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Keeping a Healthy Gut

Linshu Liu, Jenni Firrman, Johanna Lemons, and Karley Mahalak are researchers with the Dairy and Functional Food Research Unit in Wyndmoor, PA.

Welcome to Under the Microscope.

Linshu Liu (LSL), Jenni Firrman (JF), Johanna Lemons (JL), and Karley Mahalak (KM)

UM: Let's start with the basics – what is a 'gut microbiome,' and why is it important to our health?

JF: When you hear the term 'gut microbiome,' it is usually referring to the bacterial population, which is extremely dense and can be comprised of hundreds of different species. In fact, there is more bacteria living in each person's gut than there are people on the planet. When we begin to really think about this, it makes us curious as to what these bacteria are doing and how they could affect their host. 

These are questions that our team tries to address in our research because the more we learn about the gut microbiome, the more we understand that this community lies at the intersection of nutrition and human health. The gut microbiome composition and byproducts produced are reliant on the food we eat; the gut microbiota not only affects the gut but also impacts the health of the entire human body.

UM: How would you define a healthy gut microbiome? How do you test for this in your experiments?

JF: It is difficult to provide a single definition for a healthy gut microbiome.  The composition of this community is completely unique to each person. To further complicate matters, our unique microbiomes can change on a daily basis in response to food or factors such as the development of disease.

We can generally identify a 'healthy gut microbiome' by looking for biomarkers that indicate the generation of certain metabolic byproducts, the presence of bacteria generally regarded as healthy, and the absence of bacteria associated with disease. For example, the gut microbiota produces short chain fatty acids (SCFA), which are generally seen as health promoting.

There are a number of species of bacteria that are considered healthy primarily because they produce desired byproducts. Some of these species are beneficial and can be easily found in probiotic foods like yogurt. On the other hand, some bacteria are linked to disease. So, in short, a healthy gut microbiome would include a larger number of healthy species that can produce SCFAs and fewer species that are known to cause disease.  By looking at these different parameters, we can say generally what is healthy and what is not. However, it is not cookie cutter!

Bowls of sauerkraut, cucumber pickles and yogurtSauerkraut, cucumber pickles and yogurt are popular probiotic fermented foods. (Photo courtesy of Marek Uliasz, PixelsAway)

UM: What can happen if the gut microbiome is unhealthy or unbalanced?

LSL: Diet, drugs, and poor lifestyle habits can all induce dysbiosis of the intestinal microbiota. Dysbiosis is diagnosed as the loss of beneficial bacteria, overgrowth of bad bacteria, or the decrease of overall gut microbiome diversity. People in dysbiosis develop symptoms, including inflammation of the bowel, diarrhea, food intolerance, gas, and bloating.

The gut microbiota is also considered a major immune organ. Dysbiosis may result in autoimmunity and host cell damage, leading to systemic diseases and chronic diseases, such as such as diabetes (both type 1 and type 2), obesity, Crohn's and celiac diseases. Furthermore, some research indicates that dysbiosis of the gut microbiota may be linked to several mental illnesses, including anxiety and depression, which are serious concerns in society today. This is referred to as the gut-brain-axis, a bidirectional communication between the central nervous system and gut microbiota.

UM: What exactly are probiotics and how can they promote a healthier gut microbiome?

JL: Probiotics are living microorganisms that are ingested for their health promoting benefits.

LSL: You can find probiotics in yogurt, other fermented foods, and dietary supplements. The most common probiotics are bacteria that belong to groups called Lactobacillus and Bifidobacterium. Other bacteria may also be used as probiotics, and so may yeasts such as Saccharomyces boulardii.

Probiotics promote a healthier gut microbial ecosystem by, (1) helping to re-balance your body's community of microorganisms after being disturbed (for example, after using antibiotics), (2) producing substances (metabolites) that have desirable effects, (3) influencing your body's immune response and the brain-gut interactions.

Tomatoes, onions, bananas, strawberries, oats and garlicAssortment of foods high in prebiotics for healthy gut and digestive system. (Photo courtesy of Danijela, Adobe Stock)

UM: What is the difference between probiotics and prebiotics?

JF: A probiotic is, in essence, an edible form of bacteria. A prebiotic is something you eat that promotes the growth of healthy gut bacteria that are actually already present in your gut microbiome. 

LSL: You can also combine probiotics and prebiotics to create synbiotics.  Within synbiotics, probiotics and prebiotics work together. The prebiotic serves as a source of food for the probiotic.

UM: It's widely acknowledged that eating a diet high in fruits and vegetables is healthy.  Can you explain how this would affect the gut microbiome?

KM: Fruits and vegetables have a lot of nutrients that are important to overall health, but they also include the fibers that are not digestible by human cells but are digestible by the gut microbiome. Along with fibers, they include polyphenols that are also important to consume in small doses. When these bioactive compounds reach the colon (large intestine), the bacteria that composes the gut microbiome can digest these compounds. This digestion will help the gut microbial community members grow and may increase the diversity of its members, particularly those that are associated with healthier outcomes.

JL: And in addition to fiber, fruits and vegetables are also good sources of resistant starches and phytochemicals. Fiber and resistant starch (commonly found in potatoes, beans, etc.) are excellent prebiotics that are utilized as a source of energy to fuel the replication of many 'good' bacteria. A steady supply of these helps the beneficial microbes to dominate the microbial community.

JF: Ultimately, the gut microbiome is dependent on their host for their nutrition.    There are a lot of components in fruits and vegetables that the human cells can't actually break down and use themselves. In this case, these components enter the colon where they are available for the microbes. The microbiome combined carries an enormous number of genes that the human cells don't have; these genes code for enzymes that can break down and use these as a source of nutrition.

shime machine A SHIME (Simulator of the Human Intestinal Microbial Ecology) machine mimics the stomach, small intestine, and the large intestine. (Photo courtesy of the Dairy and Functional Food Research Unit)

UM: How do non-nutritive and alternative sweeteners (like aspartame or stevia) affect the gut microbiome?

KM: The effect of non-nutritive and alternative sweeteners on the gut microbiome depends on which sweeteners you are referencing. Not all non-nutritive and alternative sweeteners are the same.

For example, artificial non-nutritive (essentially zero calorie) sweeteners such as aspartame, sucralose, and saccharin have been shown to affect the gut microbial community in terms of its composition, its structure, and the metabolic byproducts. The alterations in the gut microbial community caused by these non-nutritive artificial sweeteners often induce glucose intolerance.

In our study, however, we learned that the compounds in stevia (steviol glycosides) did not induce measurable change in the gut microbial community in vitro.  Additionally, our in vivo experiment involving steviol glycosides and erythritol (a sugar alcohol that also functions as a non-nutritive sweetener) indicated that these compounds could help increase gut microbial diversity.   Taken together, we can conclude that the use of commercially available stevia isn't likely to cause adverse effects on the human gut microbiome. 

UM: How do antimicrobials in the environment affect the microbiota living in your intestines?  

JF: Antimicrobials are very important to disease mediation and are usually designed to target bacterial cells over human cells based on molecular differences between the two. However, these chemicals cannot distinguish between healthy and nonhealthy microbes, and additionally, bacteria are considered opportunistic, meaning that even healthy bacteria can do damage to an immune-compromised person. In this case, when antimicrobials are introduced into the gastrointestinal tract, they can cause a lot of damage to this community.

KM: Antimicrobials can enter the human body through either the food chain or through use in topical treatments, such as soaps or lotions. After these antimicrobials enter your body, they can be absorbed into your organs and tissues, which can alter the gut microbial community. Usually, this causes a reduction in the bacterial community, which can affect the diversity of that community and therefore have unwanted health effects. This is similar to having adverse effects from oral antibiotics, such as diarrhea. However, in our in vitro study we demonstrated that after receiving a high dose of a common antimicrobial (triclosan) for one week, the gut microbial community was able to recover from the treatment in both structure (the members of the community) and function (the metabolic products produced by that community).

UM: How can different ways of cooking food and other ways of food processing affect the gut microbiota?

JL: The term 'food processing' is used to describe any method that transforms an agricultural product into a food. It encompasses a wide array of activities including milling, pasteurizing, canning, cooking, fermenting, and more. When considering cooking (depending on the harshness of the method), there can be significant decomposition of susceptible nutrients and even the creation of toxic byproducts.

We are still a long way from a complete understanding of all the mechanisms at work, but we do know from existing research that cooking and cooling certain foods like potatoes and rice increases the concentration of resistant starch, an important prebiotic. Additionally, we know that microbial communities respond differently to saturated, monounsaturated, and polyunsaturated fats, so we can hypothesize that the choice of cooking oil will impact the gut microbiota, especially in the context of overnutrition. Another form of processing, fermenting, can provide a good source of dietary probiotics. — by Georgia Jiang, ARS Office of Communications.