r/Microbiome Feb 22 '25

Rule change regarding microbiome "testing"

114 Upvotes

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 Jun 29 '23

Statement of Continued Support for Disabled Users

75 Upvotes

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 1h ago

Antibiotic related diarrhea up to 11 times a day. Has anyone experienced that?

Upvotes

Hello everyone. İ was prescribed metradinazole 500 mg twice a day and since day 5 or 6 i got so severe diarrhea. İ mean in the past i used antibiotics a lot due to different causes ( mostly tooth) but never experienced that bad diarrhea. İ ended up not completing the treatment and of course informed my doctor. She also said i should stop.

Have anyone experiences that bad diarrhea? My health status also isn't good, unfortunately i have autoimmune gastritis and chronic gerd.

İ have no drug issues, no alcohol, no smoking.


r/Microbiome 4h ago

Eating based on my lab results

0 Upvotes

Is anyone else exhausted trying to turn lab results into actual grocery lists?


r/Microbiome 15h ago

Symptoms after first week of taking probiotic

5 Upvotes

Hi everyone,
This will probably be a pretty long post. To preface, I’m a 23 year old male that has never been sick to this extent before and is otherwise quite healthy, and don’t have any known allergies (although maybe a suspected slight hayfever allergy but it’s not officially confirmed). I got some really severe food poisoning about 2 months ago (it first started on the 29th of May) and have been recovering ever since. The sickness is now out of my system and I don’t have fever or anything anymore (I didn’t vomit when I was sick though) and I am now in the process of recovering my gut and getting back to normal. I did not take any antibiotics during the time I was sick, and I don’t take any other supplements or medications.

I started taking Life Space Double Strength probiotic on Friday the 17th (I am taking it in the morning after eating breakfast) and all was well on the first day but on the second day (Saturday) I had really severe gas and bloating, leading to trapped gas in my body that gave me pains in my back and shoulder, though this subsided after a few hours or so. On Sunday I had some gas and bloating but it was much less and a lot more manageable, there were no pains. However, on that same Sunday, after eating dinner I started feeling quite lightheaded. The feeling passed after about 30 minutes to an hour, and on Monday morning after eating breakfast, I felt the lightheadedness again but it was a lot less in severity and also subsided much sooner, in about 20-30 minutes. After dinner that same day, I once again had the lightheadedness though it was very minor and subsided within 10-15 minutes.

On Tuesday, after breakfast I didn’t feel lightheaded at all but I felt slightly woozy from about 10am which lasted until 1pm or so then cleared up by itself and I was fine for the rest of the day. I did however feel quite anxious in the morning for some reason, I am not usually someone to get randomly anxious or stressed.

On Wednesday (today in Australia) I once again didn’t feel lightheaded after eating breakfast but at about 9:30am or so, I had a severe anxiety attack which lasted for over an hour, the main symptom was that it felt like my heart was pounding, and I felt very worried for no particular reason. My resting heart rate at the time was anywhere between 90 to 105 bpm. This settled and once again, left me feeling slightly woozy, where I’m still currently feeling slightly woozy now (at 2pm) but otherwise feel okay.

Some other things that I wanted to mention is that my sleep seems to be affected, over the past few days I’ve been waking up at least once in the night and today on Wednesday, overnight I woke up twice and found it difficult to get back to sleep, though eventually I was able to. I’ve also found that when I do wake up I tend to have a noticeably beating heart, which seems to be an anxiety symptom to me.

As it stands, my current symptoms really are the anxiety and slight lightheadedness, I have also been feeling fatigued and going to bed earlier but from what I understand, that is expected for now.

My stools also aren’t too bad, they’re usually formed and come at around the consistent times and amounts every day, although can fluctuate a bit in terms of how well formed they are and whatnot which I know is expected for the first week of starting a probiotic. I’m able to tolerate things like lactose without any issue too. They are a lighter colour though when wiping but are brown in the bowl.

I’m not sure if it’s worth mentioning this too, but my diet consists of high fibre low GI toast for breakfast, some slices with avocado and some with a small amount of margarine and Vegemite, with a cup of tea with milk and sugar. For lunch I would have teriyaki chicken don (white sushi rice, pieces of chicken, small pieces of broccoli, house made teriyaki sauce) and for dinner I would have rice with pieces of flake and chicken, with steamed vegetables such as carrot, green beans and broccoli. From my knowledge, I don’t have any issues with tolerating and digesting these meals. I also have a bowl of fruit every day with things like banana, strawberries, blueberries and red grapes.

On some mornings, I have oats instead of the toast with the same kind of fruits I have in my fruit bowl.

Since this is the first week of taking the probiotic (I’m currently on day 6) I understand that there are some side effects that occur and I just wanted to confirm if what I’m experiencing is “normal”, and can I expect these to clear up and stop happening in the coming days? I’ve heard that during the first week, the new bacteria from the probiotic are essentially fighting a turf war with any existing bad bacteria. These symptoms have been quite concerning for me, especially since I just want to get back to normal and feel how I did before I got sick.

All contributions are greatly appreciated, thank you so much!!


r/Microbiome 13h ago

Postpartum Gut Changes

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1 Upvotes

r/Microbiome 1d ago

Scientific Article Discussion Beyond the ‘second brain’: the gut microbiota as a constitutive co-constructor of embodied cognitive network (2026)

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frontiersin.org
47 Upvotes

r/Microbiome 1d ago

Chronic bad breath disappears completely during viral infections - any ideas why?

68 Upvotes

Hi.

I've had chronic tongue-related bad breath and taste for several years now. The problem began after using nicotine pouches for about 5 months. Before that I never had bad breath. When I stopped using nicotine the bad breath still remained. My tongue culture later showed abundant Gram-negative anaerobes, and the odor clearly comes from the tongue rather than the gums.

The part I cant explain is every single time I develop a viral illness (COVID, influenza, or even a common cold with fever/strong immune activation), the tongue odor and taste disappears completely within about 24 hours. Interestingly, this often happens around the stage where my nasal mucus turns yellow, although the odor has never originated from my nose or sinuses. The tongue stays essentially odor-free for around a day, then the odor remains markedly reduced for another 4–5 days before gradually returning as I recover. I don't change anything when this happens. I eat the same foods, drink the same things, and don't use any supplements, antibiotics, or antibacterial products. The only thing that changes is that I become ill. I also do not lose my sense of smell or taste, I can smell and taste everything normally during these episodes. This has also been confirmed by people around me: the bad breath disappears completely.

Does anyone have any insight into why this happens during an immune response? And is there any supplements or interventions you think might be worth trying?

Some relevant information:

- I have no tonsils

- Gums do not smell, the odor comes exclusively from the tongue

- I have IBS, but had that since childhood and I did not have bad breath since childhood - it started when I used nicotine products in my mouth..

- Have tried oral probiotics, didnt work

Other things that has helped my bad breath:

  • Metronidazole: 100% elimination of the odor during treatment. After stopping, the improvement lasted about 8 months before gradually returning.
  • Chlorhexidine: almost completely removes the odor, but only for about 10 hours.
  • TheraBreath: reduces the odor by roughly 50% for several hours.
  • Diet (whole-food diet): approximately 25% long-term improvement by itself.

r/Microbiome 1d ago

Starting to reintroducing foods after elimination diet

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4 Upvotes

r/Microbiome 2d ago

do we actually know what a “healthy” skin microbiome looks like

15 Upvotes

i’m 21M and deal with both acne and eczema, so my skin somehow feels oily, dry, irritated, and broken out at the same time.

i’ve gone pretty deep down the skin microbiome rabbit hole and read about a bunch of companies using postbiotics, ferments, and “microbiome-friendly” skincare. the idea makes sense, especially after years of acne washes, antibiotics, acids, and trying to kill bacteria.

but is the science actually there yet? has anyone improved acne or eczema by focusing on the microbiome, or is most of this just barrier repair with better marketing?


r/Microbiome 4d ago

Scientists tested 39 sweeteners and found unexpected gut effects

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sciencedaily.com
511 Upvotes

r/Microbiome 4d ago

Scientific Article Discussion Sweeteners shown to slow growth of important gut bacteria in lab tests

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49 Upvotes

r/Microbiome 3d ago

I’m the person who got badly inflamed by Chia. I just remembered they were slightly burnt by using a blender meant for liquids, and they smelled like plastic afterwards (I discarded the bottom portion). Zero survival instincts I know, but ChatGPT said this was the cause and not the fiber itself.

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3 Upvotes

r/Microbiome 3d ago

Streptococcus Thermophilus

1 Upvotes

Does anyone know if this strain can potentially cause flares for sensitive individuals? Does anyone know of any Greek yogurt that does not include this strain? Seems to be in everything


r/Microbiome 4d ago

Dysbiosis?

3 Upvotes

hi everyone! I’m writing here bc well.. idk where else to ask! I fear I’ve run out of options. I’ve had gut issues for a while now, mostly acting up when I’m stressed like most... but “IBS” like tendencies with mushy stool sometimes, sometimes normal.. intolerant to garlic and fodmap foods etc..

a month or so ago I took an oral iron supplement bc I have low ferritin, I’ve tolerated it great in the past before but this time, it made me gassy, bloated, and really aggravated my stomach. I was having great stool before this, and now my stool has gone pudding. it has been like that now for a month… its driving me crazy.

I’ve done a test in the past and it’s highlighted dysbiosis so my nd put me on an antimicrobial called black walnut by cytomatrix. has anyone else ever experienced anything like this?!


r/Microbiome 5d ago

Anyone here who’s had improvement in OCD by fixing microbiome?

24 Upvotes

Looking to hear positive stories if any, since the struggle w OCD is bad.


r/Microbiome 5d ago

How long before your gut normalizes after improving motility?

6 Upvotes

After previously testing positive for Sibo I have been having poor motility for a while now and struggling with constipation, I made some changes to improve the motility and the past 2weeks I’ve been more regular which is what I wanted. However I feel at the same time my gut feels more sensitive now off and on throughout the day and makes me even more careful about what I eat since things are moving faster. The gas and gut noises are a bit more now as well which I guess makes sense based on previously things were moving too slow and a lot of gas I think was trapped.

Has anyone experienced this and how long did it take for your gut to feel normal again day to day? Even after a few more weeks if it still feels sensitive like this, does it just need more time or is that a sign of some other issue?


r/Microbiome 4d ago

Persistent bloating for a month after taking 2 back to back courses of antibiotics (Macrobid)

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5 Upvotes

r/Microbiome 5d ago

Scientific Article Discussion How can I increase microbiome diversity when I'm stuck on a very limited post-SIBO diet?

17 Upvotes

I've been lurking here for a while and trying to focus more on improving microbiome diversity instead of just chasing symptoms. A few years ago I had a bad food poisoning episode and later was diagnosed with SIBO. I did antibiotics earlier this year and my bloating is better, but I'm still pretty reactive to a lot of foods.

Right now my baseline diet is basically rice, chicken, eggs, and a short list of cooked veggies I tolerate. Every time I try to add more plant variety, like beans, onions or garlic, raw salads, apples, or oats, I get gas, distention and then either constipation or loose stools for days. Because of that I keep sliding back to the same safe foods, which I know probably isn't great long term for microbiome diversity. It's frustrating and feels like a catch-22. I have also kept a Physicians Choice probiotic in my routine, but I am treating it as one small piece rather than a fix.

I'm not looking for stool test interpretations or a diagnosis, just practical ideas and real experiences. A few specific questions:

1) Is it better to try tiny amounts of many different plants (like a bite or two of each) or to focus on one new food at a time and slowly build the dose? 2) Do fermented foods help with diversity if you can't tolerate much fiber yet, or is that a myth? 3) Any low FODMAP plants or fibers people have used as a bridge without flaring symptoms?

If you've been stuck in the limited diet -> symptoms -> limited diet loop, what actually helped you expand variety in a sustainable way?

Not asking for medical advice, just looking for experiences and general microbiome-friendly approaches.


r/Microbiome 5d ago

Scientific Article Discussion Rebuilding my microbiome after multiple antibiotics: bloating and constipation

7 Upvotes

Hey all, looking for real-life recommendations from people who actually recovered their gut after several courses of antibiotics.

Background: Over the past year I had a dental infection treated with antibiotics, then a couple of back-to-back courses for sinus infections. Since then my gut has been a mess: daily bloating, slow transit constipation, and this weird feeling of being full after small meals. I also get reflux on and off. I read in the SIBO and guthealth subs and I am trying not to chase every supplement I see mentioned.

What I have tried so far:

- A basic grocery-store probiotic (ended up making me gassy)

- More fermented foods (sometimes helpful, sometimes made the bloat worse)

- A low FODMAP diet for a few weeks (did reduce symptoms, but I worry about long term restriction)

- Psyllium was too harsh for me; magnesium helps a bit with stool consistency

What I am looking for:

1) Practical, sustainable strategies for microbiome recovery: diet approaches, prebiotics, timing, and how to reintroduce foods without flaring symptoms.

2) Specific probiotic types or strains that people with constipation and bloating tolerated well, or reasons to avoid probiotics entirely.

3) Testing that actually helped you decide on treatment (stool tests, breath tests, etc) versus tests that just added confusion.

I am not asking for medical advice, just what worked for you and what you wish you had tried earlier. I can take suggestions to my doctor. Thanks.


r/Microbiome 5d ago

Scientific Article Discussion Paper On How Ancient Societies Consuming Monoculture Diet Negatively Affected their Gut Microbiomes And Drastically Reduced their Reproductive Fitness

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7 Upvotes

r/Microbiome 5d ago

When will this stop?

4 Upvotes

Hello all,

Has anyone gone through the same symptoms as me? and if yes, then can you please provide me some hope as to when this will end?

3 weeks ago, i had a bout of sulfur burps, diarrhea and stomach cramps. the doctor gave me Ofloxacin + Ornidazole and Rifaximin for 3 days. I felt better immediately the next day and life was smooth for the next 4-5 days.

Then I ate some pizza and things went haywire. My diarrhea came back but the sulfur burps were gone. I even had a vommiting session after eating chicken rice. The doctor continued the above meds for few more days and then the meds stopped.

Now I am post 4-5 days into my last medicines. And early morning i have semi solid stools. Except today, i ate some fried egg whites and boom, the diarrhea was back. Extremely frustrated about this whole ordeal. I make progress for 3-4 days and then it comes back when i eat something i shouldnt have.

anyone faced this before and is there a light at the end of the tunnel?


r/Microbiome 4d ago

VOWST fears - please give me some hope

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1 Upvotes

r/Microbiome 5d ago

Scientific Article Discussion Roasted and browned: how gut bacteria break down heated foods

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lmu.de
11 Upvotes

r/Microbiome 5d ago

Ideas for probiotics to take after a very long course of antibiotics?

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0 Upvotes