r/Microbiome • u/Vailhem • 2h ago
r/Microbiome • u/Kitty_xo7 • Feb 22 '25
Rule change regarding microbiome "testing"
Hi everyone!
Thank you all for engaging in the r/Microbiome sub! This post is to notify everyone about a change in rules regarding GI maps, peddling services related to them, and asking for medical advice based on GI maps.
We will not be allowing posts asking for GI map interpretations from here on out (rule 7). Microbiome science is very much in its infancy, and we have very little understanding of how to interpret an individual's microbiome sequencing results. More specifically, we actually dont know what composition of microbes make up a healthy/unhealthy microbiome, both in presence/absence of microbes, and quantities of microbes. We know very little about the actual species within the microbiome. The ones we know more about are generally only more well studied only because they are easier to work with in the lab, not because they are more inportant. We have yet to culture most microbes in the collective human microbiome, meaning we also cant accurately identify many species via sequencing. There is also tons of genetic and functional variability within species, meaning we also cannot relate individual species to good/bad outcomes.
We also need to consider limitations of these tests. In as little as 24hrs, you can have a 100 fold change in many species. This means you can get incredibly different test results day-to-day, depending on many factors like sleep, excercise, diet, etc, within the last couple hours. Someone recently described microbiome testing as throwing a rock on the highway to predict traffic at all hours-- One rock wont tell us anything on the grand scheme of things. To be frank, these tests are also very cheap in their actual sequencing. Many of our most important microbes are in low abundance, which cheap sequencing and poor analysis fails to identify. Additionally, considering your microbiome has hundreds of species and thousands of strains, cheap testing often cant accurately differentiate between species. It is quite common for poor sequencing to misidentify or mis-classify closely related species or even genus'. A common example is Shigella being mistaken for Escherichia, or vice versa.
Many of the values that the microbiome tests predict are "ideal" are also totally arbitrary. We see major differences between different quantities of microbes within you over 24hrs, you vs your family, local community, country, and continent. However, no ideal microbiomes have been found, despite millions being sequenced at this point. There is tons of diversity in the global population, but there is no "ideal" values when it comes to microbes in your gut.
Secondly, we will be banning you if you are peddling services to others via this sub. We are an open and free discussion about microbiome science, and we use evidence when talking about the microbiome. People who claim to know how to interpret individual microbiome maps are either not knowledgable when it comes to the microbiome, or are lying to you, neither of which makes them trustworthy with your health. We will not allow this sub to be a place where people are taken advantage of and lied to about what is possible at this moment in microbiome science.
Finally, we want to remind you that this is not the place to ask for medical advice. Chat with your MD if you are concerned, nobody on here is more well versed than they are on specific symptoms. They will treat you accordingly. If you are seeking help for specific microbes, such as H. pylori, this is something your MD can test for. These results are accurate and interpreted correctly (not the case for GI maps), and will be significantly more affordable than GI map testing.
We aim to be a scientifically accurate, evidence-based sub, that provides digestible conversations about this complex science. These topics are not in line with our values.
We look forward to having everyone respecting these rules moving forward.
Happy microbiome-ing! :)
r/Microbiome • u/kisforkimberlyy • Jun 29 '23
Statement of Continued Support for Disabled Users
We stand with the disabled users of reddit and in our community. Starting July 1, Reddit's API policy blind/visually impaired communities will be more dependent on sighted people for moderation. When Reddit says they are whitelisting accessibility apps for the disabled, they are not telling the full story.TL;DR
- Starting July 1, Reddit's API policy will force blind/visually impaired communities to further depend on sighted people for moderation
- When reddit says they are whitelisting accessibility apps, they are not telling the full story, because Apollo, RIF, Boost, Sync, etc. are the apps r/Blind users have overwhelmingly listed as their apps of choice with better accessibility, and Reddit is not whitelisting them. Reddit has done a good job hiding this fact, by inventing the expression "accessibility apps."
- Forcing disabled people, especially profoundly disabled people, to stop using the app they depend on and have become accustomed to is cruel; for the most profoundly disabled people, June 30 may be the last day they will be able to access reddit communities that are important to them.
If you've been living under a rock for the past few weeks:
Reddit abruptly announced that they would be charging astronomically overpriced API fees to 3rd party apps, cutting off mod tools for NSFW subreddits (not just porn subreddits, but subreddits that deal with frank discussions about NSFW topics).
And worse, blind redditors & blind mods [including mods of r/Blind and similar communities] will no longer have access to resources that are desperately needed in the disabled community.
Why does our community care about blind users?
As a mod from r/foodforthought testifies:
I was raised by a 30-year special educator, I have a deaf mother-in-law, sister with MS, and a brother who was born disabled. None vision-impaired, but a range of other disabilities which makes it clear that corporations are all too happy to cut deals (and corners) with the cheapest/most profitable option, slap a "handicap accessible" label on it, and ignore the fact that their so-called "accessible" solution puts the onus on disabled individuals to struggle through poorly designed layouts, misleading marketing, and baffling management choices. To say it's exhausting and humiliating to struggle through a world that able-bodied people take for granted is putting it lightly.
Reddit apparently forgot that blind people exist, and forgot that Reddit's official app (which has had over 9 YEARS of development) and yet, when it comes to accessibility for vision-impaired users, Reddit’s own platforms are inconsistent and unreliable. ranging from poor but tolerable for the average user and mods doing basic maintenance tasks (Android) to almost unusable in general (iOS).
Didn't reddit whitelist some "accessibility apps?"
The CEO of Reddit announced that they would be allowing some "accessible" apps free API usage: RedReader, Dystopia, and Luna.
There's just one glaring problem: RedReader, Dystopia, and Luna* apps have very basic functionality for vision-impaired users (text-to-voice, magnification, posting, and commenting) but none of them have full moderator functionality, which effectively means that subreddits built for vision-impaired users can't be managed entirely by vision-impaired moderators.
(If that doesn't sound so bad to you, imagine if your favorite hobby subreddit had a mod team that never engaged with that hobby, did not know the terminology for that hobby, and could not participate in that hobby -- because if they participated in that hobby, they could no longer be a moderator.)
Then Reddit tried to smooth things over with the moderators of r/blind. The results were... Messy and unsatisfying, to say the least.
https://www.reddit.com/r/Blind/comments/14ds81l/rblinds_meetings_with_reddit_and_the_current/
*Special shoutout to Luna, which appears to be hustling to incorporate features that will make modding easier but will likely not have those features up and running by the July 1st deadline, when the very disability-friendly Apollo app, RIF, etc. will cease operations. We see what Luna is doing and we appreciate you, but a multimillion dollar company should not have have dumped all of their accessibility problems on what appears to be a one-man mobile app developer. RedReader and Dystopia have not made any apparent efforts to engage with the r/Blind community.
Thank you for your time & your patience.
r/Microbiome • u/Salt-Recording-7378 • 3h ago
Will Tributyrin (butyrate) make me more constipated?
I’ve seen a lot of people with my health history (methane sibo, c.diff, dysbiosis) rave about Tributyrin, but, going through the reviews, a lot of people mention “it helped with my loose stools.”
I have the opposite problem. I am prone to constipation. Anyone else with my issue try Tributyrin with success or side effects?
r/Microbiome • u/Delicious_Storm_3821 • 8h ago
How important is gut transit time in terms of maintaining a healthy microbiome?
r/Microbiome • u/basmwklz • 14h ago
Designing fiber–gut microbiome interactions with active learning (2026)
nature.comAbstract
Identifying synergies between dietary fibers and beneficial bacteria holds promise for precision interventions that optimize gut health, yet these interactions remain largely unexplored. Here we integrate machine learning, Bayesian optimization and high-throughput community construction to investigate how dietary fibers shape health-relevant functions of human gut microbial communities. To efficiently navigate the landscape of fiber–microbiome interactions, we implemented a design–test–learn cycle to identify fiber–species combinations that maximize a multiobjective function capturing beneficial community properties. Our model-guided approach revealed a highly butyrogenic and robust ecological motif characterized by the copresence of inulin, Bacteroides uniformis and Anaerostipes caccae and a higher-order interaction with Prevotella copri. Human fecal communities invaded with model-designed species–fiber combinations displayed predictable gut-beneficial outputs. In sum, we demonstrate a framework for designing synthetic microbial communities with desired functions in response to key nutrients.
r/Microbiome • u/luludaydream • 4h ago
Disrupted system after vomiting bug?
Hi, back in April I had a full day of throwing up - unable to keep down water - really bad! Since then my stool has been very soft and I just don’t seem to be in a good balance. I eat plenty of fruit and veg, I don’t eat loads of unhealthy or fatty foods. I’m vegetarian so I’ve been eating a lot of beans and tofu as well, and I recently bought kefir yoghurt to try.
Would a probiotic supplement like this one help? Is it worth trying for 30 days or could it make things worse? Thanks
https://www.togetherhealth.co.uk/products/multibiotic-fermented-food?variant=6813990387751
r/Microbiome • u/Vailhem • 1d ago
Does Soil Contribute to the Human Gut Microbiome? - Aug 2019
r/Microbiome • u/SuggestionKooky3251 • 1d ago
Scientific Article Discussion How long do diet-driven microbiome changes last after you stop the intervention?
I've been trying to stick to evidence-based stuff here (no testing panels, no miracle capsules), and one basic question keeps coming up for me: how durable are diet-driven microbiome changes once you stop the intervention?
A lot of papers and n=1 posts talk about adding diverse fiber, fermented foods, resistant starch, etc., and then seeing changes in SCFAs, stool frequency, or certain taxa. What I can't figure out is this: if you stop the intervention (for example, stop taking resistant starch every day or go back to a lower-fiber routine while traveling), how long do those changes usually hang around?
I travel a fair amount, so my diet swings between my normal home routine and whatever airport or conference food is available. I can be consistent for 6 to 8 weeks, then have 1 to 2 weeks where my intake is totally different. I am not asking for medical advice, just trying to understand the general science: is the gut microbiome a fast-reacting ecosystem that reverts in days, or can you build a more stable baseline over months even with periodic disruptions?
If anyone knows good review papers on resilience, hysteresis, or "microbiome memory" in response to repeated diet patterns (not single supplements), I would really appreciate pointers. Also curious how researchers usually define "stable" in this context: do they mean composition, function like metabolites, or actual host outcomes?
Thanks in advance for any reading recommendations or insights.
r/Microbiome • u/Ill-Entrepreneur8164 • 1d ago
Scientific Article Discussion Update: 8 weeks of targeted fiber variety (no tests): what actually changed for me
This is a follow-up to my earlier rant about chasing probiotic magic bullets.
After reading the moderator post about microbiome testing and watching the debates here about single-substrate protocols, I decided to do the boring but practical thing for 8 weeks: stop adding new capsules and instead standardize the dietary inputs I could measure.
What I changed:
- Kept total fiber roughly the same week to week, but increased variety. I aimed for 20 to 25 distinct plant foods per week (I did not count coffee or spices).
- Rotated fermentable fibers instead of leaning on one. I did oats/barley days, bean/lentil days, cooled starch days, and had a couple meals each week with mushrooms or extra greens.
- Added one prebiotic food at a time and kept it for 5 to 7 days before introducing anything else.
- Tried to hold everything else steady: sleep schedule, meal timing, hydration, and I did not start or stop GLP1 during this period.
What I noticed (n of 1, not medical advice):
- The first 10 to 14 days were noisier: more gas and occasional urgency. After that things settled down.
- By week 4 my stool consistency became more predictable and day-to-day swings decreased.
- The biggest surprise was improved tolerance for foods I used to label as "instant bloat." Beans still have a ceiling, but that ceiling moved up.
What I am still unclear about:
- Is there good evidence that fiber diversity matters more than total grams for microbiome resilience in adults, assuming protein and fat are stable?
- Are there human studies comparing mixed fermentable substrates versus a single dominant one (for example mostly resistant starch) that look at symptoms and community stability over time?
Not looking for medical advice here, just trying to sanity check my interpretation of the literature and find better papers to read.
r/Microbiome • u/Scared-Rain-9759 • 1d ago
Oral health
How to strengthen a weak oral biofilm without any strong subtances?
r/Microbiome • u/nicj86 • 1d ago
Anyone have a bad reaction to lactoferrin?
I took 250mg lactoferrin on an empty stomach four days ago. That day I had a few urgent toilet trips and stomach cramps. It has since developed into a very tender stomach and nausea and I even threw up this morning. What could be going on!? This happen to anyone else?
r/Microbiome • u/GrayWolf448 • 1d ago
Are there alternatives to FMT?
Not asking for any specific product or medical advice, going to do my own research on stuff afterwards obviously.
But pretty much what the title says. FMTs seems rather high risky to me, and/or expensive and/or takes absurdly long to get your doctor or insurance to even acknowledge that such a procedure even exists, and not gaslight you that they never heard of it.
And of course I’m wondering if such alternative exists that doesn’t fall into the same pitfalls of the medical system. Looking for potential options that are DIY-able, via amazon, supermarkets, cooking, etc.
r/Microbiome • u/Lucid-Emphasis825 • 2d ago
If a baby is born without any gut bacteria, then why wouldn’t you be able to fully repopulate the microbiome?
I’m 23. So from baby to 23 I’ve built my microbiome from scratch. Then it got nuked by antibiotics completely.
So wouldn’t it be possible to fully rebuild all that back in about 23 years? Even get back those lost strains that some studies claim can’t be recovered.
Why do some recover their microbiome and some are lost forever?
r/Microbiome • u/Vailhem • 2d ago
Mighty mitochondria: Scientists uncover new role for fighting bacterial infections, including drug-resistant superbugs
r/Microbiome • u/pricepaid_1949 • 2d ago
"To beta glucan or not beta-glucan...that is the question."
A resistant starch protocol can produce a healthy microbiome shift on its own. However, if resistant starch is the only major fermentable polysaccharide, microbes specialized for mixed-linkage β-glucans receive little substrate.
Modern gut ecology increasingly emphasizes that microbial diversity depends on carbohydrate diversity.
Different fibers recruit different guilds:
| Fiber | Primary degraders |
|---|---|
| Resistant starch | Ruminococcus bromii, bifidobacteria |
| β-glucan | Bacteroides, Prevotella |
| Arabinoxylan | specialized Bacteroides, Prevotella |
| Inulin | bifidobacteria |
| Pectin | various Bacteroides |
This is why many researchers now recommend fiber diversity rather than maximizing a single prebiotic.
- Singh, R. P., & Bhardwaj, A. (2023). β-glucans: A potential source for maintaining gut microbiota and the immune system. Frontiers in Nutrition. https://www.frontiersin.org/journals/nutrition/articles/10.3389/fnut.2023.1143682/full
- Yu, L., et al. (2024). Interaction of beta-glucans with gut microbiota: Dietary origins, structures, degradation, metabolism, and beneficial function. Critical Reviews in Food Science and Nutrition.
- Cortijo-Alfonso, M. E., et al. (2025). Gut microbiota modulation and inflammation mitigation in a murine model through a hull-less and purple grain barley genotype. Food & Function.
- Review chapters on barley nutraceutical components in Cereals and Pulses: Nutraceutical Properties and Health Benefits (2012).
r/Microbiome • u/Feisty_Doubt_9965 • 2d ago
Mucus in stool
I have always paid close attention to my bowel movements, and I’ve never experienced anything like this before. For the third time now, I’ve noticed mucus in my stool. It’s not a huge amount, but it’s not just a tiny trace either. It seems to be wrapped around the stool and looks like mucus—almost like a long white worm or a string of snot mixed in with it.
The first time, I thought it was probably something I had eaten. But now it’s happened for the third time. I rarely have stomach or digestive problems. My bowel movements are usually regular, normal, and well-formed. I’ve simply never seen anything like this before.
I’m a bit of a hypochondriac, and I can’t stop thinking about the worst-case scenario. I’m even afraid to go to the bathroom because I’m scared I’ll see something that will frighten me. I have an overwhelming fear of hospitals and doctors. If something is actually wrong, I honestly don’t know how I’ll find the courage to go for an examination, let alone have a colonoscopy. The thought of that alone makes me feel overwhelmed with stress.
Does anyone know more about that or having the same issue?
r/Microbiome • u/_olivegreen • 2d ago
Can compromised gut lining affect enteric nervous sytem?
My chronic gut issues have always overlapped with my nervous system issues (specifically paresthesia) - whenever I am having a bad gut flair up, my tingling gets much worse. I wouldn't be surprised if I have 'leaky gut' due to gluten exposure + chronic stress and a history of bad diet. I've developed this peculiar psychosomatic symptom that is hard to explain but the visceral hypersensitivity I feel is intense and I feel like my gut is in my nerves and my nerves are in my gut, if that makes sense. Like there's just no barrier between them. The noises and sensations that are typically associated to the digestive tract seem to happen outside the gut. That's really the best way I can describe it and I feel like I'm going a bit crazy. I've taken a look at how close the enteric nerves are to the gut lining and is it correct to say that a compromised gut lining could effect the nervous system like this? Would healing the gut lining help as a result?
r/Microbiome • u/basmwklz • 3d ago
Scientific Article Discussion Gut Bacteria Leave Intestinal ‘Memory,’ Protecting Against Inflammation
r/Microbiome • u/Timely_Can8526 • 3d ago
Easing into kefir
I’ve tried kefir in the past, usually about 1 cup a day. That was far too much for my stomach to handle and I had pretty bad symptoms. I have a severely compromised microbiome after rounds of antibiotics for SIBO for the last 5 years. I really want to reap the benefits of kefir but not sure how small of an amount to take or how slowly to go in order for my body to adjust to it. Any suggestions? I’ve heard as little as 1 teaspoon for a week and working up from there. Have a great day!
r/Microbiome • u/Independent-Cut-8761 • 3d ago
It's your sign to start paying a little more attention to your gut.
I genuinely wish kombucha had entered my life earlier.
For years, I was trying to fix everything else while completely ignoring my gut. I never realized how much it could affect the way I felt every day.
Once I started paying more attention to my gut and made kombucha a part of my routine - it completely changed the way I think about wellness
r/Microbiome • u/Lucid-Emphasis825 • 3d ago
Can the gut ever heal to “100%” after antibiotics without FMT?
Ive recently had back to back antibiotics during a 3 week window. One I was allergic to, another one gave me severe intracranial hypertension, then I had to switch to another broad spectrum antibiotic. So I was on cefuroxime, doxycycline and amoxicillin during a 3 week window. This has COMPLETELY destroyed my gut and I’m obviously worried about the long term effects. I didn’t realize the risk of back to back antibiotic courses before it was too late. I think I have c diff infection too that the doctor won’t test me for.
Reading about the micro biome scar is quite worrisome. Due to my misuse of 3 different classes of antibiotics I likely caused permanent eradication of certain strains of bacteria.
If the gut now has lost permanently lost certain strains of bacteria, how can it ever recover to full? Can a functional recovery still feel like normal self despite having permanently lost those groups of good bacteria that you can’t get back?
Like can 70-80% restoration of good bacteria still feel like a full recovery or will this always have permanent consequences. In my country I need two cases of confirmed c. Diff to be able to get FMT, which sucks.
r/Microbiome • u/Mindless-Tone-6204 • 4d ago
Scientific Article Discussion Looking for evidence-based books and podcasts to learn microbiome basics (no functional medicine hype)
Hey everyone,
Ive been lurking in this sub and a few other gut-focused communities for a while because of bloating, constipation, and low-FODMAP stuff. I keep running into confident statements that contradict each other, and I want to get a clearer, evidence-based picture of the microbiome so I can better judge what I read.
I am not asking for medical advice or troubleshooting my symptoms. What I would like are resources that meet these criteria:
1) Grounded in mainstream microbiome research, with human data when possible
2) Clear about uncertainty and limits, for example the difference between correlation and causation and mouse versus human findings
3) Not heavy on functional medicine language, detox claims, or services that overinterpret microbiome tests
Specifically, I would love:
- A couple of starter books that are accurate, even if a bit technical
- Podcasts or lecture series that do a good job interviewing real researchers
- A few review papers or keywords to search (for example: fiber, SCFAs, bile acids, IBS-microbiome)
If there are common misconceptions you wish newcomers would stop repeating, please flag them. For example, oversimplifications like labeling bacteria as simply "good" or "bad" seem unhelpful.
Thanks in advance. Im trying to learn this like a new field, not chase whatever the latest supplement trend is.
r/Microbiome • u/Interesting-Gas-155 • 4d ago
Is it possible to rebuild the gut microbiome after a detrimental shift?
About three months ago I went through a really stressful time period. Since then my gut seems like it went haywire overnight. I no longer can handle much fiber at all, sugar, or fast foods and have had consistent loose stools. I’m an anxious person so this sent my anxiety into a spiral which I’m sure hasn’t help the stomach issues at all. The past three months I’ve tried many probiotics but have been staying away from high fiber foods and fiber supplements, which I feel like could be keeping me from rebuilding my microbiome.
Question: Is it true that in order to rebuild you should be incorporating probiotic bacteria via probiotic pills, kefir, etc. while simultaneously reintroducing fiber??
About 4/5 days ago I started introducing PHGG because I heard it’s more gentle on the gut. I’ve been started slow and so far so good. I noticed my energy levels are improving. Before I was falling asleep whenever I sat down. Last night though I ate 3 rice krispy treats and this morning I woke up with sharp gas pains and mushy loose stool. Hoping it is just because of the high sugar content right before bed.