, in one study, a number of men ingested large quantities of healthy bacteria. When interviewed four weeks later, these men reported a decrease in stress and an improvement in memory. In another instance, scientists managed to turn timid mice bold and shy mice social simply by altering the composition of their bacterial ecosystems. In yet another study, mice were given bacterial samples from depressed humans--and began to exhibit signs of depression themselves.

These examples--all taken from an article published in that our mental health could possibly be affected by our microbial health. While more research is needed to determine cause versus correlation, it is interesting to think about, knowing that we have some level of control over our microbial health and none of us are slaves to the microbiome we currently host.

To learn more about recent developments in the ongoing study of the human microbiome and way beyond, visit the CosmosID website or check out our blog.


The Home Microbiome

Though the full extent of the microbiome’s effect on human health is yet to be explored, it is increasingly apparent that understanding the microbiome will lead to important advances in a number of distinct health related fields.  It has recently been documented, for example, that the microbiome may have direct impact on issues as diverse as weight gain and brain development.  Understanding what factors influence the makeup of the human microbiome is, therefore, an important goal moving forward—and this was the prime objective in Argonne National Laboratory’s recent Home Microbiome Project.

Nearly everyone spends a large portion of their time in their homes; and with new trends such as cyber commuting the importance of a healthy home environment is only going to increase. What’s more, the home is, for most of us, the environment that we have the most control over. All of these factors contribute to the importance of understanding how and why the home environment influences the human microbiome.

In this study, researchers followed seven families during six weeks.  They monitored the microbial ecosystems living within each participant, as well as the microbes that lived around the home (on surfaces such as countertops, doorknobs, light switches, etc.) The most impactful finding of the study was that the relationship between the human microbiome and the microbial ecosystems existing within the home is reciprocal.  We influence the microbial ecosystem that surrounds us just as much as it influences our internal microbiome.  In fact, when researchers had three families move to new locations, they found that the new homes contained the exact same microbial makeup within just one day!

This means that family members (and even pets, which were also included in the study) have an enormous effect on each other’s microbiomes. Not surprisingly, this effect is especially great between couples, and between parents and young children.

CosmosID is proud to have been a part of the publication and to be on the cutting edge of microbiome research; helping to identify and analyze the microbes that inhabit the places where we live and work in hopes of building a better, healthier tomorrow for all.

The Development of Civilization and How it Affected the Human Microbiome

An interesting health concern to ponder: for most of human evolution, our ancestors lived a lifestyle that was extremely different from our own.  Case in point: agriculture first developed in the Fertile Crescent around 10,000 B.C.E., and then developed independently in many other areas of the world over the following millennia.  These past twelve thousand years were, of course, the mere blink of an eye in evolutionary terms; and it is safe to say that our bodily systems developed and adapted to match a hunter-gatherer diet and lifestyle—not a settled, agricultural one. 

How might this affect our health here in the modern world?  One important consideration is the microbiome.  In recent years, scientists and researchers have been compiling a growing amount of evidence that the microbes that inhabit our digestive systems affect nearly all aspects of our health and development.  The makeup of this microbial ecosystem is affected greatly by our diet, and therefore it stands to reason that the enormous changes brought about by the dawn of civilization must have had a dramatic effect on the human microbiome.

In order to confirm this concept, and to develop an idea of what exactly those changes were, scientists at the J. Craig Venter Institute conducted a study on the digestive microbes of two distinctive communities in the Central African Republic: the BaAka, (a hunter-gatherer group that lives on wild plants, game, and fruit) and the Bantu (an agricultural community that has frequent contact with the western world.)  The study also compared the findings in both communities to the typical microbiome of an American.

Not surprisingly, the researchers found significant differences between all three groups.  The abundance of Bacteroidetes is perhaps the most representative (and most telling) difference between the three groups.  This microbe is extremely helpful in breaking down fiber rich foods; and a deficiency in Bacteroidetes is often associated with obesity.  The microbe was found to be most abundant in the BaAka community, less abundant among the Bantu, and least abundant in Americans.

Though our distinctive modern diets can cause certain health concerns, they also offer numerous benefits, and reverting to a hunter-gatherer diet is obviously neither viable nor desirable (unless maybe you prefer the Paleo Diet).  With the use of advanced microbial identification and careful study, however, scientists hope to understand and solve the microbial deficiencies experienced by millions of people around the world.  Here CosmosID, we are dedicated to furthering that mission.  Visit our website today to learn more about the exciting work we are driving.

A Healthy Start: How Exercise Can Help Set Kids On The Right Track For A Diverse Microbiome

A new study out of the University of Colorado Boulder suggests that exercise may be even more important for young children than previously imagined, as it has a positive impact on metabolism, brain development, and diversity of the microbiome.

The study examined the development of juvenile rats and found that there was a special window toward the beginning of life during which an active lifestyle would have powerful and long lasting effects on a number of health outcomes.  Researchers are exploring whether or not these results can translate to human experience.

Researchers also noted that the microbial diversity may have an effect on the relationship with associated optimal brain development and metabolism, as a well-developed microbiome can add up to five million genes to a person’s genetic profile.

A word to the adults who may be reading this article and despairing about their relatively sedentary childhoods: there is still a great deal of plasticity in the human microbiome, and this can be affected by diet and lifestyle in addition to exercise.

Of course, the important question moving forward will be how to best take advantage of the “special window of opportunity” that makes childhood exercise so beneficial to the microbiome.  The study didn’t produce an exact age range that was most important for developing rats--and even if it had, translating the results to humans would be impractical at best.  For now, it appears that the earlier the better; and indeed, beginning exercise early is an important component of developing lifelong habits for good health.

Understanding the microbial ecosystem and its relation to early lifespan development will also allow scientists to improve plasticity in adults, which is another important goal for future studies.

For more information on exciting new microbial research, visit the official CosmosID website.

4 Exciting Benefits of Researching the Microbiome

According to some estimates, there are between one and two pounds of bacteria living in your gut right now!  No need to worry, though— most of these bacteria are extremely beneficial, and in fact you wouldn’t be able to live without them!

That being said, not all bacteria are created equal.  The bacterial ecosystem that inhabits your digestive system is made up of hundreds of distinct species; and each of these species plays its own special role in your body.  Maintaining the right balance bacterial species is very important to your health.  Unfortunately, due to a variety of factors such as diet and disease, this isn’t always possible. 

Thankfully, a growing body of scientific research is being dedicated to understanding exactly how the microbiome works, and how doctors can fix potential problems.  The ability to manipulate the makeup of the bacterial ecosystem brings about a number of exciting new possibilities in medicine.  For example:

·       Making sure bacteria work in conjunction with medication.  Using prebiotics, doctors can boost the abundance of certain microbes within the digestive system in order to optimize the way the body interacts with certain medications.  This can help reduce side effects, improve safety, and more.

·       Adjusting the microbiome instead of using medication.  Some health problems are caused by imbalance in the microbiome.  Restoring healthy diversity to the body’s microbes can be an important component of addressing certain issues.

·       Targeting harmful bacteria.  Improving diversity in the microbiome can also help decrease the presence of potentially harmful bacteria.

·       Targeting skin problems. The bacteria within the digestive system have an impact on many functions of the body beyond the breakdown of food; and studies suggest that cultivating a healthy microbiome can help alleviate problems such as acne and rosacea.


As microbiome research continues to explore new and exciting concepts, CosmosID will be there to assist doctors, scientists, and organizations identify and understand the microbes that affect our health.  Visit our website for more information.

Blood Glucose Levels and the Microbiome

If you are one of the twenty nine million Americans affected by diabetes, the odds are good that you know first hand just how difficult predicting food’s effect on blood glucose levels can be.

Of course, the most important factor is the number of carbohydrates that a given food contains.  Carb-rich dishes are sure to have a proportionally larger effect on blood glucose than low-carb alternatives.  Additionally, you’ve probably learned to consider the complexity of carbohydrates: simple sugars found in white bread, soda, desserts, etc. tend to cause an immediate blood glucose spike; whereas complex sugars found in whole wheat, brown rice, oats, etc. tend to break down more slowly. 

However, you’ve probably noticed that these are only guidelines--sometimes food has unexpected effects. New research now points to the composition of the microbiome as a cause of this unpredictability.

How Tiny Microbes have a Huge Effect on Blood Sugar

            In a recent study published by Cell , researches conducted one of the most comprehensive studies on blood glucose levels and microbiome to date.  By continuously monitoring the blood glucose levels of 800 participants over the course of an entire week, scientists were able to record the reactions of each participant to various meals.  The results were extremely divergent.

In what is perhaps the most telling anecdote from the study, two participants experienced the exact opposite reaction to eating a cookie and eating a banana.  For one participant, the banana caused a spike in blood glucose levels and the cookie had virtually no effect; for the other participant, the banana had no effect and the cookie caused a spike.  How can it be that two people can have such starkly different reactions to the exact same food?  The role of each individual’s microbiome in the digestive process is a likely culprit. 

The Importance of Further Research on the Microbiome

Eran Segal, PhD, one of the authors of the aforementioned study, later speculated in an interview with Scientific American that, through careful study of the microbiome, scientists will be able to develop specialized diets catered to the needs of each individual.  “If it’s done in the proper fashion,” he remarked, “it has the potential to really improve people’s health.”

Here at CosmosID, this study was a perfect reminder of why we do what we do.  By aiding in the research and identification of microbes, we play an important role in the development of a constantly improving understanding of how the human body works.

How Does Fiber Intake Affect the Microbiome?

New Findings Point to the Importance of a Fiber-Rich Diet

            When many people think of fiber, images of strange breakfast cereals and powdery supplement pills may come to mind.  Most know enough to associate the nutrient with healthy bowel movements.  The full truth, of course, is more complicated.  Potential sources of fiber are far more diverse; and the health implications are much farther reaching.  By cultivating a better understanding of what fiber is and how it affects the body, public attitudes (and thus public health) can be improved.

Fiber and the Microbiome

            The human microbiome is comprised of trillions of individual microbiota and tens of thousands of different species of microbiota. Though this may give the germaphobes out there a small heart attack, the truth is that these microbes are not only safe; they are extremely important to the healthy functioning of the digestive system. Unfortunately, the modern American diet (rife with processed foods) does not always lend itself to creating a balanced microbiome.  One area of interest that scientists are beginning to identify is the effect of fiber on the microbiome.  As it turns out, a low fiber diet can have negative effects on microbial diversity in the human digestive system.

Long-Term Effects

            Perhaps even more disturbingly, scientists discovered that this diversity is very difficult to recuperate once it is lost. Simply put, fiber can support a healthy and diverse microbiome, but it will not cultivate one. This implies that fiber intake is even more important than initially thought.

Diet as a Lifestyle

            Last but not least, it is important to note that these findings reflect the effects of a diet sustained over a significant period of time.  In other words, skipping out on fiber rich foods for a few days is not going to cause a serious long-term problem; and neither will popping a couple of fiber supplements or eating a slice of whole bread make up for a pattern of low-fiber eating.


            CosmosID is excited to be part of the ongoing scientific mission to learn more about the human digestive system.  Our company specializes in bioinformatics, and is focused on identifying microorganisms in order to aid scientists, doctors, and health-related projects of all kinds.


Microbes and Newborns: What Research Says About the Effects of Cesarean Births

The cesarian delivery method has been, without a doubt, one of the most important advancements in modern medical history.  It has allowed for the safe delivery of countless children who might otherwise have faced various risks had they been delivered vaginally. However, many scientists and doctors have pointed out a worrisome trend--roughly one in every three births in the United States is now a C-section delivery.  The ideal C-section rate among low-risk births should be closer to 15%; and with so many babies being delivered via cesarian, it’s important to understand the ramifications of such a procedure.

Risks and Benefits

Studies have suggested that C-section babies are at a higher risk of developing certain immune and metabolism disorders--including type 1 diabetes.  This means that families must weigh the risks and benefits of delivering via C-section very carefully. However, the fact remains that, for a large portion of the population, C-section births will continue being a necessity.  It is crucial, therefore, that scientists isolate the cause of these problems in order to develop a working solution.

What the research says... 

Many scientists believe that higher risks faced by C-section babies are due to the nature of the first microbes that colonize that baby’s gut and body.  Babies that are delivered vaginally are exposed to the bacteria of the mother--whereas babies delivered via C-section are first exposed to environmental bacteria. Therefore, many scientists assume that babies born via C-section lack exposure to certain microbiota that would have been critical in developing better functioning immune and metabolic systems.

Moving forward

In order to ensure optimal outcomes for the millions of babies that will continue to be delivered via c-section, researchers must identify and isolate the bacteria that allow newborns to develop without impediment and do further work to characterize the entire microbiome.  Thankfully, alongside bioinformatic leaders such as CosmosID,  scientists are approaching answers. With the right combination of technology and investment, a better future is possible for the increasing number of children who are born through cesarean delivery.