Getting the “Bugs” Out of the Microbiome
The ins and outs of gastrointestinal bacteria.
The gut microbiome is a term that’s creating a lot of buzz these days. So, what exactly are people referring to when they talk about “the gut microbiome”? There is a ton of miscommunication on types of bacteria in the gut, pre- and probiotics, and how this relates to gastrointestinal imbalances. Below are 7 facts to help you feel more clear about the gut microbiome and how it relates to your overall health:
The microbiome does NOT only refer to the gut.
The microbiome is known as a collection of organisms and their DNA from all microorganisms found in a particular environment. The gut is one of the environments that these genomes reside in and is a popular topic because the gut microbiome provides genetic material that regulates our natural immune response and protects us against chronic illness; however, the microbiome can refer to genomes in different environments in the human body such as our skin, lungs, or reproductive organs.
2. “Microbiome” and “microbiota” are not the same thing.
People are using these terms interchangeably but they do have a few differences. As said previously, the microbiome is a collection of genomes from all microorganisms that are found in any type of environment. This can be specific to an environment in the human body or expand into our ecosystem including the organisms in our soil. The term “microbiota”, however, refers to more specific microorganisms (e.g., bacteria, fungi, viruses) found in a specific environment, such as the gut. For example, the community of organisms that are found in the gastrointestinal tract are called the gut microbiota, while these organisms and their DNA are called the gut microbiome.
3. Dysbiosis in the gut microbiota may influence gastrointestinal distress, both in healthy individuals and those previously diagnosed with a gastrointestinal disease or disorder.
Healthy individuals can experience dysbiosis when they undergo a disruption in their microbiome due to stepping away from their normal routine. For example, have you ever gone on an exciting vacation filled with lots more meals dined out and perhaps more alcoholic beverages consumed than you normally would? Ever gone to a less-developed country and gotten sick after drinking their water that may have had different microorganisms in it than you’re used to? Although you might not commonly experience gut issues, the introduction of a different set of bacteria than your microbiome is typically used to may disrupt your usual balance (i.e., cause dysbiosis) which may trigger symptoms such as a weakened immune system, abdominal discomfort, or irregular bowel habits. And dysbiosis occurring in individuals who have been diagnosed with inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), or small intestinal bacterial overgrowth (SIBO) may be exacerbated because in all three of these conditions, the GI tract is already compromised.
In individuals with IBS, food gets malabsorbed and may attract water into the intestinal lumen or create gas and pressure by way of bacterial fermentation of these malabsorbed food molecules, causing heightened discomfort in an individual with a particularly sensitive GI tract. The short-chain carbohydrates that are malabsorbed (high FODMAP foods), for example, may provide the gut bacteria with a fermentable food source which can create bloating and abdominal distention as a result of the gas byproducts of fermentation (imagine a balloon expanding inside your intestines).
In IBD, people have inflammation in their gastrointestinal tract, and dysbiosis can either trigger an inflammatory flare or it can induce symptoms of IBS as explained above.
In cases of SIBO where excessive amounts of bacteria are found in the small intestine, dysbiosis could induce a recurrence of this overgrowth of bacteria in the small intestines and cause discomfort, prompting the need for treatment to reduce the bacterial overgrowth and potentially negatively affecting health in other ways.
For those that do not have IBS, incorporating prebiotics into your diet can help mitigate symptoms of dysbiosis because they are generally high in fiber which can increase the number of beneficial organisms in the colon and stimulate production of short-chain fatty acids such as butyrate and propionate. These SCFAs are released to blood circulation and promote not only optimal GI health but overall wellbeing as they are distributed to other tissues and organs of the body. However, for those with gastrointestinal disorders, it is important to choose prebiotic foods that are low in FODMAPs while working closely with a GI dietitian to determine which foods can help to best manage symptoms. Not all types of fiber have the same effect on the gastrointestinal tract. Soluble fiber passes through the gastrointestinal tract binding to water and is metabolized to hydrogen, methane, carbon dioxide, and SCFAs.² Also, certain types of fiber like FOS can cause symptoms with low doses (10 grams or less) while other fibers, such as poly-dextrose and resistant starch can be consumed at doses up to 50 grams without symptoms. ²
4. A poor diet may not be the only factor influencing dysbiosis.
Many factors can influence an imbalanced gut microbiota. Potential factors include poor diet as well as stress, lack of sleep, lack of physical activity, smoking, and the use of certain medications such as proton pump inhibitors (i.e. prilosec), nonsteroidal anti-inflammatory drugs (or NSAIDs, such as aspirin), and antibiotics to name just a few. Diet is one of the main influencers of dysbiosis, though, which is why it is important to eat a diverse range of foods that contain probiotics, prebiotics, whole-grains, and polyphenols. Probiotics are live microorganisms that can reside in the gut and provide health benefits on the host. Examples of probiotic foods that you can incorporate into your diet include yogurt, kefir, sauerkraut, and kimchi. Prebiotics are nondigestible food ingredients that benefit the host by stimulating the growth of bacteria in the colon. Food sources of prebiotics (also mentioned above) by way of dietary fiber include a variety of fruits and vegetables (ideally, low FODMAP options in those with IBS), nuts, seeds, and legumes (ideally canned or in low FODMAP portion sizes for those with IBS). nuts, beans, and potatoes also contain dietary insoluble fiber which is important for healthy bowel function. Polyphenols are are contained in certain plant-based foods such as olive oil, green tea, and cacao. These antioxidants can impact gene expression, combat cell damage, reduce inflammation, and may improve digestive issues by way of these beneficial mechanisms.
5. Don’t overload your body with prebiotics and probiotics if you’re having gut issues.
Prebiotics and probiotics are both extremely important for overall gut health; however, for those experiencing gut issues, certain pre- and probiotics (both from food and supplemental forms) may increase symptoms. Some short-chain carbohydrates known as FODMAPs, or fermentable oligo-, di-, and monosaccharides and polyols, that are malabsorbed in the small intestine and feed bacteria. Therefore, for gut issues such as SIBO and IBS, the Low-FODMAP Diet™ is recommended to both provide relief of GI symptoms by removing the GI symptom-causing culprits and to then help identify which foods are potentially triggering the GI symptoms in the individual, specifically. This diet is not meant to be followed long term and consists of a 2- to 6-week elimination phase followed by a re-introduction phase. Many foods that are high in FODMAPs are also high in fiber and prebiotics, which may be confusing as these are typically thought to be healthy foods (and they are!). A few high-fiber foods that are low in FODMAPs include oatmeal, pumpkin seeds, kiwi, chia seeds, pecans, and walnuts. A GI dietitian or registered dietitian versed in administering the Low FODMAP Diet™ can help you to incorporate these and other high-fiber, low FODMAP foods into your daily diet to ensure that adequate fiber is still consumed while you attempt to relieve your GI symptoms. If you’re experiencing gut issues, consuming a probiotic supplement may not be the best option as it may exacerbate symptoms by way of continuing to introduce high FODMAP foods, or highly fermentable foods, into your gut. It’s important to consult with a GI dietician or gastroenterologist on which supplements may be best for your symptoms, if any, as different probiotics have strain-specific bacteria that have different functions for different conditions. Just because a probiotic has the highest number of CFUs or includes a variety of diverse strains doesn’t mean it will help with gut imbalance. It may be quite the contrary, in fact.
6. It’s not as black and white as “good bacteria” replaces “bad bacteria”
A majority of mainstream talk about gut bacteria suggests that in order to live a disease-free life, we need our gut to contain large amounts of “good bacteria” with little to no “bad bacteria”. The concept of bacteria itself is tricky because even the word ‘bacteria’ connotes a ‘dirty’ environment or potential for infection or disease. The reality is that most bacteria are harmless if not beneficial to our health and to the environment, with few species of bacteria being harmful. To put this into perspective, the number of bacterial species known to cause harm or infectious disease in humans is estimated to be fewer than one hundred, whereas several thousands of bacterial species exist in the human digestive tract alone. So, we are naturally operating from a state of having favorable good-to-bad bacteria ratios, if that is the objective.
But recent trends are promoting the use of probiotic supplements and consumption of fermented foods and foods containing live active cultures with the theory that by inoculating more and more of the proposed ‘good bacteria’ into our digestive systems, we will drive out any existing ‘bad bacteria’ or prevent them from infecting our bodies in the first place. While this is a theory that may be worth entertaining, the existing evidence to support or negate the benefits of probiotic use or consumption of fermented foods in this regard is conflicting and remains inconclusive. This begs the question: should we be as quick to flood our systems with ‘good’ bacteria hoping it will replace the ‘bad bacteria’?
7. The gut is often referred to as the “second brain” and for good reason.
This nickname for the gut being the “second brain” may be of no surprise as the microbes in our gut communicate to our brain in something known as the gut-brain axis, which is a bi-directional communication pathway. Our gut microbiota is responsible for the development of the enteric and central nervous systems.1 Many of our neurochemicals reside in our gut and transmit information that assists in functions such as moving food through the GI tract, secreting specific enzymes responsible for digestion, communicating sensations or cues of hunger and satiation, and protecting the immune system1 . This is why stress management is so important for maintaining a healthy gut. Modalities for managing stress, anxiety, and depression can come in all forms, such as through meditation, exercise, cognitive behavioral or talk therapy, abdominal massage, biofeedback therapy, diaphragmatic breathing, and more. Find what works for you and add that practice into your ritual -whether it be a daily, weekly, or monthly practice, so long as it’s consistently applied - as part of your treatment plan and healing process.
FINAL THOUGHTS: What does this all mean and how can you apply this to your daily life?
The optimal range of fiber in an individual to consume is approximately 28-50 grams of fiber per day. If this amount of daily fiber intake causes GI distress or discomfort, consult your doctor or dietitian.
If you are experiencing uncontrolled bowel habits and/or bowel movements that wake you in the middle of the night, blood in your stool, significant abdominal pain, or other gastrointestinal symptoms and/or have a family medical history of Celiac disease, inflammatory bowel disease (Crohn’s disease or colitis), or gastric or colorectal cancer, it’s important to consult with a gastroenterologist or GI dietitian for proper diagnostic screening.
The Low FODMAP Diet™ is a great tool to reboot your gut and figure out what fermentable short-chain carbohydrates may affect your own digestive health. For more information on the Low FODMAP Diet™, visit www.MonashFODMAP.com or contact us!
When picking a probiotic supplement, look for red flags on the packaging such as mentioning the name of the species but not the strain. You can always ask the supplement manufacturer yourself and if they try to keep that information a “secret” , which may mean that there lacks research to support their product including effective species of probiotic strains.
Since the gut is also known as the second brain, it is important to incorporate stress reduction practices to your everyday life to help treat gut issues.
References:
Moise AMR. The Gut Microbiome: Exploring the Connection between Microbes, Diet, and Health. 1st ed. Santa Barbara, CA: Greenwood; 2017.
Pandey KR, Naik SR, Vakil BV. Probiotics, prebiotics and synbiotics- a review. Journal of Food Science and Technology. 2015;52(12):7577-7587. doi:10.1007/s13197-015-1921-1
Scarlata K. Intersection of IBS, SIBO & the Low FODMAP Diet. For A Digestive Peace of Mind-Kate Scarlata RDN. https://blog.katescarlata.com/2017/08/10/ibs-sibo-low-fodmap/. Published August 15, 2017.
So D. The Gut Microbiota. Monash Fodmap. http://www.monashfodmap.com/blog/gut-microbiota/. Published February 12, 2018.
King S, Tancredi D, Lenoir-Wijnkoop I, et al. Does probiotic consumption reduce antibiotic utilization for common acute infections? A systematic review and meta-analysis. European Journal of Public Health. 2018;29(3):494-499. doi:10.1093/eurpub/cky185