Science AMA series: Hi Reddit! We’re Dr. Mark Pimentel, Dr. Ali Rezaie, Dr. Nipaporn Pichetshote, and Dr. Ruchi Mathur. We’re 3 gastroenterologists and 1 endocrinologist from Cedars-Sinai Medical Center. We’ll be talking about the gut microbiome from irritable bowel syndrome to obesity. AMA!


Thanks so much for your questions this morning. We had a great time! IBS and SIBO receive almost no federal funding and yet these conditions affect up to 40 million Americans and almost 1 billion worldwide. These are also the most expensive conditions in gastroenterology. Doesn’t that sound important? We think so and that’s why we have dedicated our careers fighting uphill to get the answers. Too many unnecessary colonoscopies and testing for these conditions that waste money. Also an incredible cost to patients emotionally and financially. I have met a number of patients where they have spent out of pocket copays totally over $20k. That’s absurd. We will continue to do research in this area. Thanks so much for all your amazing questions! We are inspired by your interest today and this gives us more fuel to go forward in finding the causes and cures for these common and complex conditions (I know- we are nerds). For more information about our research and updates in the future visit our research webpage.


PS Special thanks to the mods for having us on again!!

Hey Reddit – Great to be back (It’s Dr. Mark Pimentel). Last year, I responded to a request to do an AMA having never done one before and was amazed by the amount of questions (and a little unprepared for the response). We knew we had to answer more questions so I’ve teamed up with a group of my colleagues to answer your questions on the latest scientific research on the gut microbiome, as well as the work we are doing. While my research has focused on the association between food poisoning (gastroenteritis) and the disruption of gut flora, SIBO and the pathophysiology of IBS, our group here has researched links between the gut microbiome and diabetes and obesity to the role that the microbiome has affected our hormones.

More about us:

Dr. Mark Pimentel – Gastroenterologist – Executive Director of the Medically Associated Science and Technology (MAST) Program at Cedars-Sinai Medical Center, Professor of Medicine (In-residence series) at UCLA David Geffen School of Medicine, and Associate Professor of Medicine at Cedars-Sinai Medical Center. I’m on twitter at:

Dr. Ali Rezaie – Gastroenterologist, Epidemiologist – Director of GI Motility at Cedars-Sinai Medical Center, Assistant Clinical Professor of Medicine at UCLA David Geffen School of Medicine, Assistant Professor of Medicine at Cedars-Sinai Medical Center and Adjunct Assistant Professor at the University of Calgary Cumming School of Medicine. Find my twitter at:

Dr. Nipaporn Pichetshote – Gastroenterologist – Assistant Director of GI Motility at Cedars-Sinai Medical Center and Assistant Professor of Medicine at UCLA David Geffen School of Medicine.

Dr. Ruchi Mathur – Endocrinologist –Medical Director of the Diabetes Outpatient Treatment and Education Center, Clinical Research and Operations Director of the MAST Program at Cedars-Sinai Medical Center, Associate Professor of Medicine at UCLA David Geffen School of Medicine, and Associate Professor of Medicine at Cedars-Sinai Medical Center

*While we would love to answer all of your medical questions, we will not be answering any specific patient medical questions due to HIPAA violations. We can’t wait to hear from all of you – We will be back to answer questions at 1 pm ET, ask us anything!

Q: Very simply, how effective are biome transplants for weight loss these days? What are the benefits and risks?


Many studies have been done and are being done testing fecal microbiota transplants for various conditions, including weight loss. However, as we don't yet know what all of the different microbes in the gut do, this needs to be approached with caution. For example, we know of at least one case where a person received a FMT from a donor who was later found to have IBS-C (irritable bowel syndrome with constipation) and the recipient did get severe constipation as a result. In one other study where benefit was shown, all of the recipients who showed improvements received transplants from one specific donor, but we don't know what was special about this particular donor. So there are definite risks as well as potential benefits and donors need to be very carefully screened. The problem is, there are so many unknowns still with the gut microbiome, we don't know yet everything we need to be screening for. Much more research is needed! Here & Here are some links to current literature.


Is it possible on any level to enhance the gut microbiome? As in, add new solutions into the mix on a permanent basis that can counteract certain medical conditions like obesity or diabetes? Or maybe a much more practical benefit like helping people digest things they would've otherwise had trouble digesting? Or is the gut microbiome much more sensitive than people realize?


Humans have two computer programs for the gut movements. One is eating mode (where you eat food and the gut turns on the grinding and spreading motions to get the food in a position to break it down). The second is cleaning mode when you are not eating where the small bowel is cleaning itself with these intense waves called "housekeeper waves". These waves strip out lettuce pieces and bacteria in between meals and it occurs every 90 minutes. Its that grumbling sound in the morning. If all you do is snack, you never clean. So we recommend diets but we also recommend fasting period because that's how we were designed. Cant be eating all the time. Need to let the dishwasher run. MP

Is it possible on any level to enhance the gut microbiome? As in, add new solutions into the mix on a permanent basis that can counteract certain medical conditions like obesity or diabetes? Or maybe a much more practical benefit like helping people digest things they would've otherwise had trouble digesting? Or is the gut microbiome much more sensitive than people realize?


As of now, there is no known way to enhance the gut microbiome. That is why more research is needed, and is ongoing to discover the connection between the microbiome with the diseases you mentioned like obesity and diabetes. We want to get there eventually, for sure!


Good morning doctors! This is an area that has been of great interest to me but I find it to be particularly challenging to research in a truly applicable way - mostly because there is not a good way to identify how one may supplement at home (information reliable and effective brands in particular is very difficult!). I have so many questions but will try to stick to just three.

1) Is it possible for an occurance of gastroenteritis or food poisoning and the related microbiome die-off to trigger more long term problems? (Ex - manifestation of celiac, sudden dairy intolerance, ibs, sudden inability to lose weight)

2) If it is, is it possible to recolonize the gut with oral probiotic supplements in such an instance? Are more rigorous recolonization efforts required?

3) Are there any particular bacteria strains that are more helpful to supplement than others, specifically in the instance of obesity? (If you're able to suggest brands I would love it but I understand the credibility risks doing so creates, especially on reddit)

Thank you all for your contributions to this area of research! It seems so promising in the world of health. I look forward to learning from this AMA.


  1. This is a great question. Most certainly during a bout of food poisoning, the bacteria such as Salmonella can have a great immediate impact on the microbiome. However, this should reconstitute in a week or two after resolution of the illness. When we talk about the development of IBS, what we know in 2017 is that a toxin on food poisoning can through autoimmunity lead to changes in the nerves that control the gut long term. When the flow of the gut changes (particularly the small bowel cleaning waves reduce), bacteria build up and causes small intestinal bacterial overgrowth and chronic complaints. Check out this figure to see this more clearly.
  2. We don’t know the best probiotic or supplement that helps prevent this sequence from occurring.


For those of us who have undetermined gastrointestinal complaints (loose stools, gas etc) and get given a blanket diagnosis of IBS, without much medical testing - are you able to offer any hope that we can soon receive a definitive diagnosis as to the cause of our symptoms? I have heard of the IBSChek test, but many gastroenterologists here in the U.K. dispute it's usefulness.

Thanks so much, I love following your work!


There is so much hope for IBS. IBSChek is a great way to diagnose IBS. It is my understanding that you can get IBS in Europe in two ways. Functional Gut Diagnostics in London provides those services for the UK I believe. Also Unilab just launched IBSChek in Europe but starting in Switzerland with the eye to expand over shortly. When you haven’t used something, it’s easy to be critical. The test has a positive predictive value of over 95% in a trial of nearly 3000 patients. That’s pretty well validated!! Maybe they should read this paper.


I'm wondering what effect, if any, a plant based diet would have on the gut microbiome. I only have first hand experience having been vegan for a year and half but I've lost a significant amount of weight and generally feel more energetic. Is this all positive (as I'm seeing in my personal experience) or am I missing out on other benefits or overlooking potential problems? Thanks for doing this!


In California, we see a great number of people on plant-based diets. This can be handled in a healthy way as long as the protein is sufficient. The only problem with plant-based is that it can cause bloating and distension. This is particularly true if you eat lots of legumes (beans, etc). We suggest root and fruit veggies because they have less fiber.

There is evidence that the better the diversity of plants you eat, the better the effects on your microbiome. In a recent study, this was the single strongest influence on the diversity of microbes in the human gut. The greater the diversity, the better the functional redundancy.


Thank you guys so much for taking time of out your schedules to do this! Research is busy!

A couple of questions I've had on my mind for a while (and wonder if others do too)

  1. Is the diarrhea folks have from lactose intolerance related to the hydrogen they produce when the lactose is fermented?

  2. There was a paper published recently about cdiff inducing IBS. My question is this: is there evidence that this IBS is caused by the same mechanism as IBS induced by campylo where the body attacks its own proteins due to molecular mimicry (in this case vinculin)?

  3. Is the vinculin link in IBS you discovered similar to the effects of Myasthenia Gravis (MG) in some ways? Do you think drugs treating this disease could be used off-label in IBS?

  4. Are there any anti-vinculin therapies in the works?

  5. Any new fronts on reducing the cost associated with sampling the microbiome of the small intestine?

Feel free to pick and choose what to answer -- I know you folks are busy! Thanks so much guys!


Hi Isaac, thanks for your question(s)! 1. While production of hydrogen is these patients are problematic it is unlikely to explain all the symptoms. Gut microbiome likely produces a myriad of side products that will affect us in numerous ways.

  1. All gram negative baccilli (GNB) including Cdiff and campylobacter have CdtB protein. However the constitution of CdtB in all GNBs are not the same which may explain the variable rate of post-infectious IBS after GNB infections.

  2. Very similar concept. We are using the same approach to find the treatment of choice to decrease anti-vinculin Abs.

  3. We are working hard on this. We have ongoing pilot trials targetting anti-vinculin antibodies using immunosuppression or actively clearing it from blood circulation. We have some promising preliminary results but too early to call.

  4. We are working hard on this as well. We are aiming to develop simple, safe and uncontaminated techniques for assessment of small bowel microbiome. I do not foresee a non-endoscopy-based way of assessing small bowel microbiome in near future.


How does the gut biome of someone who is obese compare to someone who is not? Are there future implications for treating obesity?


Many studies have been performed comparing the gut microbiome in persons with obesity vs. persons of normal weight. We know that the gut microbiome is altered in obesity, but it is more difficult to say which changes are causative and which result from obesity. Methane-producing organisms in the gut have been specifically linked to obesity, and we showed in a small pilot study that treating obese pre-diabetic subjects with specific antibiotics improved cholesterol and insulin parameters, but we don't know yet if this would result in longer term improvements like weight loss. We also know that, in general, patients with obesity (along with other chronic diseases like diabetes) have less abundance and variety of gut bacteria. So, in one sentence... we don't know what the exact compositions are, we have some "candidate" organisms we are looking at, and variety and abundance is a good thing. Here and here are links to related studies. Best to you. RM

Cool! What role do you think the gut microbiome has in hormone regulation - specifically thyroid auto-immune conditions like Graves' and Hashimoto's?


THIS IS A GREAT QUESTION.... for which I have no answer. We are starting to see links with GI diseases like IBS and autoimmunity specific to the GI tract (nerves), and we know that there are other autoimmune diseases that affect the gut. These autoimmune diseases may be associated with microbial changes. However, at present, there is no link with thyroid autoimmune diseases.... you just gave me a great idea for a new research project. Thank you!


Thank you for coming back (and bringing others) to answer questions!

Wondering if you could discuss a little about auto immune diseases that impact digestion, specifically Celiac Disease. Many others in this thread have asked interesting questions about the impact a stomach virus or an imbalance of gut flora could have on the impact to triggering the disease. (Which I would love to know as well)

Are there any studies or theories that show a major shift in a persons microbiome could help after they have Celiac? Either to help heal the intestines or possibly reverse Celiac?

I know there are currently multiple clinical trials to create medicine for Celiac - any information or opinions you could share about these, their viability would be wonderful to read!

Thank you again!


There are connections being drawn between IBS and celiac and also small intestinal bacterial overgrowth (SIBO). For example patients with celiac who do not respond to gluten free completely might have a component of bacterial overgrowth. Checking for that and treating it can be of great benefit in some.


How has your research affected your own behavior? For example, have you changed your diets or decided to donate to a certain cause?


Thanks for your question. We have absolutely changed our behavior. We are more cognizant of what we eat. We avoid food poisoning at all costs to prevent IBS in our patients, friends and family. As far as donating goes, we have a challenge right now until June 30 with a matching donor and what I can tell you is that every single person on our research team not only fights for these conditions but we also all donated money to reach this goal. All hands on deck for IBS and SIBO given the poor funding environment.


Is it possible for the gut microbiome to go through population 'cycling' similar to how predator/prey populations get out of balance in cycles? Example: mouse plagues in Australia

Could this be the source of some episodic gut pain/digestive issues?


Do you need a job in our lab? This is the kind of stuff that needs to be studied in humans. I absolutely believe these types of events are happening.


I have a couple of questions:

  • Does pesticide or herbicide use affect our gut microbiome?

  • Does the microbiome play a role in autoimmune diseases? What diseases are affected by the microbiome?


It is unlikely that it doesn't . Pesticides and herbicides have been linked to myriad of health issues. I summarized the evidence of oxidative stress and pesticides several years ago and it has received a lot of attention. It should be noted that studying pesticides in the setting of microbiome is very hard due to various different pesticides and dosing used globally.

We're going to answer the autoimmune in a big block -- it's a long answer! I'll answer soon.


Can you talk a little bit more about the new research that is coming out about gut bacteria being linked to mood disorders like depression?


Needless to say that research in this field is in its infancy. "Psychodelic bacteria" is indeed an interesting concept. While this is not something our group is studying, however there are a number of people in the field that are - suggest you watch Dr. John Cryan (twitter: @jfcryan) presentations on this! AR

Are probiotic supplements effective in regulating the gut microbiome? Would you recommend their use after a course of oral antibiotic therapy?


Currently I do not recommend probiotics after antibiotic therapy! This is based on the PLACIDE trial results (please read here my editorial on this paper). In short placide trial is the largest randomized placebo controlled trial with probiotics that showed probiotics do not decease the chance of diarrhea or Cdiff after antibiotics in over 3,000 patients. Patients on probiotics got more bloating and flatulence!


Has any of the research looked at PCOS and how it is affected by gut biome, diabetes, and obesity?

I'm sure many would be happy to see some sound/solid science that can be used to battle against PCOS.


Studies have shown that the gut microbiome is altered in PCOS, and and alterations to the gut microbiome have also been linked to obesity and and diabetes. A recent study using a rat model did suggest that estrous cycles in a PCOS rat model normalized following fecal microbiota transplants. However this is VERY preliminary and in rats only, it is too early to say if this is something that could work in humans. Our group is actually quite interested in this area of research as it combines both Endocrinology and Gastroenterology- which is essentially what we do. Hopefully if you ask this question again in a year or so, we will have a more definitive answer for you.

Association between PCOS and Microbiome paper


How do artificial sweeteners in diet drinks impact gut biome?


Generally speaking artificial sweeteners which are sugar alcohols are extrememly fermentable and affect the gut microbiome. However the artificial sugars which are protein such as aspartame are absorbed quickly and do not affect the microbiome (at least theoretically).


I have so many questions! How long should an intense course of probiotics be taken until Flora is rebalanced? And is bloating/gas ever normal/expected (like with beans) or is it always a sign of food intolerance? What are the symptoms of low stomach acid that could be mistaken as leaky gut?

Thank you so much for all you do!


Probiotics have benefits but also problems. One problem is that there are more types of probiotics than randomized controlled trials to study them. This makes it so confusing for patients. But the PLACIDE study in the lancet showed that the probiotic they used only caused bloating and did not help patients. MP

Hey Docs, glad you're doing this. How much is true about gut bacteria and specific food cravings? And what about it's relationship with hunger control?


This is a really good question. We have already published data saying that small intestinal bacterial overgrowth of the hydrogen type are associated with hypoglycemia which is a driver for eating. Dr. Mathur has shown that the methanogenic bugs are associated with obesity and hyperglycemia. So there is a lot going on to figure this out in our lab and around the country. MP

Hey Docs, glad you're doing this. How much is true about gut bacteria and specific food cravings? And what about it's relationship with hunger control?


Interesting question. There is research underway looking at the brain gut axis and seeing if gut bacteria plays a role in central hunger signaling. The relationship is quite plausible but still to be proven. Regarding specific cravings, a bit less likely. Thanks! RM

Often times individuals with Autism Spectrum Disorder have poor digestive systems. I have heard this is because their gut flora is different. Is there any truth to that? What could be causing it the difference?


There is currently research that is ongoing regarding this subject, but no definitive information regarding this just yet. That is why research is so important!!! NP

Fasting is a major part of religious practice. Is there any research that shows the positive/negative impacts of fasting on the GI system?


We are currently in Ramadan and during this important religious time fasting all day is practiced for an entire month. We do believe fasting is beneficial to gut microbes and had started an interesting study on this. Unfortunately, the study was poorly recruited and we did not complete it. The point is, humans are feast and famine animals and we need to fast at times of the day or year to maintain health.


Do you dismiss digestive tract candida overgrowth, or do you consider it a possible source of gut dysbiosis?


Candida is poorly studied but there is growing interest and actual data in yeast in the last few years. Some researchers such as Dr. Satish Rao in Georgia have coined the term small intestinal fungal overgrowth (SIFO). However, this is seen in the minority of IBS patients compared to small intestinal bacterial overgrowth (SIBO). We need more studies and data to clarify these.


What do you feel about a tentatively established link between the microbiome and Alzhiemers?


There is a growing link between the gut, its microbiome, and neurodegenerative diseases. For example, in Parkinsons, constipation predates the neurodegenerative changes by even a decade or two. Some have found specific bacteria are important in this event. Stay tuned because more is coming here.


Any thoughts on the importance of food combining? Combinations, timing, order of eating, etc.


There are a number of diets recommended for #IBS. One of these is the low FODMAP diet. This diet is good at controlling symptoms but cannot be used long term since it is not well balanced. We use a low fermentation diet. Ours is based on restricting fermentable products and combining that with gaps in eating so there is time for the bowel to clean itself. We are feast and famine animals and we need hours between eating so the bowel is not continuously bathed with food. The bacteria grow when they are not cleaning.


I'm really looking forward to reading your research on IBS! I was recently diagnosed and it is such a struggle. Is there anything you've learned that you think all IBS sufferers should know in regards to treating/controlling it?


IBS is not in your head! I think that is an important fact that all people with IBS need to know.


Hi there! Every day there are two or more posts here about how the gut biome is responsible for everything from depression to obesity.

Is there any truth in this or is this just another fad?


I hope it's not a fad because we have a number of research projects looking into many aspects of the gut microbiome! As with any relatively new area of research, we need to approach it cautiously and not jump to conclusions...and not sell snake oil. So, without going through details, let's think about it from an evolutionary prospective. We have lived and harboured these microbes for thousands of years. We are symbiotic with them. We provide them a safe haven to live and reproduce, and in turn they help us with energy harvest, immunity, vitamin production, and metabolism. When we disrupt them, it would make sense that there would be consequences. Dr. Blaser wrote a book called Missing Microbes which might be of interest to you. I appreciate your drives honest and good science. Best to you!


I have read a hypothesis that weight loss surgery impacts the gut microbiome and could possibly be the reason why diabetics who undergo gastric bypass are immediately cured after surgery (before any weight has been lost). What are your thoughts on this? Do you think it will be possible for patients to alter their gut microbiome, without surgery, to obtain a similar result?


There is definite evidence to support this. For example, Roux-en-Y gastric bypass (RYGB) alters the gut microbiota, and these alterations have been shown to contribute to weight loss and metabolic changes. However, while we have shown some specific miccrobial populations are changed following surgery, we dont yet have a good way to change these without surgery. We also do not know for certain whether this contributes to the immediate blood sugar benefit we see right after surgery (which is independent of weight loss). This is a very active area of research.... so do stay tuned! Research here and here


Hello! Thanks for your time. What are steps for finding a cause of acid reflux? Proton pump inhibitors seem to just be treatment for a symptom and not a cause. What are alternatives to being stuck on proton pump inhibitors? Are they bad long term?


Long term use of proton pump inhibitors have been associated with osteoporosis, dementia. There is a clear connection with osteoporosis and PPIs in people who are postmenopausal of who have kidney disease. The dementia association is not so clear. There are alternatives to chronic PPI, surgery, diet, lifestyle changes. Sometimes evaluating the motility of your esophagus is helpful in finding the cause of acid reflux.


Why is depression a common symptom to people with IBS?


IBS is a chronic illness with waxing and waning symptoms. Given it's chronicity and unpredictability it is very common for patients to have depression associated with this disease. IBS also has a negative stigma attached to it and I think this also contributes to people's depression.


Thank you for doing this! What role do food allergies (and associated inflammation of the GI tract) play in affecting the biome for gut bacteria?


Imagine you have 1000 bacteria in the gut that are producing an immense number of chemicals which will produce reactions or things in you. Add to that food with chemicals and breakdown products from bacteria breaking food down at the same time you are. All of this makes for challenging research to figure food allergies out altogether. I am sorry for this obscure answer but what we do know is that food allergies are increasing especially in children.


Thank you for doing this! What role do food allergies (and associated inflammation of the GI tract) play in affecting the biome for gut bacteria?


There is ongoing research assessing the role of allergies. For example, antihistamines (ebastine) have been shown to decrease visceral hypersensitivity.


As some are finding a link between your gut and depression, what effect does the American super sugary diet have on your gut and therefore depression?


Yes, there are links between gut bacteria and anxiety and depression but the corollary is also true. A recent study by Dr. Talley from Australia showed that patients develop depression after the onset of IBS for example. If you had to run out in the middle of dinner to the bathroom for 30 minutes, that can make people anxious also.


Hi Dr Pimentel,

Thanks for your important work in this area. I donated to your efforts. I have a question on the natural/holistic approaches to SIBO and dysbiosis that are everywhere online. There are a lot of anecdotal reports that 'natural' antimicrobials like certain essential oils, antimicrobial foods and teas, and supplements like allicin from garlic are more effective and less dangerous than antibiotics in culling bad bacteria. But it seems like we'll never know because expensive clinical trials are not investigating things that can't be patented and then sold for maximum profit. Also, there seems to be no incentive to actually cure, just treat symptoms, since cured people are not good future customers.What do you think of this common criticism of the modern medical system, where the profit-motive and the public good seem so often misaligned? The logic makes sense to me, but I'm open to being proved wrong. As someone coming from this establishment system, how will any solution you developed be different?


So sad. Natural products are being marketed so aggressively and there are so many options but they need to fund studies so we know all the answers about these. But, I do know that allicin for example has an inhibitory effect on methane which is a cause of constipation. Work we are now doing is showing that lovastatin (which is a natural statin from aspergillus) blocks methane production and helps constipation. Allopathic and naturopathic companies both need to step up to the plate and help fund work around their product and other studies. You can't just say it works...prove it. There are many researchers that will to do that work.


Thanks for doing an AMA! What types of bacteria affect obesity and diabetes? Do we know the mechanism by which the bacteria affects these conditions? And lastly, are there any probiotics that are shown to be effective at lowering diabetes/obesity?


Both obesity and diabetes have been linked to changes in many different microbial populations, but the key question is whether these changes are cause or effect, which is what researchers are working actively to tease out. Methane-producing bugs (which are archaea not bacteria) have been linked to obesity and reducing them using specific antibiotics has been shown to reduce blood cholesterol and improve insulin parameters. The postulated mechanisms by which gut bacteria can impact metabolism are varied... from harvesting excess calories that are presented to the human host, to effects on bile acids, to mediating inflammation. There are no probiotics which have been shown to be effective at this time. In the future, one can imagine a "designer" probiotic to target specific microbes... but this is still a long way off. Thank you for your question.... stay tuned.

Two research articles on this topic found here & here


I was told that Irritable Bowel Syndrome was as much psychological as it was biological; that stress and anxiety were very much to blame for the physical symptoms.

But...I'm not severely stressed (no more than normal) and have some anxiety, but it still doesn't explain why I can't drink coffee/eat beef/use mustard, etc. without having diarrhea.

So, is it psychological, or is it physical?

Thank you. :)


This is wrong. The US military study proved that deployment caused IBS but it wasn't the stress. So this is the one and only level 1 massive study that says "no". What caused IBS was food poisoning. If they got sick with food poisoning overseas was when they developed IBS.


I saw a report on a study yesterday linking intestinal bacteria to type 2 diabetes and the related high blood pressure, high cholesterol, etc.. Do you know how far along they are in that process? Much more work going on?


This is a very active area of research. Many studies have been performed which have shown that gut microbial populations are altered in type 2 diabetes, and alterations in gut microbial populations occur in subjects at high risk for diabetes, even in the prediabetic stage. Specific reductions in levels of butyrate-producing bacteria have been demonstrated in T2D, and a recent Danish study demonstrated that insulin-resistant individuals have higher circulating levels of branched-chain amino acids (BCAAs), which cannot be synthesized by humans and are largely produced by two specific species. One study showed that transferring intestinal microbes from lean donors increased insulin sensitivity in recipients with metabolic syndrome, but this is only one study and fecal microbial transplants are still associated with a lot of risks. So there is a lot of work going on and the complicated relationships between microbes, diabetes and cholesterol are still being teased out. We also know that reducing gut methane-producing microbes specifically lowered cholesterol in a pilot human study (see answer to Lover_Of_The_Light), which is very promising....This is a link to a related study. Thank you for your question. It's a fascinating area of research, isn't it?


Hi there. This maybe be slightly out there...

What kind of long term effects can a bout with H. Pylori have on your stomach's bacterial flora? Any suggestions after treatment to return to normal?


That is not yet known how the bacteria H pylori affects the stomach's bacterial flora. Since we don't know how it affects the flora, we unfortunately don't have any suggestions on how to return it to normal. As it might seem with many of the answers, there is just so much we do not know in this field. H. Pylori has been associated with disease outside of the gut, but still relatively unclear in the current literature.


Does temporary (24 hour) food poisoning have any long term effect on the body?


Unfortunately, any food poisoning, even 24-hour food poisoning, can cause long term effects. 10% of people who get food poisoning will develop IBS.


Does temporary (24 hour) food poisoning have any long term effect on the body?


Yes. But fortunately only 1 in 10 people with food poisoning develop IBS. The more severe the food poisoning the higher the chance.


You likely won't see this, but IBS has ruined my life with vomiting/diarrhea reactions to the point where I'm scared to eat anything but my safe foods (carrots, dairy free cheese and tuna). Is there any hope of IBS just going away?


We did see it! So sorry you are having such trouble. There is a lot of hope for IBS. If you have bacterial overgrowth causing your IBS, that is easy now. You need to see someone who specializes in motility to do a good workup and assess it. There is a motility program in many major university hospitals. Good luck.


You likely won't see this, but IBS has ruined my life with vomiting/diarrhea reactions to the point where I'm scared to eat anything but my safe foods (carrots, dairy free cheese and tuna). Is there any hope of IBS just going away?


You are not alone. We have a long way to go but our knowledge on IBS has been revolutionized in the past 10 years. That is why we have moved away from calling IBS a psychosomatic disease. We are working hard on the microbiome-related IBS cure.


Is there any link between the microbiome and PCOS/PCOD and infertility, and if there is, is there a way to reverse the damage?


See our answer to ShovelingSunshine - the microbiome has been shown to be altered in PCOS, and a recent study using a rat model did suggest that estrous cycles in a PCOS rat model normalized following fecal microbiota transplants. While encouraging, this is very preliminary and it is too early to say if this could work in humans.



Is there any link that you've found between IBS/gut flora disturbances and Ehlers-Danlos?


EDS type 3 (hypermobility type) patients have significant GI symptoms. This includes bloating, distention, alternating bowel habits, nasuea and vomiting. At this point these symptoms are considered to be a consequence of dysmotility in these patients such as delayed gastric, small bowel and colonic transit. While I am not aware of a formal study on microbiome of EDS patients, given their dysmotility, it is very unlikely that gut microbiome is not disturbed. Please read our case-report on this at ACG conference


How effective are stool transplants?


A recent study was presented at DDW (the international gastroenterology meeting) that showed that fecal transplant in IBS was not different than placebo. If IBS is associated with an overabundance of bacteria, why add more? I have seen some patients with IBS worse after transplant.


It's a common belief that IBS does not have a specific cause. Can you explain what medical science does know about the causes of IBS?


That is exactly what we want to change. We have shown specific autoimmune and microbiome-related pathways that lead to IBS.


I know this is a simple question, I'm not well-versed in these fields. Are there proper dietary ways to manipulate your gut biome? Are there any "super foods" for your gut?


This is not a simple question. Diet has an immense effect on the microbiome. If you live in a particular country and eat a country specific diet, your microbiome will adapt to that. Now imagine modern living where you can eat at a Greek restaurant one night, Indian restaurant the next and then Italian the next. How does your microbiome figure that out. They (the bugs) must be so confused. As a result, some have advocated a simple diet. Others a low carbohydrate diet, low FODMAP, gluten free and so many others. We don't know yet which is best.


Are there difference in gut bacteria in different regions of the world? Would moving to another country alter your gut bacteria composition together point it affect your health in some way?


Here’s a study by Yatsuneko et al that examines this. The authors found differences in gut microbial profiles of individuals in the US vs the other countries starting from infancy but with sustaining effects into adulthood. Many factors can affect changes to your gut microbial profile. In this study, the effect of diet is a pronounced factor, but we know of some definitive other reasons as well such as antibiotic usage.


This may not be within your scope, but does the gut microbiome cause/have any effect on diabetic gastroparesis or ketoacidosis, especially for individuals with type 1 diabetes? If so, how does it work and can it be managed or prevented?


Dr. Henry Parkman at Temple University has published work showing bacterial overgrowth is common in gastroparesis and that the motility disorder does not stop at the stomach but involves the bowel as well. Regarding ketoacidosis, I am not aware of any direct relationship. Thank you for your question.


Is eating too clean a bad thing? Always washing your hands before eating and eating food that is cooked well. Does that somehow lower your body's ability to fight food-borne illnesses?


You should wash your hands before eating and eat at establishments that would not give you food poisoning (which unfortunately is sometimes hard!). 10% of people who get food poisoning do develop IBS.


Hi. Where is the research on CVS (cyclical vomiting syndrome) and other types of functional conditions like this?

Has there been recent advances in treatment? Is there any promising therapies out there for dealing with it?


There are new studies coming out that are looking at people with cyclic vomiting and their genome. It has been shown that some genes are associated with cyclic vomiting syndrome and that would explain, for example why some people who use marijuana develop cyclic vomiting syndrome and some people do not. See this very interesting article


Why are GI docs not given more background in food and nutrition? Doesn't food affect the health of the gut, and gut health affect how food is digested?


Yes food does affect the gut and how we feel. We definitely know more now than we did 10 years ago, but we are still learning new things every day.


Dr Mathur:

Thank you ahead of time for this.

Women with osteoporosis face awfull decisions regarding the available medicines. They are as bad as the disease! Fracture from the disease or fracture from the medicine! What to do?

Please give your opinion on the drugs.


Thank you for your question. I know Dr. Pichetshote answered your question... and I'll chime in as an Endocrinologist. Osteoporosis management itself can cause GI upset and can be associated with bone benefit in the hips and spine, but potential fractures in the long bones. There are specific guidelines for length of treatment and switching between treatments (bisphosphates, Prolia, etc). I suggest you speak directly with your MD about possible long-term options for managing your bone issues. And... don't forget about weight bearing and calcium intake. Best to you.


Dr Mathur:

Thank you ahead of time for this.

Women with osteoporosis face awfull decisions regarding the available medicines. They are as bad as the disease! Fracture from the disease or fracture from the medicine! What to do?

Please give your opinion on the drugs.


It is very difficult! That is why it is important to only take medications that you truly need. There are times that medications are started, like proton pump inhibitors, but then are continued even though they are no longer benefiting you.

NP (Going to get Dr. Mathur to answer it in a few...)

How much of what you study can be "fixed" or brought back in line within their normal range by people simply choosing diet and exercise?

Basically, what I mean is... If people didn't have sedentary lives and poor eating habits, would you have to find a different field to study?


It all depends on the underlying cause of the SIBO. For example if SIBO is caused by opioids or bariatric surgery, it is hard to control it alone with diet and exercise. Having said that I have a lot of patients with mild SIBO that are controlling their symptoms only with diet and aerobic exercise.

And to answer the second question: LOL... I doubt it. Even if you have the healthiest life, you may still be affected by SIBO.


Dr. Rezaie: what do you think about this recent study from your alma mater (UofC) assessing the impact of prebiotic fiber (oligofructose inulin) on limiting weight gain in obese children? P.S. You're the best!


Thank you :) This is a fascinating study and I am not just saying that because it is done at my hometown at the University of Calgary. Given the results of this study, larger trials are needed to validate the results. One issue with prebiotic research is that their effect is dependent on each individual's native microbiome; hence, given the diversity of microbiome in different individuals, the efficacy of prebiotics becomes unpredictable (even more than probiotics). We need more studies like this.


Do you guys have any opinions or theories about Cyclic Vomiting Syndrome? Causes and Treatment?


We do see patients here in our GI motiltiy clinic with cyclic vomiting syndrome (CVS). Chronic marijuana use has been a suggested cause of CVS and so I do counsel people with CVS to stop marijuana to see if they can see an improvement of their symptoms. There are some medications that are sometimes used to treat CVS: tricyclic antidepressants, coenzyme Q10 and L carnitine, serotonin agonists, histamine antagonists. You should ask your doctor to see which medications would be right for you.


Trying to top a Jim O'heir AMA?



Typical Jerry/Gary Gergich!!

Can gut bacteria react to low blood sugar levels ans cause "cravings" accordingly i.e sugary food


There is no direct evidence specifically regarding cravings yet, although we know that specific gut microbes are altered in type 2 diabetes, including butyrate-producing microbes. There is also evidence that butyrate, acetate and other short-chain fatty acids (produced by gut microbes by breaking down dietary fiber) appear to affect satiety and influence appetite suppression. So it seems very possible that gut microbes may indirectly cause 'cravings'. Related studies can be found here, here, and here.


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