We're a group of microbiome researchers here to answer your questions on the gut microbiome and digestive health (IBD and IBS). Ask us anything!

What habits improve gut micro biome and which ones are damaging?

Hi /u/Critical-Survey-2202,

Thanks for the great question! While this list is not exhaustive, here are a few things that have been associated with improving or harming your gut microbiome.

Improvement of 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 healthy bacteria need to survive.One dietary pattern that has been associated with improved gut microbiomes 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, kimchi, to your diet. Fermented foods contain live, beneficial bacteria that can lead to improvements in your gut microbiome. In addition, contain 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 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/

Cheers,RM

You stated that certain fermented foods contain healthy bacteria. I eat sauerkraut from time to time. Should I avoid heating the sauerkraut, to avoid killing the beneficial bacteria? Same with kimchee - if it is in a stew, does this mean the beneficial bacteria is dead and there is no benefit from a bacteria standpoint?

While cooking the fermented foods is likely killing off the beneficial bacteria, there are still a variety of beneficial compounds in these foods that are produced during the fermentation process.

RM

Any idea if marijuana smoking via flower or oil cartridges is harmful here as well?

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.

RM

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?

Hey /u/Ambivertigo!

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 flareups 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. This is believed to be because of the fact that such a diet may promote the growth of non-beneficial bacteria that actually trigger the immune system.

As I mentioned in a comment about Ulcerative colitis above, the unfortunate part of this is that it is highly personalized. A diet that might help with psoriasis in one person might not help someone else. What there is consensus on though is that common triggers such as stress, processed sugar, alcohol, and dairy should be first eliminated from the diet prior to larger diet changes.

I am actually working with a team of doctors, data scientists as well as autoimmune patients on an app that allows patients to track their symptoms and lifestyle in order to quickly discover lifestyle and dietary triggers and help them manage their illness. This of course is not a substitute for medication in treating things such as psoriasis, but can be highly beneficial when used in combination.

Cheers, RK

Is there a way to probe the microbiome without testing stool? Are there any stomach scanners for that, like how we have brain scanners?

Not currently ! But perhaps in the future someone will find a way. For now, stool tests are the way to go.

Cheers, RK

Is it true that germs inside our guts control our mood?

Hi u/ripthatsong, thanks for the question. 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. There's tons more we could discuss on the topic of mental health, mood, the gut microbiota, and gut disorders, but I hope this provided a brief synthesis of some evidence to answer your question! -LC

The gut is also physically connected to the brain by the Vagus Nerve, which can be bound by bacterial produced molecules like the short chain fatty acids, which then send impulses to the brain to modulate our brain, which is also implicated in depression, anxiety etc!

Absolutely! The vagus nerve has a major role in this, which is a very interesting and large discussion!

What are your thoughts on Fecal Microbiota Transplant (FMT)?

Hey /u/king-schultz!

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, for example: 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 example, 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.

As I mentioned in another post above, the microbiome is only 1 of 3 components that mediate chronic autoimmune 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 autoimmune illness will have a much lower chance of success than to a patient with 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.

Thanks for the great question again! RK

Hi. Thank you for doing this!

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?

Hey /u/Just-Olive-2599,

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.

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 at the same time has been shown 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.

Thanks,

RK

As a regular IBS haver I have been following strict 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 my stupid ass breed out the methane producing bacteria.

Ty xoxo.

Hi /u/dudespock ! Super interesting question.

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 or methane 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.

Ill 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/

Cheers! RK

Methane itself is odorless.

Corrected ! Thanks

Since the interaction of microbiome and IBS/GI-health has been well-documented and supported via clinical research, why is it so hard to get a doctor to even look or acknowledge that relationship? I (now realize that I) have had IBS for most of my life - but I’ve been through a myriad of doctors that can’t even acknowledge that microbiome may be an issue. I have a PhD in biology, and so I’m well-versed in how to find good studies/research.
However every time I bring up the notion that “maybe my microbiome is playing a role here”, every doctor dismisses it as pseudo-science or “voodoo science” (direct quote). One doctor acknowledged there may be a relationship - but that

“we won’t figure out how the microbiome influences GI health until after I’m (the GI MD) dead, so I’m not going to worry about it with your issues” (verbatim quote).

I can understand your frustration, especially since you know you can comb through the literature and find good studies to learn from. However, it's important to remember that often times, there is a gap between scientists/what the science is showing and doctors, especially ones that have been in the field for some time. Although this is not always the case, it's enough of a problem that patients aren't getting the support they need, based on the questions they're asking and the hopes they have for their health. This is especially a problem with IBS, since some doctors still don't really 'believe' in it and aren't working towards finding meaningful solutions for their patients, which can only make matters worse.

But not all GI docs refuse to discuss the microbiome, and based on your curiosity and repeated questioning about the role of the microbiome in what you're experiencing, it might be worth finding someone who will address your concerns with an open mind. I recognize that accessibility to adequate healthcare and/or the ability to pick your doctor is not a reality for everyone.

To self-advocate for yourself, I would encourage you to come armed with your knowledge and the research you've gone into in order to convey to your doctor(s) that you are serious about finding solutions and want this to be discussed further, or at least to receive a more thoughtful response than 'it's just voodoo medicine'. It's the doctor's job to help you, the patient, and answer your questions respectfully. Also be prepared to ask them follow-up questions to have them justify why they won't look into your microbiome health further, such as "can you explain why you...", "what have you learned/read about the microbiome to convince you that the science isn't there", etc. This could help you find a common ground or find a new approach to solving your health issues.

All in all, problems like these, with unsuccessful GI appointments or barriers to adequate healthcare or health information, I'd just like to mention that this is part of why we created Phyla. We want to help patients learn about their health in a personalized way, reshape the narrative of healthcare, and reduce the need lean on physicians to receive the care and attention that you require in order to feel your best.

Keep self-advocating! I hope you find the relief you deserve! -LC

I heard a lot about how probiotic yoghurts or even pills don't tend to survive digestion (which makes sense for not getting horribly ill everytime 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?

Hi /u/APiousCultist,

Thanks for the great question!

A recent study looked more closely 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/

Cheers,

RM

What role does the microbiome play in ferritin absorption? Is there anything the average anemic can do to make it better?

Hey /u/Drakorre!
Great question.

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 malnutrition as well as due to intestinal inflammation, which can impair iron absorption from the diet. This is why for many gastrointestinal patients, oral iron supplements simply dont work. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959949/).

Ferritin is actually 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 study30560-1) 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.

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.

Cheers! RK

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.

Thank you so much for doing this AMA, by the way!

Hi! I'm really pleased you've asked what you can do to advocate for yourself, because that is something I am very passionate about and an important aspect of being a patient is finding ways to be empowered and get the answers you need. 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 antibiotic 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! Happy to provide more information on this if you're curious. 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 .

-LC

would love to hear more about the at-home microbiome tests :)

Hi u/REIRN and u/flower_gnome! Sure! At-home microbiome tests are an emerging tool to help people monitor their gut health long-term, without the need for excessive utilization of healthcare resources, which are a common occurrence among chronic, relapsing diseases like inflammatory bowel disease. With such diseases, monitoring is incredibly important, yet many patients can't get the consistent, frequent support they need, which is why the ability to test the microbiome through a home-based stool test makes sense. By providing an option to put your health journey in your power through health tracking that can be done from the comfort of home, the goal is to help patients (and curious non-patients) learn more about their gut, leaving them feeling more empowered by the decisions they can make for their well-being.

The Phyla gut microbiome test sequences your gut bacteria through stool tests taken over the course of about two weeks in order to get the best picture of what's going on in your ever-changing microbiome. With this data, a detailed and informative but clear microbiome report is generated, where you can learn about how how your gut bacteria could be affecting your well-being (in terms of levels, diversity, and more). This comes with personalized recommendations on how to improve the composition and balance of your gut bacteria, which are known contributors to a host of symptoms. This is paired with information in the Phyla digital health app, where you can monitor your sleep, exercise, diet, symptoms, medications, etc. daily :) -LC

I was diagnosed with colitis in April, followed all my GI Doctor's instructions and prescriptions and I'm still pooping up to 22 times a day! What the hell is wrong with me?

Hey /u/bizguyforfun!

Sorry to hear about your diagnosis,. For the sake of this post I will assume you have Ulcerative colitis and not another form of colitis. IBD-type illnesses such as Crohn's disease or Ulcerative colitis (UC) are complicated to treat as they are highly personalized and multifactorial. Increased stool frequency such as 22 times/day is one of the many difficult symptoms experienced by UC patients.

In general, there are 3 components to an illness like UC. The immune system, the microbiome and the external environment (lifestyle, stress, diet, etc.). Most but not all medications given by a GI doctor will impact the first component, which is the immune system.

The unfortunate truth is that it is not uncommon that a UC patient will have to trial multiple medications before they find one that helps them with their symptoms. This can be a very difficult period, but many patients eventually experience a reduction in symptoms once the right medication is applied.

In the meantime, you can try to address the other contributors to the illness. Diet and lifestyle can play a large component in UC. Indeed, many patients find relief from symptoms by applying dietary changes. Unfortunately, yet again, this is highly personalized. One diet may work for someone else with UC but it might not necessarily work for you.

To help discover what could be a potential trigger for the UC, many patients benefit from keeping a log of their diet and lifestyle to determine which factors actually contribute to their symptoms so that they can exclude them. I am actually working with a team of doctors, data scientists and IBD patients on an app that allows patients to track their symptoms and lifestyle in order to quickly discover triggers and help them manage their illness.

I hope this was helpful and wish you the best in managing your UC.

Cheers, RK

Will pro biotic drinks help me if I drink one every day?

Will pro biotic drinks help me if I drink one every day?

thanks for your question u/superjeegs!

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 :)

Ill 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/

Thanks!

LC

Not OP, but it depends on what you're looking for by "help". There's a wide variety of probiotics on the market right now, and a lot of them are crap. I believe legit probiotics need to be refrigerated. I was on long term steroids last year, and when I came off, a doctor recommended a specific one. It brought the bloating down--I feel like I have my body back again. Also, probiotic poops are the best thing in the world, no joke.

Just saw this, you pretty much nailed it u/knightofbraids

Visbiome is one of the few probiotics that actually has rigorous science behind it. Here's a link to their website / research!

https://www.visbiome.com/pages/15-clinical-trials

LC

I've experimented with cutting down on consumption of inflammatory foods and it really seems to have improved some of my symptoms (e.g. lifelong problems with constipation). The things that seem to have made the biggest difference are cutting down on gluten and inflammatory oils (canola, sunflower, safflower). However, I have no idea what the science behind inflammatory foods is, this is just my anecdotal experience. So my question is - is there any research and evidence on the impact of inflammatory foods' on the health of our gut microbiome? Are inflammatory foods even a real thing or it's just individual reactions to certain foods?

Hey /u/knitra,

Great questions and I'm happy to hear that the diet shift helped with the constipation. Specific foods, such as the oils you mentioned, have actually been proven to be linked with increased inflammation in the body. This is such a well studied field in fact, that researchers have come up with a way to grade the inflammatory potential of any food via different scoring methods.

Amongst other methods, there is the Dietary Inflammatory Index. Therefore, processed foods such as canned foods, excessive meat consumption and sugary foods are all considered pro-inflammatory, whereas foods such as garlic and ginger are anti-inflammatory.

The impact of the food on the microbiome is not fully understood but it is believed that aside from the food's own anti/pro-inflammatory properties, it is also broken down by the gut microbiome into compounds that are either pro-inflammatory or anti-inflammatory.

I am actually working on an app with a team of doctors, researchers, and IBD patients, where people are able to track their diet and figure out their triggers, such as you did yourself. Part of what we want to integrate is an inflammation calculator for different foods. So the idea is that you will be able to enter a picture of a specific food and it will give you that food's inflammation score. We hope this will help people figure out their potential triggers faster and with less experimentation.

Thanks! RK

Hi u/knitra, great question!

Diet certainly can lead to inflammation. Inflammation and the gut microbiome are linked to many health issues, such as obesity, celiac disease, and inflammatory bowel disease. The gut microbiome and the intestinal immune system work together to help keep inflammatory responses in check, but this can be impacted by poor diet or a really heavy meal, among several other factors. For instance, diets high in fat and sugar can impact the composition of the gut microbiome and affect immune signals, leading to inflammation. As an example, high sugar consumption can impact the amount of Proteobacteria versus Bacteroidetes, which can trigger pro-inflammatory responses and affect the intestinal wall itself, making it more porous and inflammatory. Affecting the balance of gut bacteria can lead to a host of symptoms, for example nausea, but what affects this balance depends on numerous factors, with food being one important piece.

While many foods are considered 'inflammatory' or even 'anti-inflammatory' with good reason, you make a good point- it's important to realize that everyone's body is different and what works for one might not work for the other. It's incredible what modern blood and stool testing can reveal about food sensitivities and gut health on a personalized basis! Research must continue in this field in order to further cater diet plans and other health considerations to help people reduce inflammation, monitor their disease, and more. This is especially critical for people with health conditions linked to the gut microbiome (which is a lot more diseases than many may think!), so it's super helpful to have a personalized diet that keeps your gut bacteria at healthy, stable levels with enough diversity. It's incredible how this can vary between people!

Here's some research on the gut microbiome and the role of foods known to cause inflammation if you're interested to check them out for yourself!
High Intake of Sugar and the Balance between Pro- and Anti-Inflammatory Gut Bacteria: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7284805/
The Microbiome in Celiac Disease: https://celiacdiseasecenter.columbia.edu/wp-content/uploads/2020/10/2019-The-Microbiome-in-Celiac-Disease.pdf

Thanks! -LC

I'm seeing a lot of studies popping up on the relationship between chronic inflammation, autoimmune diseases, and microbiome dysfunction. what is your group's view on this topic?

Hey /u/Ambivertigo!

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 flareups 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. This is believed to be because of the fact that such a diet may promote the growth of non-beneficial bacteria that actually trigger the immune system.

As I mentioned in a comment about Ulcerative colitis above, the unfortunate part of this is that it is highly personalized. A diet that might help with psoriasis in one person might not help someone else. What there is consensus on though is that common triggers such as stress, processed sugar, alcohol, and dairy should be first eliminated from the diet prior to larger diet changes.

I am actually working with a team of doctors, data scientists as well as autoimmune patients on an app that allows patients to track their symptoms and lifestyle in order to quickly discover lifestyle and dietary triggers and help them manage their illness. This of course is not a substitute for medication in treating things such as psoriasis, but can be highly beneficial when used in combination.

Cheers, RK

Hey /u/MarshallBlathers,

Check out my response above, did a quick write up on microbiome and autoimmune disorders.

Thanks! RK

Could you recommend any resources for learning and practising in bioinformatics analysis of the gut microbiome? An aspiring bioinformatician also extremely interested in the field :)

Dr. Dan Knights from the University of Minnesota has a great introductory YouTube series covering different ways to analyze microbiome data (https://www.youtube.com/watch?v=6564K4-_DBI).

QIIME2 (a common tool used for the analysis of microbiome data) also provides some excellent tutorials that you can work through with actual microbiome data (https://docs.qiime2.org/2021.4/tutorials/).

In addition, the QIIME2 forum has a great community that is able to answer questions and provide advice and suggestions on ways to improve your analysis (https://forum.qiime2.org/).

Cheers,

RM

Can you say some things about the link between the gut microbiome and autism, if there is one?

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.

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 at the same time has been shown to reduce autistic symptoms in mice.

Hey /u/ghidfg! Check out my answer to /u/Just-Olive-2599 above!

Thanks! RK

What exactly does Remicade (Infliximab) do to the body? I receive it as a IBD treatment.

Hi /u/flamestar_1,

Thanks for the great question!

Remicade is a name for the biologic drug Infliximab, which is an antibody targeting the inflammatory protein tumour necrosis factor alpha (TNF). So now what exactly does that mean and how does it help with the IBD.
One of the defining characteristics of IBD is the increased activation of your immune system and elevated inflammation in your gut. TNF is produced by cells within your gut and promotes inflammation and immune activation. One way we can reduce inflammation then is if we are able to prevent TNF from doing its job. This is where Infliximab comes into play. Infliximab is designed to be able to capture the free TNF and prevent it from promoting inflammation. By reducing inflammation in your gut, Infliximab is able to reduce disease activity and help keep you in remission.

Cheers,

RM