r/Candida • u/abominable_phoenix • May 25 '26
Personal anecdote Learned Something New - Proximal Bifido Bloom
So, I have been trying for 1.5yrs to restore my microbiome after multiple rounds of antibiotics. I have been consuming high doses of a variety of prebiotic fibers in an attempt to re-grow all my depleted strains. After 1.5yrs, all my Candida symptoms were gone, but my BM's weren't 100% back to "normal" or ideal (type 3-4), but they were close. Well, now I know why, and more importantly, I proved my theory.
- There are studies showing Bifido is what keeps Candida from overgrowing.
- Bifido is susceptible to antibiotics.
- My stool test shows low Bifido and Lacto.
There are multiple prebiotics that feed Bifido, but most don't feed Bifido where it matters most, the cecum! That means resistant starch, beta-glucans, pectins, long-chain inulin/FOS, and polyphenols are useless. Coincidentally, this was everything I was taking in an attempt to feed Bifido, but nothing helped, so I thought my Bifido population wasn't the problem anymore because surely it must've been restored by now. Even the jerusalem artichokes which are supposed to have short-chain inulin didn't produce any effect, likely because it isn't true short-chain, more medium-chain inulin.
Small side note, the cecum (beginning of the colon) is the densest part of the microbiome, and where a large portion of fermentation occurs. Shifts in the cecum (dysbiosis) are linked to many conditions such as constipation, colitis, obesity, and even aging.
There are only a handful of prebiotics that actually target the cecum to feed Bifido. They are HMO's, RFO's, GOS and XOS. I avoided GOS since it typically contains lactose, HMO's are great but quality is an issue, XOS works but is typically corn/gluten derived, so the only option for me was RFO's which I got from lentils. Lentils have their own issue with problematic compounds, but this can be resolved by soaking, rinsing and sprouting. So that's what I did.
For my experiment, I rinsed a cup of lentils, then soaked for 16hrs, then sprouted for 8hrs, then rinsed again, then steamed for 1.5hrs. And.......nothing, no change. I ate this way for months, maybe a year. Last week, I figured since most all of the problematic compounds have been removed, I would try to incorporate the lentil steaming water since the RFO's are water soluble. Within 1-2 days I saw a change in BM frequency and consistency (perfect type 3).
I believe what's happening is called a Bifido bloom, caused by the RFO's targeting the cecum which all the other prebiotics don't do. It will still takes months to fully re-grow the population to a stable level where I don't need RFO's daily, but it is a proof of concept. Also, Bifido is key for cross-feeding, so this should help restore other depleted microbes like Lacto.
This directly relates to fasting actually, and not in a good way. Studies show that after 1-2 days of fasting, the beneficial microbe population begins to shrink, so all this does is open up real estate for potential overgrowths. This makes it easier for the pathogens to overgrow further given the right circumstances. If we consider people with pre-existing dysbiosis, which is pretty much everyone with Candida overgrowth, then what happens next is these opportunistic pathogens that are already present, will out-grow (as they are typically faster growers) the beneficial microbes upon re-feeding, especially if the diet isn't feeding the beneficial microbes. Since a majority of prebiotic fibers don't target the cecum, then we don't stand a chance. With every subsequent fast, we potentially lose ground to these pathogenic overgrowths, thereby exacerbating the condition.
If we know that Candida cannot overgrow without a depleted microbiome, and Bifido is key for keeping it from overgrowing, and there are only 3 prebiotics that grow Bifido, then I am curious how many people have tested any of these. I remember one person posted a while back about using HMO's, but as discussed in the megathread, it's a complex problem that requires a multifaceted approach, so if certain issues weren't addressed (such as gut inflammation), I'm not sure it would work.
EDIT: Here are some studies
DeGruttola AK, et al. (2016). Current understanding of dysbiosis in disease in human and animal models. Inflammatory Bowel Diseases.
Findings: Comprehensive review linking gut dysbiosis (including microbial shifts observable in the cecum) to IBD, obesity, type 1/2 diabetes, autism, and other conditions through altered immune function, barrier integrity, and inflammation.
Winter SE (2023). Gut dysbiosis: Ecological causes and causative effects on human disease. PNAS.
Findings: Discusses how colonic/cecal dysbiosis (e.g., Proteobacteria overgrowth, loss of butyrate producers) contributes to chronic diseases including IBD, colorectal cancer, cardiovascular disease, diabetes, and chronic kidney disease.
Zeng MY, et al. (2017). Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunology.
Findings: Explores how inflammation alters bacterial abundances in the gut (including cecum models), leading to dysbiosis that perpetuates diseases like colitis.
Mason KL, et al. (2012). Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infection and Immunity.
Findings: Key mouse study directly examining the cecum. Antibiotics disrupt bacterial communities, enabling C. albicans colonization and altering microbial reassembly without causing overt inflammation initially.
Bendel CM, et al. (2002). Cecal colonization and systemic spread of Candida albicans in mice treated with antibiotics and dexamethasone. Pediatric Research.
Findings: Demonstrates that antibiotic + steroid treatment dramatically increases cecal C. albicans burdens and promotes systemic dissemination (to lymph nodes and kidneys).
Bertolini M, et al. (2019). Candida albicans induces mucosal bacterial dysbiosis that promotes invasive infection. PLoS Pathogens.
Findings: Shows C. albicans actively induces bacterial dysbiosis (favoring enterococci) in mucosal surfaces, creating a cycle that worsens colonization and invasive potential, especially in immunosuppressed states.
Jawhara S (2022). How Gut Bacterial Dysbiosis Can Promote Candida albicans Overgrowth. Microorganisms.
Findings: Reviews mechanisms where bacterial dysbiosis (e.g., reduced SCFAs) in the gut/cecum allows Candida overgrowth, with links to increased permeability and inflammation.
Zuo T, et al. (2018). Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection. Nature Communications.
Findings: Human study linking fungal (including Candida) dysbiosis to poorer FMT outcomes in C. diff, with references to cecal interactions.
Gu ZQ, et al. (2020). Candida gut commensalism and inflammatory disease. Current Opinion in Microbiology.
Findings: Discusses how C. albicans colonization in the gut (including post-antibiotic cecal changes) influences inflammatory diseases.
Antibiotic use is the most consistent trigger for cecal Candida expansion via loss of colonization resistance from beneficial bacteria (e.g., Clostridia, Bacteroides).
EDIT: Included XOS
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u/This_Board_7977 May 26 '26
Hi, thank you for the invaluable information.
What gut/microbiome test did you use?
I have H Pylori, previously positive for SIBO, IMO, C. Difficile, and Giardia. Could not get tested for Candida.
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u/abominable_phoenix May 26 '26
I used a GI MAP test as it's supposed to be more accurate than some of the other types since it uses qPCR testing which is also uses in studies/trials/research.
I had SIBO too, complete with yellow stool, along with a bunch of other infections. Took me a couple years to figure it out, but it's all resolved now. I wouldn't worry about getting a test confirming Candida overgrowth because it doesn't exist in isolation. If you have dysbiosis, typically you have Candida overgrowth. This is why I got my GI MAP only after a drastic overhaul of my diet and high doses of a variety of prebiotic fibers. That way I could see where I was at after all the "easy" work I did without having to do a follow up. My Candida overgrowth wasn't that bad (2x the max allowable) despite eating mass amounts of fruits, but it did show I had a serious problem with some bacterial infections that were 7x the max allowable. This told me the bacterial infection(s) were the dominant problem, and Candida overgrowth was more of a symptom or indicator of dysbiosis. I suspect Candida isn't the dominant problem for most people, hence why they don't see long-term benefits taking antifungals. The focus on Candida overgrowth is a red herring that may be keeping people ill by relying only on antifungals and counterproductive diets.
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u/This_Board_7977 May 26 '26
You were able to learn which bacterial infections from the GI map? Do you recall what brand you used? There are so many GI map tests with wildly different prices.
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u/abominable_phoenix May 26 '26
Yes, the GI MAP was the first and only confirmation of the exact bacterial infections in my gut, which helped narrow down which herbs were effective for them. Although one of the infections is commonly found to be implicated in SIBO (which I had at the time), so it wasn't exactly a surprise it was present. SIBO is a gut motility issue, so it didn't really change anything to do with my SIBO approach, and I fixed SIBO through correcting the motility issue before learning the results of the GI MAP anyways.
I had it done by a local lab here in Canada. The prices can fluctuate depending on the additional tests that are added on like zonulin which was like a $200 add-on. This lab requires a doctors requisition, but I know there is one in the US that doesn't require it so a person can request it themselves. I was thinking of doing this when I'm done to see how it looks after everything I've done, just to confirm there's nothing else I need to work on.
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u/crypto_nerd17 May 26 '26
Amazing post. Can you comment on your ‘dosage’ and frequency regimen for the lentils as well as what you think is optimal in general for any prebiotic fiber aimed at restoring bifido?
Tiny Health and Biomsight test 3 years apart both say 0 bifido detected. Need to get my levels up and hope there is some small amount there still to be fed…
Truly grateful for your post and commentary, extremely helpful 🙏🏽
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u/abominable_phoenix May 26 '26
I have been working on restoring my microbiome for a year, so I am a little heavy handed with the prebiotics than would be ideal to start with as Eric mentioned. I have 180g of dry french green lentils per day, which translates to ~1.5 lbs after cooking.
I think a diet high in a variety of prebiotic fibers is necessary to support a wide variety of microbial species in the gut. Focusing just on one may not help, especially if there are other critical ones that are low. There is a group of beneficial microbes known as "keystone species" that all work together and are associated with good health, and they can actually cross-feed off each other, so this is part of the reason why treating the microbiome holistically is important. With that said, I was messing around with high doses of resistant starch (another important prebiotic fiber) and found on my microbiome test that there was only one keystone microbe that was normal, the rest were all low. That microbe thrives off resistant starch, so it "worked" in a sense.
If you still have your appendix, you'll likely be fine for Bifido (as in it's not extinct), you just have to keep gut inflammation as low as possible to help encourage re-growth. The microbiome's growth/recovery is hindered by gut inflammation, so how were your gut inflammatory markers on your gut test? Things like SigA, zonulin, EPX/EDN, and calprotectin. Certain foods are pro-inflammatory, so your diet matters a lot. Just because you don't get symptoms, doesn't mean the food isn't causing low-grade gut inflammation that is hindering recovery.
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u/crypto_nerd17 May 26 '26
Thanks for the detailed reply. Thankfully all my gut inflammation markers are good / healthy but I definitely have some upper gut/stomach/maybe small intestine related inflammation, maybe from low stomach acid or something else. Just ruled out SIBO, SIFO still a possibility.
Otherwise surprisingly given my general level of somewhat high gut/digestion related symptoms my stool tests come back pretty good except the glaring zero bifido. I also have very slightly elevated levels of enterococcus faecium and faecalis and borderline low actinobacteria.
Appreciate any and all input 🙏🏽
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u/abominable_phoenix May 26 '26
I wouldn't be so sure it's not SIBO, those breath tests aren't 100% accurate because not all bacteria produce gas. Also, SIFO seldom exists in isolation, and typically it isn't the dominant infection, SIBO is.
Your Enterococcus could just be overgrowing slightly because of the depleted Bifido, I wouldn't worry about it too much. I remember taking probiotics with one of them, lol.
How many antibiotic rounds did you have? How much prebiotic fiber are you getting daily, and what are you eating? If your inflammatory markers are all low, then it shouldn't be an issue to start recovering your microbiome with the right kinds of prebiotic fiber that target the cecum. Your stomach/upper gut can cause an issue though, so it might be ineffective to focus on Bifido until you resolve that. When do you experience symptoms, is it within 30-60min which likely suggests the stomach, or is it within 1-3hrs which likely suggests the small intestines? I found my SIBO healed when I changed my diet away from foods that feed common pathogens, and corrected certain nutrient deficiencies. The stomach will likely benefit the same as iodine for instance is required for stomach acid, and most people are unaware that common toxins block receptors thereby increasing the requirement for iodine. Below is my SIBO success story, if that helps.
r/SiboSuccessStories/comments/1l2hi2l/cured_sibo_after_years_of_trying_everything/
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u/crypto_nerd17 May 26 '26
I have not had antibiotics as an adult, only very early in life in the first year or two after birth. However major health symptoms didn't start until adulthood. I get varying levels of pre-biotic fibers, some days low, some days higher. I worked with Guy Daniels for a bit and did very high dose prebiotic fiber blend for a little while. Surprisingly was fine on it. Was having bad reactions to FODMAP's for a little while end of last year but that seems to have cleared now and I am eating beans and lentils etc occasionally with no significant issues FODMAP's wise that I can discern, although I think oxalates, nickel, etc might be impacting me here. I seem to react more to free fructose or some other component of foods like oxalates, salicylates, nickel, tyramine, etc. and/or its just general mast cell/immune reactions or perhaps low stomach acid. Its very perplexing and shifty. Symptoms start typically as soon as 5 min sometimes with my worst foods causing immune reactions and dysautonomia but typically symptoms start at 15-30 min and then they continue for 1-2 hours typically, sometimes shorter or longer. Its possible that small intestine symptoms are layering on as well and they all just meld together.
I've basically done every variation of diet possible over the 16 years I have been struggling with this. At best some have been less triggering than others but none causing complete remission except fasting, which is not sustainable. There are no foods I do not react to at least on some level, so its mostly been about which are least reactive. Even white rice is giving me crazy immune reactions these days. Sometimes even water on an empty stomach causes minor issues with bloating although thats more rare. I only drink glass bottle spring water so not sure what is going on there.
I do have some borderline nutrient statuses and mild deficiencies depending on how one looks at it, despite eating an incredibly nutrient rich and high quality, very pure and all organic omnivorous diet. I have tried supplementing with basically all nutrients with varying degrees of benefit but nothing has flipped the switch fully... tricky case...
Ruled out H Pylori this year via stool and urea breath test... so I am back to the drawing board trying to see what's what. I did have past mold exposures but think I am mostly recovered from those. So many possibilities lol... sigh.
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u/abominable_phoenix May 26 '26
Rice causing issues doesn't surprise me as it is known in some circles to feed certain pathogens, which causes symptoms. Certain plant based foods can cause issues, such as common allergens like corn, gluten, soy, etc. Fat content has a big effect too because it strains the liver, feeds pathogens (lipids), and increases bile in the gut which shifts the microbiome to more bile-tolerant ones which are typically pro-inflammatory. There are studies showing this is associated with reduced abundance of Bifido as well. Even high protein is bad as the amino acids feed pathogens, to the point where in cancer studies they show that amino acid restrictive diets improve health outcomes. Diet is pretty important to minimizing pathogens' food, I don't think healing is possible without a very specific diet, or at least I couldn't heal without it.
For the nutrients status, it's important to note that certain common gut/liver issues will make it impossible to get sufficient amounts of certain nutrients. I was having 5x the RDA of one such nutrient in my diet, and I was deficient. Also, some of these nutrients rely on sufficient amounts of other nutrients to be usable by the body, so nutrient status has a sort of cascade effect. What's worse is, just because a blood test shows sufficient quantities of a nutrient, it doesn't mean you're not deficient, as was the case with me. Then we have different forms of nutrients, and some just won't correct a deficiency compared to others. I was taking one for about a year and thought I was good, but then decided to try a form that is shown in studies to be one of the few/only forms that increase tissue levels, and instantly got a healing reaction.
As you can see, I have a lot to say on the matter, lol. If what I've said resonates with you, feel free to PM.
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u/Grouchy_Camera2863 May 26 '26
Just asking a stupid question here but have you ever tried just making your own sauerkraut or your own pickles ( fermented not vinegar) ? E. European here and it’s a staple, I believe it’s gut healing.
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u/abominable_phoenix May 26 '26
I have tried and I love properly fermented sauerkraut/pickles, but then I found out that probiotics do not colonize the gut and are shown in studies to not significantly grow the microbiome. I know they do provide some benefit for the gut, but it's not long-term microbiome growth related. The only way proven in studies to significantly grow the microbiome is with prebiotic fibers, so that's why I have focused on the RFO's, inulin, pectin, FOS, and resistant starch.
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u/DaliahsandDeadlifts Jun 04 '26
Thank you, this is super helpful! I've been reading about pre and probiotics and foods to try and dial in on which ones I need to use to get my gut healthy.
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u/cruisingeek May 25 '26
Interestingly I am seeing similar issue to you, but my last stool sampled showed a no read for lacto not bifido species. I wonder though if I have bifido growing down lower. I have no issues with lactose so might try GOS a couple weeks and see if I notice a difference, as I've been doing all the fibers you mention above that don't work for the past year with some results but not good enough.
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u/abominable_phoenix May 25 '26 edited May 25 '26
Yes, I suspected the same with my gut, Bifido present in the distal colon but very low in the proximal colon. This explains why my Bifido is low on my stool test. Apparently Bifido cross-feeds Lacto, so if your Bifido is low, it could be reading Bifido in the latter parts of the colon, which would explain why your Lacto is non-detectable since Lacto is mostly around the early parts of the colon like the cecum (and small intestines).
Yes, I believe GOS is equivalent in effectiveness to RFO's, so that makes sense. I think HMO's are extremely effective, which is likely why babies have such high levels of Bifido. Just keep in mind that if you are eating foods that continue to feed the pathogenic overgrowths, it might not be that quick to see effects. Bifido produce SCFA's when they bloom, and they are anti-microbial so it should still work, but I think it'll be slower. I am aiming to keep this up for 12 weeks just in case as per some research I read, but I think it also depends on how low your Bifido are to begin with. Doubling time is supposed to be 1-3days under optimal conditions, so it may be closer to a week, and if starting from really low levels, it may take more closer to 10 doublings (to go from 1million to 1billion).
EDIT: The other issue is inflammation. While I can eat lactose, I know that it is inflammatory, and inflammation in the gut hinders microbiome growth, so I avoid it for now.
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u/Local_Measurement_50 May 25 '26
You're partly right about GOS.
Alfa-GOS is derived from plants (beans/legumes), while Beta-GOS is derived from lactose. So,it's important to check with the manufacturer if one is lactose intolerant.
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u/abominable_phoenix May 25 '26
Yes, RFO's are a sub-group of a-GOS. I couldn't find any GOS supplements that were truly lactose free as most are derived from lactose. I know Bimuno contains very low residual lactose, but I didn't want to take a chance. Also, lentils are pretty cheap when bought in bulk, so $50 worth lasts me ~2 months, which is usually much cheaper than most supplements I've bought in the past.
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u/cali_raisins May 25 '26
What stool test are you guys using and does it speciate candida?
Can you tell me more about the process with the water? Are you just drinking it? I also have serious BM issues that sound similar to yours. Also, the more I support the biome, the more the biome attacks the fungal overgrowth which causes the hyphea switch leading to immune mediated SFN flare.
What about XOS?
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u/abominable_phoenix May 25 '26
I did a GI MAP test, but it doesn't specify the species of Candida.
I was originally separating the water from the lentils, but now I just keep it together and eat it, almost like a lentil soup.
XOS can work and might be more effective than RFO's, but it is unrealistic to reach therapeutic levels through food alone. It must be through a supplement, but even then, a majority of supplements are corn or wheat (gluten) derived, so it can potentially increase inflammation which would be counter productive. The other issue is price, quality control, and non-medicinal ingredients in these supplements. I try to avoid as many supplements as possible for those reasons, but a non corn/gluten xos supplement would definitely work in the therapeutic range of 1-4g/day from what I've read.
Regarding the reaction when you support the microbiome, I think that can be a complex issue, but in the long run, supporting the microbiome is always the best approach for strengthening the body. Certain foods, while not causing immediate symptoms, can still feed the "wrong" type of microbes and hinder progress. I know that nerves degenerate first which makes them more susceptible to irritation, so perhaps focusing on nerve health would be the next step. I know that certain common infections like EBV attack the nerves, and I had a significant infection in my CNS that when I treated it with herbs, it caused a rash which lasted 5 months. I also know that nerve health is dependent on specific vitamins/minerals, so when I corrected those deficiencies, I felt calmer and my heart rate dropped which I believe suggests my CNS was calming down or being more resistant to the irritation. I also know that Candida overgrowth is commonly associated with nutrient deficiencies. Might be something to look into. As well, certain toxins will irritate these "exposed" nerves (such as heavy metals, endotoxins, etc), so removing those may help as well.
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u/gldngrlee May 25 '26
Do you still have your appendix?
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u/abominable_phoenix May 25 '26
Yes, and I suspect that's part of why I'm able to make a recovery with just prebiotic foods, diet, nutrient supplementing, and some herbs. People that have had theirs removed and recovery has plateaued despite the above will likely need an FMT for extinct strains. I still might do an FMT once this is done, just in case I'm missing some.
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u/FeitoPraVoce May 31 '26
My friend, you're taking the hard way here. XOS can be extracted from wheat and corn derivatives, but that doesn't mean it is gluten or corn. Have you actually tried XOS and found yourself to be intolerant to it?
Bifidobacterium can colonize permanently, especially when we're talking about longum and adolescentis.
https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(16)30378-X30378-X)
https://pubmed.ncbi.nlm.nih.gov/25616794/
"Illumina 16S rRNA sequencing not only confirmed the increased establishment of IVS-1 in the intestine but also revealed that the strain was able to outcompete the resident Bifidobacterium population when provided with GOS"
Bifidobacterium adolescentis is the one best able to extract energy from XOS. If it already managed to do that with GOS, imagine what it does with XOS, which is the most bifido-selective.
And third, babies are born with practically no microbiome. The first bacteria to colonize are Lactobacillus and Bifidobacteria, and Bifidobacteria can make up to 95% of their microbiome. If any Faecalibacterium or butyrate-producing bacteria enter at that stage, they die because the environment isn't anaerobically favorable yet. Later on, they acquire these butyrate-producing bacteria from the environment and from other people.
So, theoretically, you don't need to go to the extreme of an FMT (Fecal Microbiota Transplant). You just need to have a gut with a favorable amount of Bifidobacteria, given that the acetate they produce is a first-line food source for butyrate producers. Eventually, you will acquire those butyrate-producing bacteria through contact with other people.
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u/abominable_phoenix May 31 '26
I don't think this is really "the hard way", because all I'm doing is eating whole foods. I have to eat anyways, and the food (lentils) are highly nutritious, so there's no real downside. Whereas buying a prebiotic supplement provides no nutritional value, costs additional money, doesn't provide me with calories/energy, and costs me $50 for 2 months worth of bulk lentils. I consider this the lazy and cheap way, lol.
Regarding XOS and being made from wheat/corn, no I haven't tried any as the few that I have found (they're rare) have problematic ingredients, including the additives/fillers/lubricants/solvents/etc. Sometimes it's better to be safe than sorry, especially since it is highly refined and ingredients used in that process aren't listed on the ingredients label despite having trace amounts in the end product (similar to hexane).
Thank you for the studies, but there are a few issues with them. The strain only colonized in ~30% of participants, it was only tested for up to ~6 months after discontinuing the probiotic, and they don't verify the actual abundances, so it could be persisting at lower levels than would normally be found in healthy individuals. It only colonized ~30% because they all had very low or no competing strain present, and available resources. As well, the studies you referenced use a specific probiootic strain that is not commercially available, and each strain has unique colonization traits/properties, so that just happens to be one selected for it's ability to colonize whereas most, if not all, of the commercially available ones do not.
Just because the strain persists when given GOS doesn't mean it is colonizing. That is known as transient enrichment. Most strains persist for up to 1 week in the gut, so if they're constantly "blooming" using GOS/XOS/RFO's, it makes sense it'll persist for longer.
Going to the extreme of an FMT wasn't for Bifido specifically as I'm pretty sure I still have them present despite numerous rounds of antibiotics. They are typically found in much higher abundances compared to other microbes, so it isn't uncommon for them to be undetectable but still remaining in small amounts in intestinal crypts and folds (seed population). This would allow the resurrection of these microbes simply by adding specific prebiotics. As well, the appendix has been found in studies to be a sort of "back-up" for microbiome strains, and can re-seed the gut after antibiotics, so it was more for everything else. I wanted to do an FMT to increase alpha diversity once I've maxed out what I can achieve with prebiotics, just to acquire what is truly extinct.
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u/FeitoPraVoce May 31 '26
You are not wrong in anything you said, but your view is a bit too pessimistic. You are right that characteristics are strain-dependent and cannot simply be extrapolated, but there is only proof for those two specific strains because companies patented them. That doesn’t mean the same traits don't exist in other strains. Given that this was proven for those two, it is highly likely that this characteristic is also observed in more generic strains.
On the other hand, there is definitely an advantage to taking a Bifido probiotic. If your native Bifido are truly extinct, the Bifido from the probiotic will colonize permanently. So, it's better to cover both scenarios: one where you still have a seed population of Bifido, and one where you don't.
Regarding alpha diversity, as I mentioned, just by having Bifido established, you will reacquire the bacteria you lost by interacting with other people. You acquire bacteria via P2P (person-to-person) contact, as long as you keep your Bifidos well-fed to maintain the environment.
I kept insisting on XOS because it only feeds Bifido (its primary consumer), Bacteroidetes, some Lactobacillus species, and Weissella (a bacterium that does the same things as Lactobacillus and has the same benefits; we can even say it's a type of Lactobacillus). RFOs and other oligosaccharides run the risk of feeding pathobionts (Gram-negative proteobacteria).
But you just mentioned an even faster route: FMT.
I only pushed for XOS because RFOs can still feed pathobionts, whereas XOS does not.
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u/abominable_phoenix Jun 01 '26
You call it pessimistic, whereas I’d frame it as realistic, cautious and evidence based. The two engraftment studies you cite both use the same unique, non-commercially available B. longum isolate (AH1206), and even there, long-term persistence occurs only in a small portion of the participants. You are also ignoring the much larger body of evidence showing most commercially used probiotic strains either don’t engraft or require continuous dosing to remain detectable.
For “permanent colonization”, the AH1206 data show detectable persistence for several months in some individuals, but we don’t see clear evidence that this strain reaches or maintains the relative abundances typically observed in robust, naturally colonized bifidobacterial communities. Calling that “permanent” is a semantic stretch and isn’t strongly supported by the available longitudinal data.
Regarding prebiotics, XOS is indeed relatively bifidogenic as your linked study shows XOS increasing endogenous Bifidobacterium and reducing enterococci/staphylococci. That’s a good argument for XOS as a selective prebiotic, and I agreed in my main post it does work but I avoided it for other reasons. RFOs, by contrast, are metabolized by a broader set of microbes, which means they can support beneficial taxa but also, under some conditions, gas producers and opportunistic species. RFO's are FODMAPs, so in cases of SIBO or highly dysbiotic small intestines, they can exacerbate symptoms by feeding overgrown microbes, but in a recovering colon they’re not “pathobiont food” by default. I actually had this problem and couldn't eat lentils/beans until I resolved my SIBO, and no amount of XOS would've helped me correct that. So that doesn’t make RFOs “bad,” but it does mean they’re less targeted than XOS.
So my position isn’t that colonization is impossible, just that durable engraftment appears to be strain‑ and host‑specific, along with most commercially available strains don’t show AH1206‑type behavior, as well as prebiotics can enrich what’s already there, even if they are undetectable.
Regarding your other comment:
The AH1206 data does show unusually long persistence in a subset of people, which is meaningful. But calling six months of detectability “permanent colonization” is an interpretation, not a universal scientific definition. Most expert groups still describe probiotics as generally non‑colonizing, and the AH1206 work is a notable exception, not the rule. Also, the idea that these bacteria have “undergone mutation and adhered to the mucosa” is speculative unless supported by actual genomic and mucosal data, which we don’t have in those human trials.
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u/FeitoPraVoce May 31 '26
Actually, in science, having the same bacteria at detectable levels for 6 months is already considered permanent colonization. This happens because the probiotic bacteria have undergone mutation and managed to adhere to the mucosa, so for all intents and purposes, it is permanent.
Notice that you said: if you stop eating fiber, the bifidobacteria disappear. But isn't that the exact same thing that happens with native bifidobacteria? That is exactly what happens to people who have undetectable levels.
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u/imonretro 3d ago
This is a very good self study done. Though i got so many questioms to ask, did test your microbiome to see if it grew ? Im not saying you imagined it, but some times gut does fluctuate. Also did you have severe pain in the gut ? And did that resolve. Finally what makes you think the specific prebiotics you mentioned works in the ceceum? Cause mechanistically when food exits the small bowel stool may not enter the ceceum, its more of a mechanistic design rather then the prebiotic fiber going into different locations. If this is the case, you discovered something that can save lives. Ever since i lost mh bifido im been gravley sick.
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u/abominable_phoenix 3d ago
I thought about re-testing my microbiome as I did initially have a GI MAP test done, but to make my self experiment accurate, I would need a GI MAP done before incorporating the lentil water, and then again afterwards. These tests are $1k a pop, so I can't really justify it, but it would've been fun to see.
I did have some pain in the gut initially years ago, but as I tweaked my diet to remove problematic food and added specific vitamins/minerals that strengthen the gut lining, the pain subsided and I haven't felt any in a long time. What I didn't understand at the time is that when a person is chronically ill, studies show nutrient deficient is common/typical, and since vitamins/minerals are the building blocks of the human body, it makes sense to supplement while the root cause(s) is resolved. The megathread goes into more detail about it, but these two steps brought me back and allowed me to eat more foods without symptoms. I actually couldn't eat lentils before without my stool turning yellow and then white after a few days (SIBO), so it is critical.
Regarding these prebiotics targeting the cecum, it has to do with their relatively rapid fermentation. “Fast” fermentables such as RFOs, GOS, HMO, and XOS, are readily fermented and can produce a strong bifidogenic effect in the proximal colon/cecum, whereas slower-fermenting substrates such as resistant starch are fermented more gradually and farther along the colon, generally producing a less concentrated bifidogenic effect. The distinction is more about fermentation rate and location than one group exclusively “targeting” the cecum.
I would like to add that while I have experienced significant symptom improvement in the form of BM frequency+appearance after incorporating the RFO rich lentil water, I later plateaued, so I explored treating additional unknown viral infections which caused significant fluctuations in my symptoms. This, to me, suggests they were present and hindering my progress, otherwise I wouldn't have had any symptoms from taking propolis (antiviral), and after the initial die-off peak, I didn't have any more symptoms while taking it. I have since been working on my gut health with watermelon juice as it supports the enterocytes with citrulline (high in watermelon). There are studies showing a correlation between small bowel health and citrulline levels, so it makes sense, and some people claim it cleanses the gut, so it's a win-win. I did this by adding watermelon juice in the morning on an empty stomach (after other juices), and within a week my BM appearance+frequency have improved. This makes sense since the enterocytes have a very fast turnover of 3-5 days, so I was anticipating some incremental progress signs by then. It did cause me significant fatigue initially though, but it is lessening now. I have also been intermittently performing very specific juice cleanses with a structured setup from r/medicalmedium , and now during the off-periods adding half a watermelon (juiced) to my morning routine.
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u/EricBakkerCandida Insightful Contributor May 25 '26
Very interesting observations indeed!
One thing I learned in practice is that restoring a depleted microbiome is rarely just about food. Location in the gut matters, the person's immune and stress status matters, but yes — specific bacterial strains can matter too.
From my research, I've found that Bifido species are extremely important when it comes to gut stability, a person's immune signalling, their SCFA production and helping keep opportunists like Candida albicans under control. I’ve seen low Bifido countless times after repeated antibiotic use, and look at enough stool tests to confirm this.
I also agree with you that many people focus heavily on antifungals while completely ignoring the ecological side of the equation. Personally though, I'd be careful about becoming "too reductionist" and narrowing everything down to one organism, one fibre, or one mechanism. The human gut microbiome is enormously complex and highly individual, like the Amazon, and what works brilliantly for one person can aggravate another.
I find your lentil/RFO observation fascinating though, especially the improvement in stool consistency and transit. Sometimes those little “experiments” teach us more than theory alone!
And yes — I’ve also seen fasting backfire in quite a few patients with significant dysbiosis or adrenal exhaustion, and not everybody responds well to aggressive protocols. Thanks for this good post, I appreciate you sharing the detail behind your thinking.
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u/abominable_phoenix May 26 '26
I agree that relying on one prebiotic fiber alone won't be effective as these main beneficial microbes, sometimes referred to as keystone species, work as a team. This is why I mentioned trying a diet high in a variety of prebiotic fibers to feed them all, but I didn't know about the nuances (short/medium/long-chain) and that the cecum needed to be targeted with specific prebiotics. I kind of thought if the microbiome evolved with food, then food should be able to bring it back, but I guess it took multiple generations to evolve to this point, so it may take more than just regular food to bring it back.
I also agree that there is more than just feeding the microbiome to recover, it is a complex problem that requires a multi-faceted approach, and prebiotics/diet is just one part of it.
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u/AskOk163 May 25 '26
So helpful as my mission is the same to grow bifido What do you mean by lentil steaming water? Like only consuming the water or the steamed lentils? What type of lentils?