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If you’re like most folks, you probably didn’t start hearing about your “microbiome”  or “gut health” until recently. We are starting to realize the far-reaching effects of the health of our digestive system, or “gut,” and a big part of that are the microbes that live there.

What is the microbiota?

Your microbiota is a completely unique-to-you blend of bacteria, fungi, protozoa, and viruses. 90-95% of it is found in your digestive tract, primarily in your large intestine. Microorganisms are also found on the skin and in the mouth, nose, lungs, urinary tract, and the vagina.

As soon as we enter the world, our microbiota begins to develop. It is immediately influenced by the way we are born, vaginally or by C-section. After that it is continued to be built by our food and even the people we live with.


What is the difference between the microbiome and the microbiota?

The term microbiome refers to the genes within the microbes that determine what they do and how they interact with our cells. Microbiota refers to the community of microbial cells.

Due to the fact that more folks are more familiar with the term microbiome than microbiota, we will use the abbreviation GM to refer to the gut microbiome or gut microbiota for the rest of this article.


How does the gut microbiome affect our health?

Our GM is very beneficial to us. Some of the ways it improves our health include…

  • The production of many byproducts that are essential to our body’s wellbeing, such as short chain fatty acids (SCFAs) and certain vitamins
  • Helping us glean energy from foods by digesting them for us
  • Improving our gut motility (the movement of food through the intestines)
  • Improving our gut function
  • Reinforcing the gut barrier (lining of the intestines)
  • Protecting against pathogens (bad microbes)

While some microbes are health-promoting, others may cause undesirable symptoms or even make us more susceptible to diseases. Having enough of the “good guys” in a diverse community makes your GM less hospitable for the “bad guys.”

The microbes that we WANT to have in our GM are commonly referred to as “probiotics.”

Research is emerging that some health conditions are linked to an imbalance or dysbiosis of our GM. The jury is still out on whether conditions such as autoimmune diseases, diabetes, inflammatory bowel disease, and metabolic syndromes cause or are caused by this imbalance. It’s a chicken or the egg situation. We do know that our GM talks to our immune system, about 70% of which is found in the gut!

Your GM might be disturbed by…

  • Antibiotics (which kill good and bad bacteria alike)
  • Proton pump inhibitors (stomach acid reducers)
  • Gut infections such as food poisoning or the “stomach flu”
  • Environmental stressors (pollutants and toxins)
  • Mental stress
  • GI surgery and more

Often times some of these things can’t be avoided or are necessary to prevent worse things from happening (I’m all for taking antibiotics appropriately!). Taking probiotics or eating fermented foods with live cultures can help rebalance it.

When your GM is over-colonized in the wrong place, it can cause issues as well. For instance, when too many microbes start growing in your small intestine it is called Small Intestinal Bacterial Overgrowth (SIBO). This can cause significant pain and bloating, among other symptoms.


How does what I eat affect my gut microbiota?

Our GM is sensitive to the food we eat and the environmental stressors in our life. The bacteria that thrive in your gut will likely be the ones that like the food you’re currently eating. One of the reasons that it’s a good idea to eat a variety of plants is that the bacteria that likes to eat fiber produce a lot of byproducts that are very beneficial to us.

The fiber that the bacteria metabolizes is called “prebiotics.”

We can also consume probiotics through our food. Fermented foods are made through the introduction of microorganisms and, if not heat treated, will still contain live microorganisms when we eat them.

Some examples of fermented foods that contain live probiotics include yogurt, kombucha, non-shelf stable pickles and sauerkraut, kimchi, miso, and raw cheeses.

While foods like sourdough bread, chocolate, and most cheeses are made through fermentation, the end product does not contain live microorganisms. But this does not mean they are without benefit. The process of the microorganisms fermenting the food can make it easier for us to digest as well as produce beneficial bioactive compounds, just like the microbes do in our intestines.

If you are experiencing digestive issues, it is important to consider your GM as a piece of the puzzle. However, it’s not a good idea to start taking a general probiotic blindly.


Should I take a probiotic all the time?

Unfortunately, many people taking a probiotic supplement are likely wasting their money either because it isn’t necessary or they are not taking the right strains for their issues.

I usually only recommend a probiotic when my clients have specific conditions that could benefit from probiotic treatment. And even then, I try to recommend a particular strain or group of strains that has evidence to show that it benefits their particular condition. For example, there are specific strains that have been shown to greatly reduce the risk of diarrhea associated with taking antibiotics.

If you are healthy and simply want to maintain a healthy GM, taking a probiotic supplement is not necessary! The biggest and best effect you can have on your GM is through consuming a variety of foods (especially foods from plants), moving your body, tending to stress, and protecting your sleep.


How do I choose a probiotic? 

Not all probiotics are created equal. Picking out a probiotic is more nuanced than just making sure it has enough CFUs, or Colony Forming Units. In fact, more CFUs is not always better. It’s best to choose the effective dose, which is the amount that has been well researched and tested.

In addition, for the best results and to avoid potential worsening of symptoms, it’s important to tailor fit your probiotic to your digestive condition.

Think of taking a probiotic like taking a medication. You need to select the right one. Just like you wouldn’t want to take a blood pressure medication if what you really wanted was something to alleviate your allergies, you don’t want to take a probiotic that helps with constipation if what you really wanted was relief from diarrhea.

Another reason I usually don’t recommend taking a generic multi-strain probiotic is that many probiotics now include prebiotics. However this is notorious for causing digestive problems for folks who have a hard time with this fermentable carbohydrate. In fact, it is avoided in the low FODMAP diet, an evidence-based elimination diet for folks with IBS.

Prebiotics are not always named clearly on the label, but you may see it listed as galactooligosaccharides (GOS), fructooligosaccharides (FOS), oligofructose (OF), chicory, or inulin. It is often added to high fiber bars and cereals as well.  If you have digestive discomfort after consuming a supplement or food that contains one of these as an added ingredient, that just might be the culprit.


Here are some steps you can follow to choose the right probiotic:


1. Determine if there is a probiotic that is effective in treating your condition or alleviating your symptoms. One of the resources I like to consult is the Clinical Guide to Probiotic Products Available in the USA. It is also available as an app.

2. Note the specific probiotic that is beneficial. This will consist of two words, the genus and species, and a combination of letters and/or numbers to specify the strain (for example, Lactobacillus acidophilus CL1285).

3. Note the effective dose or how many CFUs have been shown to work.

4. Note how long you need to take it (most are 30 days).

5. Find a reliable manufacturer that makes a supplement containing the strain you need. I offer the ability to purchase probiotics through my Fullscript dispensary. All of the probiotics in my dispensary are made by reliable manufacturers and listed as evidence-based in the Clinical Guide mentioned above. You can view these here by creating an account and then selecting Amy Lorraine Nutrition’s Favorites. Purchasing through my dispensary gives you access to 15% off. Please note that I will earn a commission if you purchase a supplement through me.

6. Last but not least, make sure you know whether your probiotic needs to be refrigerated and whether you need to consume it with food. Many people wonder whether a sign of a good supplement is that it requires refrigeration or if it needs to be enteric coated to survive the stomach. These are not necessarily indications of a high quality probiotic. Many high quality probiotic supplements are shelf stable and it is not necessary to choose one that is enteric coated. 

The goal of taking a probiotic is not necessarily that the strains on the label will colonize in your gut, as this actually does not happen frequently. The way probiotic supplements work is by interacting with the microbes present in our gut as well as our immune system and the very cells of our digestive tract. So once you’ve taken it for the recommended amount of time and your symptoms improve, you can usually stop taking the probiotic.


Should I take a probiotic?

If you are able to eat a variety of foods and are not struggling with any health conditions, you likely do not need to take a probiotic supplement.

However, if you are dealing with certain digestive symptoms or need to follow a restricted diet for medical reasons, I recommend you consult with your dietitian about whether a specific probiotic would be beneficial for you.

There are certain situations where it is not usually recommended to take a probiotic, such as if you are immunocompromised or have short bowel syndrome. In these cases it is especially important to check with your doctor and dietitian first.


Will taking a probiotic help my immune system to prevent COVID-19?

While we know that a lot of the immune system is connected to the gut and that certain probiotic strains can help protect against respiratory tract infections, there is no evidence that taking a probiotic will prevent COVID.

If you’re interested in taking a probiotic to try to strengthen your immune defense against viral infections, the Clinical Guide to Probiotic Products Available in the USA lists a combination of L. plantarum HEAL9 and L. paracasei 8700:2 as having Grade I evidence (the highest level) to support taking it to alleviate the symptoms of or defend the body against community acquired common infectious disease. UltraFlora Immune Booster by Metagenics is the supplement they list. 

You can view UltraFlora Immune Booster in my dispensaryDisclosure: Purchasing it through me will result in me earning a commission. 

Other questions?

The International Scientific Association for Probiotics and Prebiotics has some fantastic infographics you can check out here: https://isappscience.org/for-consumers/infographics/

Medical Disclaimer

The contents of this blog are for informational and educational purposes only and not for the purpose of medical advice. The contents of this blog are not to be used as a substitute for medical advice. While I take efforts to ensure the information on my website is up-to-date, I cannot guarantee that the information on my website reflects the most recent research. As always, consult your doctor and dietitian for personalized medical advice.