This page was created to provide anyone, regardless of their background, with the foundational knowledge to understand the current scope of the microbiome and related fields. Research into the microbiome has only become mainstream in the past decade. As a result, the news coming out of the labs and industries related to the microbiome tends to be mostly hard-to-read scientific literature, or hyped up articles which present the danger of overextending the truth.

With this in mind, we decided to compile some of the necessary information we believe anyone interested in the microbiome should know.

Below are straightforward summaries and translations of selected research articles representing an assortment of microbiome-related topics. In light of wanting to be unbiased we stress that the information below is merely a foundation. Should you be interested in learning more, we recommend diving deeper in to your topics of interest and expanding your knowledge base further.

That being said, please do not hesitate to contact us for recommendations on further reading material! Also follow the MicroPredictome Facebook and Linkedin pages where we will be constantly uploading new and interesting information we find relevant. We hope you enjoy the learning experience and thank you for taking the time to aid in making the world a more informed place. 

Happy reading!

– The MicroPredictome Team


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The Microbiome

Simply put, the microbiome is the vast bacterial world we share our bodies with. It has been estimated that the microbiome contains around 100 trillion microbes and 3.3 million unique genes (a gene is a unit of instructions made up of DNA). To put this in perspective, this is around 3 times the amount of cells that make up the human body and around 143 times the amount of genes found in the human genome.

The word microbiome is most frequently used in reference to the gut microbiome, but in fact there are several microbiomes found all over our body, such as in our mouths, on our skin, and even in and around our reproductive organs. The relationship between us and our microbiome can vary. Some microbiota simply live in us, while others perform actions such as shaping our immune response and aiding in our ability to metabolize food products, thus impacting our daily lives.

What makes the microbiome so interesting is its susceptibility to change over time. Even during infancy, studies have shown that factors such as antibiotic treatment, diet (breastfeeding versus formula), hygiene, and the method of child delivery (C-section versus uterine birth), all influence the development of the microbiome. Then, as infants begin to mature into toddlers, their bacteria begin to stabilize, meaning the differences between a toddlers microbiome and their mother’s become less drastic. To a lesser extent, changes in one’s microbiome continue to occur over the natural course of life. For example, as a result of changes in one’s environment or diet, or more substantially as the result of disease.

Although there are still many details yet to be fully understood regarding the impact of the microbiome on our well being, it is clear that a relationship exists between the make-up of the microbiome and disease. This relationship is currently studied by comparing a healthy individuals microbiome to that of a sick patient. For example, it has been reported that patients with inflammatory bowel disease (IBD) have a reduced amount of bacterial diversity compared to healthy individuals. Meaning that certain types of bacteria are pushing others out of their normal space, therefore changing the overall composition of the microbiome as a whole, resulting in health implications. Other examples of diseases being connected to the microbiome can be found here.

In summation, the microbiome is a massive collection of bacteria found all across our body that possesses the ability to impact us in both positive or negative ways. The microbiome is a truly amazing living and changing ecosystem worthy of its description as a human organ. It is for this reason we are so dedicated to uncovering the secrets of the microbiome in relation to our health and how the microbiome can be exploited for the enhancement of diagnostics, gut health, and treatment!

Updated on 2019-08-31

Bacterial Genera

When it comes to naming the different forms of life there are eight levels of classification (taxonomy) used. In order they are:

Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species

To put this in a perspective familiar to everyone, here is how Homo sapiens are classified:

Eukaryote > Animalia > Chordata > Mammalia > Primates > Hominidae > Homo > sapiens.

This might seem complicated, but taxonomy allows us to categorize biological information so it can be easily shared and communicated. That being said, the main taxonomic classification people are presented with are the genus and species, such as Homo and sapiens. In the case of bacteria, the genus species pair may look something like Lactobacillus rhamnosus or the abbreviated L. rhamnosus.

Some common bacteria genera you might come across include:


These genera can be further classified by species like so:

Lactobacillus acidophilus
Bacteroides fragilis
Clostridium difficile
Streptococcus mutans
Escherichia coli
Salmonella enteritidis
Vibrio cholerae
Bacillus brevis
Staphylococcus aureus

Notice that the genus is capitalized while the species is not. Additionally these names are sometimes abbreviated, a popular example would be E. coli.
The difference between species within the same genus can be quite great. For example, a snow leopard (Panthera uncia) lives in a drastically different environment than its relative the tiger (Panthera tigris). For this reason, it is important to understand taxonomy, especially in the case of bacteria. So the next time you find yourself confronted with a slew of bacterial names, as is the case with probiotics and supplements, use this new information to seek out the species you are specifically interested in!

For deeper information on this topic, check out these links!


Updated on 2019-08-31

Diet and the Microbiome

Key takeaways:

    • Microbiota can influence our appetite in various ways
    • Diets must be personalized to an individual to have a higher chance of impact

Mouse Studies

In 2013, researchers wondered whether or not the microbiota found in obese mice could have an impact on the weight of lean mice. To test this, researchers transferred fecal samples from obese mice into lean mice through a process known as FMT (Fecal Matter Transplant). Why would researchers want to remove fecal samples from obese mice in the first place? Well, the fact is that feces (stool, poop…) contains trillions of microbiota which can be used to determine which types (strains), and how many of each type are present within the digestive tract. Some strains of microbiota you have probably heard of include Escherichia coli and Salmonella enteritidis. Getting back to the story of our mice, researchers observed an increase in fat in the lean mice within one week of the FMT, suggesting that the microbiota from the obese mice were the cause of the significant change.

This mouse study was then taken a step further by taking advantage of the fact that mice are coprophagic (meaning they eat poop). The researchers wanted to determine if simply placing an obese mouse in the same cage as a lean mouse could have an impact on weight. This was achieved by using twin pairs of obese and lean mice. While one lean mouse and one obese mouse were placed in a cage together, their twins were left separate, allowing the researchers to see how each mouse gained weight compared to its twin. Sure enough, it was seen that the obese mouse exhibited a significantly lower ability to gain weight than its obese solitary twin following a 10-day diet partially composed of lean mouse feces. Once again suggesting that microbiota are able to have an impact on weight.

By uncovering this causal relationship between gut microbiota and body weight regulation, the power of the microbiome over the body as a whole was further solidified. Today, there are plenty more examples regarding the impact of the microbiome on mood, inflammation, and gut diseases to name a few. Here is the link to the entire mouse study if you are interested in more details.

So what does this mean for humans?

In the previous section, we discussed the impact of FMT on body weight regulation in mice. Don’t worry, the following section will not include eating feces of any sort (although there is research suggesting this could one day be a solution for certain conditions…).

Just like us, the microbiota in our gut need to eat to survive; in short, what we eat, they eat. Furthermore, microbes in the gut have a preference for certain types of foods and even possess the ability to manipulate us into getting exactly what they want. So the question becomes, how do our gut microbiota influence our eating behavior and how does our eating behavior influence our gut microbiota?

To answer this question we must first understand that not all bacteria desire the same foods. Some prefer carbohydrate-rich diets while others are more partial to specific forms of fiber or certain types of fat. As a result, the food we eat can dramatically impact us via its impact on our gut microbes.

For this discussion, we will mainly be pulling from a 2014 article which compiled information related to the question of how eating behavior can be manipulated by gut microbiota. Frankly, there are many ways in which this could be happening within our bodies, most of which will not be discussed here; so as always, links will be provided below for those interested in further reading.

Similar to the way in which an infant cries when hungry, bacteria are also able to motivate us to feed them. For example, there is evidence suggesting that our eating behavior can be influenced by the way we feel pain. Pain, as described by the International Association for the Study of Pain, is “an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage”. As we all know, pain can be an extremely motivating sensation, and by exploiting our underlying ability to sense pain, our gut microbiota is able to influence our eating habits.

So how exactly do they achieve this? Well, it turns out our microbiota is actually quite active, it can help us digest certain foods, produce certain necessary vitamins, and most importantly for this discussion, they can release toxins which stimulate pain. When faced with low levels of the nutrients needed for their growth, microbes can produce toxins which directly injure the gut. This, in turn, results in a sensation of pain which can motivate us to eat. However, this is simply one potential explanation for the pangs of hunger we all experience.

There is also evidence suggesting microbes may influence our dietary habits through the manipulation of a major sensory control center known as the vagus nerve. The vagus nerve is an extremely important component of the nervous system. It is the tenth of the twelve cranial nerves and is responsible for controlling many of the organs which allow us to live, such as our lungs, heart, and digestive tract. Evidence also points to the vagus nerve as being an integral regulator of appetite and thus body weight. To keep things simple, let us assume that increased activity in the vagus nerve results in overeating, while reduced activity leads to a loss of appetite. To understand what we mean by activity and how it can be influenced, let us take a brief detour to discuss hormones. Hormones are chemicals which are created in one part of the body and then transported to another location, frequently through blood, where they can then have an impact. You have probably heard that hormones are produced in glands such as the pituitary, which is located in the brain, or the adrenals, which are found above your kidney, but interestingly, these same hormones, and chemicals resembling them, can be produced by certain microbiota in the gut. As a result, these microbes are able to create their own chemicals which increase the activity of the vagus nerve and thus influence one’s appetite. It is for this reason that bacterial strains such as Lactobacillus are of interest due to their potential to reduce the amount of hunger-inducing hormones present in the body, however further research is needed to determine how this could be effectively used as a weight loss or weight gain strategy.

Clearly there are many ways in which our microbiome could be influencing our diet. Although we have provided some examples above, it is important to understand that the true reason may be something completely different or even a mixture of many reasons. As a result, it is important to keep up with the current field of research, especially for a field such as the microbiome which is rich with development. 

Updated on 2019-08-31

The question everyone wants an answer to…

In today’s world where we are constantly bombarded with different types of diets, it can be quite intimidating when it comes to figuring out what works best for ourselves. Unfortunately, the truth is not nearly as clear and exciting as we would like it to be. The reality is that determining the relationships between diet, microbiota, and conditions such as IBS or any gastrointestinal discomfort is extremely complex. For example, think of 5 people you know. Do they all eat the same thing? Are there certain foods one person can eat while the others avoid? Even if everyone eats similar foods, are there still considerable differences between everyone’s weight? By asking these very simple questions it becomes strikingly clear how different we all are, especially at the nutritional level, whether that be in terms of one’s dietary decisions or capacity to consume certain foods.

To further illustrate the complexity of these relationships, let us discuss some dietary regimens commonly suggested to those diagnosed with IBS. Although the causes of IBS and its subtypes are not fully understood, the disorder is considered to be the result of the interaction of various internal and external factors including stress, diet, intestinal dysfunction, and the microbiome to name a few. Some studies even suggest that up to 63% of IBS related symptoms are caused by dietary choices. As a result, it is common for people to try to initially restrict certain dietary aspects such lactose, gluten, and fructose, found in items such as spicy dishes, fatty foods, alcohol, and dairy products. Additionally, diets have been developed to limit specific dietary components for those with IBS. We will discuss a few such diets in the paragraphs below.

One diet that some IBS patients have benefitted from is the low-FODMAP regimen. FODMAP stands for fermentable oligo-,di-,mono-saccharides and polyols. These are a specific class of carbohydrates which are indigestible. This means that instead of being digested the normal way which allows for nutrients to be broken down and transported throughout the body by our bloodstream, these carbohydrates instead stay inside our intestine where they can then be consumed by our gut bacteria. The potential problem with this is that these bacteria are major producers of gases such as hydrogen. Resulting in increased intestinal pressure and discomfort in the form of cramps, bloating, or flatulence. Furthermore, the bacteria known to produce high amounts of gas have been found to be more abundant in IBS patients, making the digestive symptoms even more severe. To combat these symptoms, those with IBS remove certain FODMAP-containing foods from their diet, including certain grains, beer, sweeteners, as well as specific fruits and vegetables. You might be thinking that a low-FODMAP diet sounds like it would require a lot of forethought, and it does. Interestingly, many FODMAP foods are normally quite healthy options, such as apples, asparagus, and beans. As a result, those interested in trying the low-FODMAP diet should consult a doctor or dietician to make sure they restrict the proper foods while simultaneously still consuming the necessary daily nutrients. Although this is significantly more drastic than the usual no chocolate or no bread diets we are accustomed to hearing about, the low-FODMAP diet, when pursued correctly, has the potential to greatly reduce intestinal discomfort for those who need it most. For this reason, it is frequently suggested that people on the diet eliminate all FODMAPs for weeks then begin to slowly reintroduce certain foods back into their diet, allowing people to observe which foods result in digestive issues.

While the restrictive nature of the low-FODMAPs diet may convince you it is a cureall, this is sadly not the case. Just as is the reality with all health interventions, they do not work for everyone. Additionally, dietary approaches such as the low-FODMAP regimen lack substantial evidence for their long-term benefit, even though on the short-term symptomatic reductions are commonly seen. Future studies will certainly be needed to understand the relationship between diet and our microbiome, including the surveying of the gut microbiome over time. Especially in the case of IBS patients where symptoms are known to vary over time even for a single individual.

It is for this reason that the advice given to those who are simply looking to eat more healthily is the same advice most of us have been hearing our entire lives; eat plenty of varied and colorful fruits and vegetables, stick to whole grains, consume different sources of protein and stay away from sugary snacks and drinks. It is with these guidelines that the “Healthy Eating Plate” was developed by nutrition experts at the Harvard T.H. Chan School of Public Health.

So in summary, listen to your body, and if you encounter symptoms of intestinal discomfort, try adjusting your diet gradually. We, just like you, are extremely interested in the way diet impacts our microbiome and are constantly reading literature related to the topic. So, for further reading check out these papers below!

Updated on 2019-08-31

Stool Softness and Visual Assessment

Although we all poop, it remains as something we tend to avoid in conversation. However, by simply taking a glance at your poop, you can gain some interesting insight into your current state of health.

How often do you glance at your poop? What does it look like? How does it feel when you poop? These are all questions commonly asked by one’s general practitioner during a check-up, but what information do your answers truly hold? It turns out that information regarding the consistency, frequency, and shape of your stool are all impacted by your diet and lifestyle. As a result, the Bristol Stool Chart was developed to categorize what different bowel movements might mean.

Take a look at the chart in the link above for cartoon images of each stool category.

The chart is broken down into 7 types of stool. 1-2 are indicative of constipation, 3-4 represent optimal stools and 5-7 indicate diarrhea and urgency. To better understand these categories let us first discuss the meanings of constipation, diarrhea, and urgency.


Constipation is generally described as having less than 3 bowel movements a week. This is frequently the result of your colon removing too much water from your food, making it difficult for it to move through your digestive tract. This then causes a cycle where the food begins to move slower and slower through the gut and therefore loses more and more water.

Constipation is normally associated with difficulty in passing stool or the inability to pass more than a small amount of stool at a time. This can also result in discomfort in the forms of cramps or the feeling that a movement was incomplete.

There are many reasons one may become constipated including but not limited to: low fiber intake, dehydration, drug side effects, and spinal cord injuries. Those who are experiencing constipation may be prescribed options to increase the regularity of their bowel movements, such as stool softeners, supplements, or lubricants such as mineral oil.


Diarrhea is the opposite of constipation and is associated with loose, watery, and frequent bowel movements. Interestingly, liquid stool can also be the result of severe constipation resulting in a hard to pass stool becoming lodged in the digestive tract. This causes a partial blockage resulting in watery stool flowing around the blockage leading to unexpected diarrhea-like events. However, this is technically not diarrhea but instead a side effect of constipation. There are many potential causes of diarrhea including but not limited to: infection, disease, antibiotics, allergy, and intolerance (lactose).

When most of us think of diarrhea we are commonly referring to a single event, however diarrhea can actually be much more serious. In 2016 it was determined that diarrhea was the eighth leading cause of death among all ages. This is mainly due to severe dehydration and nutritional imbalance resulting from the inability of the digestive tract to absorb the contents passing through it, also known as malabsorption. It is for this reason that diarrhea is especially dangerous for elderly and infant populations.

So what are the treatments? At its core diarrhea represents a fluid retention problem, so treatments commonly include supplements, antidiarrheal medications, or fluid replacement through an IV line.

As for urgency, this involves the inability to control one’s bowel movement resulting in stool leaking from the rectum. Urgency is also referred to as urge incontinence and is primarily caused by muscular or nerve damage to the rings of muscle at the end of the rectum.

The Bristol Stool Chart

Now that we are on the same page regarding these terms, the Bristol Stool Chart begins to become more clear. Types 1 and 2 are defined by hard and lumpy stool, this makes sense considering constipation includes the difficult passage of dehydrated and compressed stool. At the bottom of the chart, types 5-7 are defined by soft, fluffy, and liquid stool representative of malabsorption during diarrheal episodes.

So what about types 3-4 which are defined as being relatively smooth and consistent in shape throughout. What makes these the healthy types? First and foremost, when we talk about having regular bowel movements there is a misconception that all people should have the same bowel habits, but this is false. What ‘being regular’ really describes is having soft, well-formed and easily passed bowel movement at least 3 times a week.

Other indications of good bowel function listed on the continence foundation of Australia’s website include: being able to comfortably get to the toilet without any mishaps (minimal urgency), being able to pass stool within one minute of sitting down, and passing completely with minimal strain thus minimizing return trips after a short period of time.

For further information feel free to check out these links:

Updated on 2019-08-31

Prebiotics vs. Probiotics vs. Postbiotics

In today’s world of food crazes, cleanses, and health food supplementation it can be hard to determine which options are valid and which are merely side effects of misinterpretation and pseudoscience. This is especially the case when it comes to microbiome-related products.

Each of the above -biotics are used with the intention of manipulating the balance of the microbiome; however, each category of -biotic represents a different means of accomplishing this goal. Let’s take a look at some definitions before diving in further. We will present the different categories in the order of decreasing public awareness.


According to the National Institute of Health (NIH), “probiotics are live microorganisms that are intended to have health benefits,” including orally ingested foods and supplements. Additionally, probiotics fall under the category of a health food and as a result are not regulated by the Food and Drug Administration. For probiotic bacteria to be useful they must be able to survive the journey from the mouth to the gut. This includes being able to withstand the acidic environment of the stomach before moving on towards the less acidic regions of the small and large intestines. The most commonly selected types of probiotic bacteria are from the genera Lactobacillus and Bifidobacterium (Take a look at our earlier topic on how bacteria are named for more info!)


Unlike probiotics, which introduce live bacteria into the gastrointestinal tract, prebiotics are dietary components which stimulate the growth of beneficial bacteria over the potentially harmful ones. Similar to probiotics, prebiotics must survive the journey through our gastrointestinal tract so they can reach the bacteria they are meant to help multiply or activate. Prebiotics are primarily carbohydrates that we ourselves cannot digest but are instead consumed by certain strains of bacteria. Some prebiotics you may have heard of include inulin (not to be confused with insulin) which falls under the dietary fiber class of fructans, as well as pectins, another source of dietary fiber.

You may come across the word synbiotic while researching these products. Synbiotics are a combination of probiotics and prebiotics found in the same food or supplement. “Syn” comes from the word synergism which means that when combined these two -biotics work better than they would individually → they come together to create a whole which is greater than the sum of its parts. Most frequently this means a prebiotic helping a probiotic survive the trip to the gut.


Postbiotics represent the active products released by probiotic bacteria which are responsible for some of the advantageous effects of probiotics. For example, some bacteria may release products which fend off potentially dangerous bacteria while others may release products which help energize certain cell types.

Updated on 2019-08-31

Decisions … Decisions

People want to have a healthy diet with minimal effort, it is for this reason that the word superfood is thrown around so much…even though no scientific definition of a superfood exists. The criteria for picking the “right” food have since become more involved than simply selecting based on taste and nutrition. People are now also interested in how they can consolidate different health benefits within their diet beyond nutrition; especially in the case of gut health-conscious individuals. However, we must also consider the range of reasoning which accompanies those interested in using these products, stretching from a healthy individual interested in bolstering their microbiome, to someone impacted with a disease looking to reduce their symptoms.

Although it may seem as simple as adding a certain bacteria to a food product such as yogurt, the bacterial strains selected can have different impacts, or more commonly, no impact at all. The potential benefits of every food described as a new probiotic powerhouse should always be met with healthy skepticism. For this reason, the future acceptance of probiotic products depends on their ability to provide consumers the benefits that they promise at the present.

This is not to say that the next probiotic yogurt or supplement you take will result in the decline of your health, but rather one must take it upon themselves to do the research on the product they are purchasing and be conscious of the way they feel when the product is in use. Some guidelines to live by are reading labels properly, making sure the product (especially probiotics) have been stored properly and are of high quality, and understanding the bacterial strain in use. For those considering taking a probiotic for a health condition, make sure to have a discussion with your physician first; especially those with potential allergies to substances which may be part of a probiotic formulation. For deeper evidence-based information on the topic of bacterial strains, recommended doses, and some conditions which benefit from probiotic use, please consult this link from the World Gastroenterology Organisation. Remember, the topic of microbiome-related supplementation is quite fresh. For example, no probiotic has FDA approval for its use in treating a disease. Therefore one should always make sure to research a product of interest and talk to the relevant health professionals prior to use.

For further reading check out these papers below!

Updated on 2019-08-31


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