How To Achieve Total Gut Restoration with Kiran Krishnan (Updated with Q&A)

Microbiologist Kiran Krishnan is a SIBO SOS™ fan favorite and the creator of truly gut-changing supplements like Megaspore and Mega IGG.

In this webinar, Kiran walks us through his 3 -step “Total Gut Restoration” process. You’ll learn about the differences between a healthy and unhealthy gut and how his 3-step process helps heal the gut.

P.S. If you want to try Kiran’s 3-step Total Gut Restoration Protocol, he gave us an exclusive 15% off code!

First, register as a patient with patient direct code “SIBOSOS” HERE: Microbiome Labs (this is the first step – you can’t order directly from Microbiome labs unless you do this) 

Next, add the Total Gut Restoration products you’ll need for the protocol (3 bottles of Megaspore, 2 bottles of Mega Prebiotic, and 1 bottle of Mega Mucosa) to your cart.

Finally, enter code “GUTRESTORE15” at checkout. 

Want to try a different product? Register with patient direct code “SIBOSOS” HERE: Microbiome Labs, then use code “DIGESTIONSOS” for 15% off your entire order! But this coupon is one-time-use only, so load up your cart!

Q&A With Kiran Krishnan

After the webinar (watch it by clicking on the video above), Kiran was gracious enough to answer questions submitted by viewers when the webinar was live. Here are those questions and answers:

Leigh-Anne C. Is this something we should do during treatment or after?

Kiran Krishnan (KK): This will be a critical part of your treatment, so you would start it during.

Elena V. Thanks for your products!! I have methane sibo and am starting another round of antimicrobials. I started using megaigg, megaspore and restoreflora. My gut likes them. What products should take while taking antimicrobials can I continue use of megaigg, megaspore and restoreflora or should I add something else

KK: Yes, you can continue to use those while on antimicrobials. I would recommend adding in the MegaGuard to address bile flow issues, gastric emptying and HCL production. 

Pam M. Does Mega prebiotic have dairy in it? Or Casein?

KK: No, it doesn’t. Although the oligosaccharide is from dairy, there are no dairy proteins or fat in it. The oligosaccharides are purified extracts.

Ingrid W. If we are someone who can not take supplements easily and have to try micro doses. How long can we take micro doses of Mega IGG? Is it something you can stay on long term?

KK: Absolutely, there is no risk, only benefit. 

Pam M. Why are immunoglobulins low with leaky gut?

KK: Because of systemic inflammation and compromised immunity. 

Laurie B. P. Can SIBO ever truly be cured or is it life management once you’ve been diagnosed?

KK: I absolutely believe it can be cured. There is a mechanism that causes it and its not genetic. If we address that mechanism, it can be reversed. Unfortunately, more often than not, the root causes are not being addressed. 

Glaucia S. L. What are the best digestive enzymes and probiotic strains for SIBO? KK: Digest Gold from Enzymedica would be fine and use HU58, RestorFlora and Megasporebiotic for probiotics. 

Jeanette F.  Jeanette in Stockholm, Sweden here. Is dr Krishnan in touch with any Swedish researchers/MDs?

KK: Hi, not in Sweden.

Mary Kay A. Question: How will MegaPreBiotic affect me, given that oligosaccharides are the fodmaps to which I seem to be particularly sensitive?

KK: These are longer chains and should have less negative impact. However, go slow, use as little as ¼ of a scoop per day to start. But remember to use it after 4 weeks of the probiotic. If you have been on low FODMAP, your large intestinal bacterial are starving for fermentable carbohydrates, which are critical for maintaining gut and immune health. 

Marilyn M. Can one take the IgG product continuously with no side effects? Should it be discontinued gradually?

KK: You can absolutely take it continuously. Should you want to stop, you do not have to discontinue gradually. 

Glaucia S. L. What test is recommended to found out this problem?

KK: The problem is complex and multifactorial, if you are referring to leaky gut and barrier dysfunction. There isn’t a single test for it. You can rest assured that if you have health issues, there is a high likelihood that the gut lining is compromised. 

Robin L. C.  I had been taking Megaspore and Megaprebiotic for several months. On a recent GI Map my “Bacillus spp” was flagged high. Do you think that’s a problem? Can you overdo it with the spores?

KK: The GI Map test is archaic, inaccurate and not validated in any study. Their arbitrary flagging of strains as “high” or “low” is nonsensical. Bacillus is normally in the gut at 1X10^6 cfu/g of stool, so their threshold for “high” is way off. These strains are also transient, so they don’t accumulate beyond a certain level.

Marilyn M. I see that there are citrus flavinoids and lemonade flavoring in the Megamucsa. Will this trigger histamine reactions in sensitive people?

KK: We have not seen that at all. 

Susan G.I recently started a regime by my nutritionist for healing my gut. Started taking Aloe Vera Gel beginning of September; 2-3 Tbsp a day. I just got back my full Metabolic lab tests today, and my liver tests (AST/ALT) are extremely elevated (I am not at risk for hepatitis, I don’t drink any alcohol, and don’t take Tylenol). I searched online and it says that Aloe Vera Gel can cause adverse liver toxicity?!

KK: That may be true, but I haven’t researched aloe and liver health. Leaky gut is also a big driver of liver toxicity. It is important to use a clinically studied solution for gut healing, you should consider the Total Gut Restoration.

Robin L. C. Do you think that the GI Map is a reliable indicator for Zonulin? My symptoms say my gut is leaky, but zonulin marker is well within range. Also, I was on Megapore and Megaprebiotic for several months. My Akkermansia was still below detectable levels. Shouldn’t it be detectable by now?

KK: The test is virtually useless in detecting strains with any accuracy and zonulin is only partially correlated with leaky gut. Use a more accurate whole-genome sequencing test to more accurately detect to the species level. Tests are not the be all end all in functional medicine, follow your symptoms and how you feel as well. 

Marilyn M. Will your protocols help with longstanding autoimmune

KK: Leaky gut is a major driver of autoimmune conditions, the protocol is designed to fix leaky gut, so it should be an important part of supporting your immune system. 

May S. F.  I am currently taking megaspore and IGG for Sibo. Will I kill my good bacteria by consuming antibacterial foods like onions garlic and coconut oil, even if well tolerated? 

KK: Coconut oil will likely kill good bacteria, I would use is sparingly, the rest of the foods are ok.

Glaucia S. L. Having SIBO does it mean there is Leaky Gut?

KK: Almost certainly. 

May S. F.  And, is it true that sugar substitutes like Splenda can affect gut bacteria adversely, even affecting eyes?

KK: Not sure about eyes, but certainly gut diversity.

Glaucia S. L. Can we measure LPS in a blood test?

KK: In a lab, yes. Not in a doctors office. 

Marilyn M. Will the Mega Mycobalance assist in eliminating a systemic fungal infection?

KK: It is designed to do so. We have had success with it in people with localized and systemic issues. 

Sonja P.  Why does megaspore increase the keystone strains?

KK: Absolutely, then the addition of MegaPreBiotic increases them further. 

Ingrid W. If we can’t take Megaspore at a micro dose or Just Thrive – can we try the prebiotic instead to try to work on the gut? Can this be a back door way to recondition and build good bacteria when we have tried over months to get on the probiotics but it was too stimulating.

KK: Sure. There is no issue there. 

Karen P. N.  I am on a probiotic that was supposedly made for me based on the study of my stool sample. Can I add megasporebiotic and also your additional protocol while also on this custom probiotic? Can you use anything like Biocidin during this time for SIBO or will your protocol alone help SIBO?

KK: You can certainly use the total gut restoration as well, it will only help. Use that first and give it a single round (90 days), if the symptoms of SIBO are still present then, you can look at using biocidin.

Jordan P. what if you have Sibo? can this get rid of id?

KK: SIBO is multifactorial, this targets key underlying causes, there may be a need for other interventions, but try the system first and see how you do. 

Katie J-E. Is it ok to start with intestinal mega mucosa when starting spore probiotic or does it hinder your outcome

KK: It is perfectly ok.

Sonja P. Do you distribute your products in Europe too, i.e. Germany? I could only find products in the US.

KK: Yes, either from Romania or the UK. Look at Microbiome Labs UK

Eliza it ok to just take the megasporebiotic and megaiGG2000 or do i need the rebuild and reinforce too

KK: Ideally you would do all 3 steps, but if you do just the probiotic and MegaIGG, you will see significant benefit as well. 

Sonja P.  Do the spores settle in the colon or they are just transient – so they get excreted with a bowel movement?

They stay for about 21 days and then leave. 

Sonja P. I can barely tolerate any carbs. Do you recommend taking more than two capsules of megaspore in such cases?

KK: Go slow and build up to 2 caps. Once you are there, you can go beyond 2 to 3 or 4 to see if the extra dosing will help.

Michele V. Pimentel said not to take probiotics if we have SIBO, don’t add more bacteria to the situation. Don’t do this if we have SIBO?!

KK: He isn’t referring to spores and he doesn’t study probiotics. Spores can actually bring down the growth of bacteria in the small intestines. 

Katie J-E. What do you do if you have low lactobacillus buts have SIBO os ok to just do megaspore and not lactobacillus

KK: Megaspore increases your natural lactobacillus, so it will take care of that issue. 

Kristie R. Why are spore based probiotics listed as opportunistic in a GI Map?

KK: Because its an archaic test and is poorly designed. They clearly haven’t read studies on microbiome commensals and composition. Numerous studies clearly define bacillus as a commensal and a keystone genus. 

Jeanette F. Chronic constipation? Take full program?

KK: Yup. You should see improvement even in the first month. 

Katie J-E. How do you increase lactobacillus bacteria (especially for women) if they are low in lactobacillus but have SIBO and are taking megaspore

KK: Megaspore has been shown in a published study to increase lactobacillus. 

Sonja P. Is it possible that the spores could settle in the small intestine – when the conditions are favourable for the spores – like in case of SIBO?

KK: They do function in the small intestine, but once there they modulate the immune response and they bring down the growth of over-grown bacteria.

Glaucia S. L. How to revert it and have a healthy connexion with brain and gut?

KK: You have to fix leaky gut. 

Andrea Beth T. can they break through biofilm?

KK: Yes

Sonja P. Sometimes the spores can turn pathogenic, what helps the most from your experience to get the situation under control in such a case?

KK: They cannot turn pathogenic; this is a complete misnomer and simply false info that has been perpetuated by competitive probiotic companies. We would never develop and sell and product that could turn pathogenic. They have been completely gene sequenced, tested for virulence factors, etc. 

Sonja P. Is restore flora containing sacharomyces also good for constipation??

KK: It can be, yes. 

Sonja P. Do megaspore probiotics produce lactic acid?

KK: They produce L+ lactic acid which is then converted to butyrate and other short-chain fatty acids.

Sonja P. Do you have an idea why some people having SIBO can’t tolerate any probiotics and some do? Apart from lactobacillus strains that assists building up secondary bile salts. What are the main reasons?

KK: It likely depends on the nature of their overgrowth, what kinds of microbes are overgrown and how the immune system is responding to the presence of those microbes. 

Sonja P. Do you know why Epstein Barr virus causes slowing down of the motor migrating complex and initiating SIBO?

KK: I have not seen good evidence that EPV slows down the MMC. 



35 thoughts on “How To Achieve Total Gut Restoration with Kiran Krishnan (Updated with Q&A)”

  1. My granddaughter is 15. Will megaspore probiotics help her acne problem. She also has prob with her gut. Some days having diarrhoea. She is beginning to have acne.

  2. Hi! I was wondering what is the best time of the day to take the MegaMucosa and when to take the MegaIGG2000? I would thing the mucosa in the morning before breakfast and the igg at night to sooth the gut but would like to hear what you suggest? Does the IGG also bind any medications like for example thyroid hormone for people that are on meds? Thanks!!

    1. Hi Kasia, MicrobiomeLabs’ standard recommendation does not suggest any specific timing. Both can be taken with/without food, so they’re not very particular about what time of day you should take it.

      That leaves us with… timing it according to possible interactions with your thyroid hormone!

      Sorry, I don’t have the answer for you on that on-hand. That might be a question for your practitioner. But you might still also want to check in with Microbiome Labs if they have any recommendations as far as your other medications are concerned. They have an excellent support team that you can contact here.

      1. Thank you Clarissa. I’ve contacted them and there is no interaction with thyroid medication ( of course taking into account to leave half an hour between meds and all supplements in general) so neither the Mucosa or IGG will bind to them. Indeed the timing of the Mucosa or IGG is up to individual preferences, you are right. Only the spores are advised to be taken with food as they help digestion too. Thanks for the reply!

  3. I take these vitamins which are Gluten Free: Will they interfere with any that I have ordered?

    Coq10- 3x day
    Zinc 20mg
    Magnesium taurate 125mg
    Ester- C 500mg
    Selenium- 200mcg
    Vit. K2+Resveratrol
    MK7- 90mcg
    and sometimes Caprylic Acid 600 mg, & Niacin 500mg, off and on B12-1000mcg
    I only want to order this one time, on the Probiotics,Mega Prebiotics and then the Mega Musoca
    will try and see how these go. Thanks

    Vit. K2+Res

  4. Thank you so much for this talk, I can’t wait to start MegasporeBiotic. Would this be something you’d have to use in conjunction with a low fermentation diet, or could you just eat a varied, healthy whole-food GF and dairy-free diet without worrying about carb levels, fodmaps, etc? I hope so, I’m looking for an alternative to low-fodmap and low-carb, because after a lifetime of dieting I find that having too many food restrictions is very stressful.

    1. Hi Nina,

      Awesome to hear you’re looking to expand your diet! It is stressful! And it could really mess up the diversity of your gut microbiome… especially since you mentioned you’ve been on a restrictive diet for so long.

      I would ask your practitioner first, so you can get individualized monitoring… but we’re behind you on expanding that diet! That’s something that a lot of our featured experts really advocate for.

      AND! if you can supplement your efforts with MegasporeBiotic, which is really part of the gut-healing trifecta made by MicrobiomeLabs, that sounds like a match made in heaven!

      Good luck! Are you in the group? We have a very supportive community on Facebook. We’d really love to have you and keep in touch with your progress!
      Here’s where we’re at: The SIBO SOS® Community Group

  5. I have been prescribed restoreflora and megasporebiotics. My gut says to take them separately during the day. Should I? Do they cancel each other out? Or are they better to take together at the same time of day?

    1. Hi Linda – you say they were prescribed… in that case, you should take with the practitioner who prescribed them and see what they recommend.

  6. Beginning the 9th week of Koran’s protocol when we are to start the 4 critical amino acids, megamucosa and Megaprobiotic, do we stay on the Spore biotic and IgG also or stop taking them?

  7. Hello,
    I have severe skin reactions that gets infected as it cracks also suffering form constipation, tingling on my feet, constant burning and other gut issues. Can Kiran’s protocol help me in anyway.

    1. Hi Sakeenah,

      That’s a tricky question! Obviously, we’re not doctors and Kiran is a microbiologist, not an MD. You should definitely be consulting in-person with an MD about your symptoms. That being said, we are understanding more and more how gut health is interconnected to every part of the body! The only way to know for sure if it could help is to give the protocol a try.

  8. Hi
    My husband and I are starting the protocol with Mega Spore. I have a very sensitive gut.
    You mentioned that the Mucosa product helps with die off.
    I had bought and thought it was the Mega IgG2000 that I should take with the Mega Spore to help with die off?

    I am confused as to which one is better for me to start with? I have dysbiosis..

  9. Barbara Sowerwine

    I received an e-mail with an interview with Kiran Krishnan on October 25th. It arrived on my cell phone and on my ipad and computer. I listened to a little of it on my phone that night and determined to come back to it today (the 26th). I opened it on my ipad and listened to the program where Kiran used many illustrations but it did not sound like the program I started last night. After listening to the one on my ipad I went to my iPhone and brought up the program there. It was completely different. It began with Kiran having some technical problems and then proceeded to be a conversation with much information regarding the liver. This was very informative to me as I am having some issues in that area I believe. I went to my computer to bring up the version I listened to on my phone but it was the version I listened to on my ipad. I would really like to have the conversation regarding the liver (it was an hour and a half). Is there some way I can get this one again so I can refer to it? It was most helpful and I would like to hear it again. I am able to store the one that presented the charts. It is the other one I cant’ find. Please help! Thanks so much.

  10. Kingsley Cunningham

    If a person has sibo, can taking the prebiotic powder potentially exacerbate the sibo by feeding the microbes in the small intestine?

  11. I used VIOME testing last year. Is this the type of testing you are referring to as inaccurate and testing is not done correctly, etc.?

  12. I found that presentation quite engaging. I purchased the 90 day protocol. What is a good test to gauge the diversity of the microbiome and the effectiveness of the process?

  13. Good morning I have been suffering with reflux it is not acid based every time I eat my body brings up bile very sticky like wallpaper paste that’s the only way I can describe it I am vegan I don’t know why this is happening also my nose begins to run I sometimes fast for a couple of days just to help my tummy I would be really grateful for some advice from you about what is causing this thank you

    1. Hi John – sorry to hear what you’re struggling with! We’re hosting a free Q&A with Dr. Steven Sandberg-Lewis – who is an expert on acid reflux! – on Nov 1 at 6 PM Eastern. Free to participate – jut join our free Facebook group here: The SIBO SOS® Community Group

      1. Jeanne Formanski

        I would just like to know in regards to the meeting. I have been diagnosed with IBS and microscopic colitis therefore; I occasionally have gas and bloating would this be a beneficial Face Group meeting for me to attend and gain knowledge about how to help my conditions.

  14. I take CREON as a 24 hr stool te
    st showed I make only 87 of normal 4-500 ?? Of that Enzyme!?! AM better (have had Dumping for the 16 months since Fundoplication surgery! Advice????

    1. We’ll email you them as soon as we have them ready. Be sure you join our newsletter list if you’re not already part of it!

  15. Hi there!
    Thank you for this information this is amazing thank you.
    I will start a 9 month antibiotic treatment for a Tuberculosis dormant in my body I have lives with this bacteria for a good 17 years but as I get older I have to address it I guess although I am healthy thank God.
    My question is what supplements can help me rebuild my microbiome, if there is any that can help.
    Thank you for your tine in this matter

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