FAQ: Top Questions and Answers from Our Second Reddit AMA

15 min read



Questions and answers edited for length and clarity.


Our second Reddit AMA was a hit! This time Luca, Ryszard, and Dr. Martin answered questions from the Reddit community on the gut microbiome, artificial intelligence for medicine, bioinformatics, and more. Check out some of the most popular questions we received and responded to below. To all the Redditors who sent in questions, thank you!


Table of Contents


1. What’s the relationship between the microbiome and autoimmune disorders, and what role does

diet play?

2. Is it true that the germs inside our guts control our mood?

3. What are your thoughts on Fecal Microbiota Transplantation (FMT)?

4. What’s the relationship between autism/ADHD and gut health?

5. What are some healthy and unhealthy habits for the microbiome?

6. Any idea if marijuana smoking via flower or oil cartridges is harmful to the microbiome?

7. What role does the microbiome play in ferritin absorption and what can be done for someone

with anemia?

8. What can I do to advocate for myself when my medication isn’t working and I’m experiencing

symptoms of nutrient malabsorption?

9. Could my long-term, restrictive, low-FODMAP diet be breeding a subtype of bacteria that is

making me gassier?

10. Any foods or eating habits that do have measurable positive effects on the gut biome beyond

cutting down on processed food and sugar?

11. Will probiotic drinks help me if I have one every day?


Interested in viewing the full AMA? Check it out here. To see our first AMA, click here.


Q1: Is there a strong link between the microbiome and autoimmune disorders such as psoriasis? Is it possible to reduce flare ups with a diet change? Or conversely are there any microorganisms suspected of making autoimmune issues worse? (u/Ambivertigo)

A: There is definitely a link between microbiome and autoimmune disorders. Almost every autoimmune disorder has been linked with changes in the gut microbiome as well as its corresponding microbiome (ex: skin microbiome of individuals with psoriasis is distinct from healthy individuals). What is surprising and interesting is that something like the gut microbiome, which is so far from the skin, is linked to psoriasis.


Our current understanding of this is that the gut microbiome has some form of two-way relationship with the immune system, which in turn is the direct driver of autoimmune illness. Therefore, the gut microbiome is indirectly connected to these illnesses via the immune system.

In terms of diet, there is definitely a possibility to reduce flare-ups with a change in diet. Diet has a large impact on the microbiome and diets high in processed foods and sugar such as the Western diet have been directly linked to increases in psoriasis severity, since such a diet may promote the growth of non-beneficial bacteria that actually trigger the immune system.

The unfortunate part is that this is highly personalized. A diet that might help with psoriasis in one person might not help someone else, but there is consensus on common triggers such as stress, processed sugar, alcohol, and dairy should first be eliminated from the diet prior to larger diet changes.

Q2: Is it true that germs inside our guts control our mood? (u/ripthatsong)

A: There's a saying that the gut is your second brain, and I think that's a fitting way to get into the topic of the link between the brain and gut. The brain-gut axis is a two-way highway of communication between these regions of our bodies. This relationship is bidirectional, meaning the activity and functioning of one can affect the other.

In short, all the germs in our guts, what we call gut microbiota, have a lot to do with our mood, due to this brain-gut axis. For example, mood-related disorders such as anxiety and depression have been linked to abnormal gut microbiome activity, such as stress responses and inflammation occurring due to compounds produced by gut microbiota (for example, short-chain fatty acids). The risk of such mood disorders is also increased in people with gut issues, such as inflammatory bowel disease and irritable bowel syndrome, due to changes in healthy gut bacteria and the stress of coping with chronic, stigmatized gut health issues, among numerous other factors.

Not only can gut microbiota trigger stress responses that affect mood, but being stressed or anxious can also trigger gastrointestinal symptoms. There's a good reason why many people with gut issues are encouraged to try meditation; healing and centering the mind and body can improve symptoms! This helps to explain why we consider the relationship between the brain and the gut bidirectional.

Q3: What are your thoughts on Fecal Microbiota Transplant (FMT)? (u/king-schultz)

A: Great question, FMT has a lot of potential as a treatment for microbiota mediated diseases but the research is still in its infancy. The only approved indication for FMT is currently relapsing C. difficile infection. Use of FMT for other illnesses has only been in clinical trials.

Some trials using FMT to treat illnesses such as ulcerative colitis or Crohn's disease have succeeded while others have failed. There are many factors that have to be considered as to why this happens, such as the origin of the donor stool, the dosage of the stool, the frequency of the dosage, the nature of the recipient's illness, the recipient's medication protocol and many many more, all of which can impact trial results. For instance, FMT will be received differently by a patient who had taken antibiotics prior to the FMT. Therefore, there is no clear answer whether FMT as a standalone treatment can help chronic illness.

A study which gave FMT to ulcerative colitis patients saw a large portion of them relapse in the following months, leading researchers to question whether this is the right path forward.

The microbiome is only 1 of 3 components that mediate chronic immune-related illnesses. The other 2, the immune system as well as lifestyle (sleep, stress, diet, etc..) are also important contributors. A standalone FMT given to a patient with uncontrolled immune-related illness will have a much lower chance of success than to a patient taking medication with their illness somewhat under control.

Lastly and most importantly, the personalization of FMT is an important and understudied aspect of the technique. Similar to how a heart transplant should match the recipient's genetic profile, an FMT with bacteria that don't match what the recipient needs will have a lower chance of success. It would be beneficial, therefore, to perform a gut microbiome analysis of both donor and recipient for compatibility evaluation prior to transplant. However, the characteristics of what makes a donor and recipient compatible haven't been well outlined yet and again require more research.

Q4: Is there any clear connection between autism and/or ADHD and gut health? Will improving gut health lead to a better management of autism/ADHD symptoms? (u/Just-Olive-2599)

A: Neurological conditions such as autism and ADHD are very complicated topics, but there is evidence linking these with the gut microbiome. Indeed, those with autism or ADHD did have differences in their microbiomes when compared to healthy individuals. Here’s some preliminary evidence in mice: healthy mice, when receiving a fecal transplant from ADHD mice, develop ADHD symptoms and brain changes. The anti-diabetic drug metformin has been shown to have significant impacts on the human microbiome and also to reduce autistic symptoms in mice.

While the field connecting microbiome to neurological disorders is much less studied than microbiome and gastrointestinal illness, research is expanding in this direction. Recent studies have shown that diet changes have helped to modify the microbiome as well as improve symptoms in ADHD.

Q5: What habits improve gut microbiome and which ones are damaging? (u/Critical-Survey-2202)

A: While this list is not exhaustive, here are a few things that have been associated with improving or harming your gut microbiome, and the research supporting them.

Improvement of the microbiome:

An important habit that affects the microbiome is the food you consume. Your diet not only provides you energy and nutrients, but also feeds the bacteria living throughout your gastrointestinal tract. In order to improve and maintain your gut microbiome, it is important to provide the nutrients that healthy bacteria need to survive. One dietary pattern that has been associated with an improved gut microbiome is the Mediterranean diet, which is rich in fruits, vegetables, nuts, legumes, olive oil, and meats such as fish and poultry and limits consumption of red meats and refined grains.

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359750/

Another way to improve your gut microbiome health is by adding fermented foods, such as kombucha, kefir, yogurt, and kimchi, to your diet. Fermented foods contain live, beneficial bacteria that can lead to improvements in your gut microbiome, and a lot of compounds formed through the process of fermentation that are beneficial to you and the bacteria already in your gut.

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306734/

In addition, other lifestyle aspects have been associated with features of a healthy gut microbiome. Specifically, some studies have identified links between good sleep quality and exercise with positive aspects of the gut microbiome.

- https://pubmed.ncbi.nlm.nih.gov/32795890/

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357536/

Disruption of the microbiome:

Just like your diet can improve your gut microbiome, it can also disrupt the bacteria in your gut and allow for growth of harmful bacteria. Diets high in processed foods, sugars, and fats and with low intake of fibre and fruits and vegetables have been linked to disruption of the gut microbiome. In fact, these diets are thought to play a role in the increasing incidence of the chronic inflammatory bowel disease (IBD).

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566788/

Cigarette smoking also harms the gut microbiome and has been identified as a risk factor for chronic diseases such as IBD.

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245763/

Q6: Any idea if marijuana smoking via flower or oil cartridges is harmful to the microbiome? (u/Koda_20)

A: Currently there is not a large number of studies that have looked into the association of cannabis and the gut microbiome.

One study looked at the gut microbiome of chronic cannabis users and found an altered ratio of bacteria compared to non-smokers, but this was likely due to the different diet of those who chronically smoked (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790619/).

Two other studies demonstrated some beneficial effects on the gut microbiome of CBD or THC treatment in mouse models of experimental autoimmune encephalomyelitis (https://pubmed.ncbi.nlm.nih.gov/31356922/) and obesity (https://pubmed.ncbi.nlm.nih.gov/26633823/).

More research into these connections is definitely required before we can draw any conclusions about the effect cannabis has on the gut microbiome.

Q7: What role does the microbiome play in ferritin absorption? Is there anything the average anemic can do to make it better? (u/Drakorre)

A: In the intestinal health context, anemia is commonly seen in patients suffering from gastrointestinal conditions such as Celiac disease, IBS and IBD. This is partially due to malnutrition as well as intestinal inflammation, which can impair iron absorption from the diet. This is why for many gastrointestinal patients, oral iron supplements simply don't work (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959949/).

Ferritin is the protein that helps our body store iron. Quite a few studies have shown that the microbiome is involved in iron uptake from the intestine. In addition, it is not only the human body and the human cells that require iron for function, but iron is critical to many gut microbiome bacteria as well.

A recent study in mice has actually shown that bacteria in the gut can actually compete with the body for iron by reducing the body's own capability to absorb iron. A lay version of this article is also available for interested readers.

This research is still quite new and will take time to be brought into clinical use, however, a microbiome analysis could indicate whether there are elevated levels of bacteria that could slow your body's absorption of iron.

As a side note, It is important to find and address the cause of your anemia with a licensed medical practitioner prior to investigating outside the realm of current medical practice.

Q8: I'm visiting my GI soon because my current medicine isn't bringing me back up to 100% (dicyclomine), and I keep having symptoms of nutrient malabsorption. What can I ask to advocate for myself? Any tests? I don't want to be stuffed with antibiotics, but it seems that's always what docs want to resort to. (u/RadioactiveTaco)

A: An important aspect of being a patient is finding ways to be empowered and get the answers you need, so finding ways to advocate for yourself is definitely important. Nutrient malabsorption can be a very serious issue, so I would encourage you to ask for the relevant tests to check on your nutrition (blood tests, stool tests, etc.) and given the data you receive, ask if it would be in your best interest to get a registered dietitian, or if there is something you can do to fix the issue right now. If you're having gut issues and have been using dicyclomine to try to solve the issue, it doesn't seem that antibiotics would be the next best course of treatment. You have a point saying that doctors tend to resort to this, but if you go to your appointment armed with knowledge about antibiotic usage and how it can negatively impact healthy levels and populations of gut bacteria and trigger gut symptoms, you can start a larger discussion with your GI about options that work best for you, your goals, and your lifestyle. Writing down a list of your specific questions and your goals for the appointment can help you and your GI set expectations so you get the most out of your visit.

If you leave the appointment feeling dissatisfied with how your situation was handled or you're motivated to dive deeper and learn about your gut health further, that's when an at-home gut microbiome test might empower you and help you find the answers you're looking for! I'm happy you appreciate what we're doing, and hope I've provided some good tips! Good luck with your GI appointment!

On a final note, here's some extra info on dicyclomine and nutrient malabsorption, which are commonly related to IBS: https://www.uptodate.com/contents/irritable-bowel-syndrome-beyond-the-basics/print.

Q9: As someone with IBS, I have been following a strict low-FODMAP diet for years now. Somehow along the way my farts stopped smelling. Like I'm at the point where my farts never smell (even if I go wild with eating). Could my abusive eating restrictions breed out a subtype of bacteria in my intestines? As far as I know, gas can be either hydrogen or methane. Could I be breeding out the methane producing bacteria? (u/dudespock)

A: Gas is usually a byproduct of the fermentation occurring when the bacteria in your gut digest the foods you are giving them. Indeed, as you mentioned, some of the products of this fermentation are carbon dioxide, hydrogen, methane as well as sulfur. Sulfur is known to create pungent odors which is part of the reason why our farts smell. A great review on this can be found here: https://link.springer.com/content/pdf/10.1007/s11894-013-0356-y.pdf.

To answer your question, it is entirely possible that your diet has changed your microbial composition in such a manner that there might be less sulfur producers. However, without performing a gut microbiome analysis it would be difficult to say. In addition, it is not really possible to say whether this is a bad thing or a good thing, but some research has linked sulfur-producing bacteria such as Desulfovibrio with illnesses such as IBS and IBD: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508456/. Therefore, excessive levels of such a bacteria may not be beneficial to one's health.

I'll leave you with one last interesting read that discusses the impact of diet on the composition of your gases: https://pubmed.ncbi.nlm.nih.gov/31520080/.

Q10: I heard a lot about how probiotic yogurts or even pills don't tend to survive digestion (which makes sense for not getting horribly ill every time we eat something with less beneficial bacteria on it) and don't have much impact on gut bacteria if any in practice. Are there, to your knowledge, any foods or eating habits that do have measurable positive effects on the gut biome beyond cutting down on processed food and sugar? (u/APiousCultist)

A: A recent study looked more closely at how fermented foods, such as yogurt (which contain probiotic bacteria), alter the gut microbiome. In this study, they showed that fermented foods increased the diversity of bacteria found in the gut. Interestingly, few of these bacteria were actually from the fermented foods in the people’s diets. The study suggested it was because of the other components of the fermented foods, such as compounds produced during fermentation, that provide a more hospitable environment to new bacteria.

- https://pubmed.ncbi.nlm.nih.gov/34256014/

While it is hard to suggest a specific food that is guaranteed to improve your gut microbiome, some broader dietary patterns have been associated with healthy gut microbiomes. One commonly associated diet is the Mediterranean diet, which is rich in fruits, vegetables, nuts, legumes, olive oil, and meats such as fish and poultry and limits consumption of red meats and refined grains.

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359750/

Q11: Will probiotic drinks help me if I drink one every day? (u/superjeegs)

A: When it comes to probiotic drinks such as kombucha, the truth is there is very little medical and scientific evidence to support their benefit. As is the case for the majority of probiotics out there, very few of these 'good' bacteria are able to survive the trip from our mouths, to our stomachs, and then to our intestines. We've seen this time and time again with our clients who are actively taking probiotics, but do not see them present after taking our microbiome test (which tests for all bacteria found in stool). Ultimately, it's an area of research that still requires time to develop, but for now, I would remain skeptical of many of the probiotics out there, whether they be in supplement or beverage form.

The best way to improve your microbiome is through your diet. Our bacteria eat what we eat and even help us digest fiber our bodies themselves are not able to process.

So if you're drinking kombucha with the intention of having a medical benefit, the research is not there yet, but if you're drinking for the taste, go for it. I know I do. My two cents would be to watch for added sugars though. Some flavors have massive amounts :)

I'll drop this link here from the Mayo clinic that gives some background on the current evidence behind probiotic drinks. https://www.mayoclinic.org/healthy-lifestyle/consumer-health/expert-answers/kombucha-tea/faq-20058126

Additionally, here is another link from the Cleveland clinic!

https://health.clevelandclinic.org/what-are-kombuchas-health-benefits-and-how-much-can-you-safely-drink/


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Left to Right: Dr. Martin, Luca, and Ryszard.