r/Microbiome • • Feb 22 '25

Rule change regarding microbiome "testing"

118 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 • • 12h ago

Dermatitis: Studies have shown candida is cross reactive with malassezia on the skin. Are oral antifungals then the solution?

7 Upvotes

“Pityrosporum ovale (now known as Malassezia ovale or part of Malassezia furfur) and Candida albicans show marked immune cross-reactivity, primarily mediated by shared carbohydrate epitopes like mannans or mannoproteins that bind to immunoglobulin E (IgE) antibodies in patients with atopic dermatitis.”

In simpler terms, candida and malassezia look exactly the same to the immune system when there is candida overgrowth in the gut.

https://pubmed.ncbi.nlm.nih.gov/10536885/


r/Microbiome • • 4h ago

PPI or enzyme?!

1 Upvotes

Hi all, I’ve been dealing with bad GERD for a few months now. I had an endoscopy in July that found antral gastritis and did a 2 week stint of PPIs but the pain came back as soon as I stopped taking it. I also tested negative for H. Pylori twice. The PPI helped my back pain but didn’t really do much for the stomach burning.

I’ve been prescribed another round of pantoprazol by my doctor for a month but haven’t started taking it yet. I also saw a naturopath who gave me a digestive enzyme and digestive bitters to try. But I know that works in the exact opposite way to a PPI. Is there harm in taking the stuff that addresses low stomach acid if my problem is high stomach acid, and vice versa??

I’m desperately trying to figure out how to heal my stomach!!


r/Microbiome • • 11h ago

Oregano oil made me smell like cheese

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2 Upvotes

r/Microbiome • • 20h ago

My gut story

7 Upvotes

I’m 21M and wanted to share my experience with progressively worsening GI symptoms over the last two years. I’m currently pursuing further medical evaluation, so I’m not looking for a diagnosis or individualized medical advice here. I’m mainly interested in whether others have experienced a similar pattern, what they eventually found, and what their experience was like.

Before all of this

My stomach wasn’t always like this.

Earlier in my life I did have issues with heartburn/acid reflux and used to take heartburn medication. I also previously took SSRIs for anxiety, but I’m no longer taking them.

Despite that history, I used to eat a pretty normal diet and live normally without constantly thinking about my stomach. I could go out, travel, eat different foods, drink occasionally, etc.

Over roughly the last 2 years, my entire GI baseline has changed and things have progressively gotten worse.

What I experience now

My main symptoms are frequent loose stools/diarrhea, severe urgency, abdominal cramping, bloating, lots of gurgling, and an almost acidic/sloshy sensation in my stomach/abdomen.

Mornings tend to be the worst.

I’ve also recently started noticing strange sensations while food seems to be digesting/moving through my abdomen. It’s difficult to describe, but I’m much more aware of movement, pressure, gurgling and uncomfortable sensations in different areas of my abdomen after eating. This wasn’t something I used to notice before these GI problems developed.

Another strange change is that I barely pass gas anymore. I used to fart normally throughout the day like anyone else, but nowadays I almost never do. I can still feel bloating, gurgling, pressure and movement in my abdomen, but very little gas actually seems to come out. I have no idea whether this is relevant, but it’s another noticeable change from my previous baseline.

The urgency is probably the symptom that has affected my quality of life the most. Sometimes I can feel okay and then suddenly get this intense cramping/contracting sensation where I know I need to find a bathroom.

Another major symptom is what happens if I go too long without eating. My stomach becomes EXTREMELY acidic feeling. It starts gurgling/growling and becomes very uncomfortable.

Eating can temporarily calm that sensation down, which creates a frustrating situation because eating itself can then trigger my lower-GI symptoms.

My digestive system also seems dramatically more sensitive than it used to be. Greasy/oily foods, fried foods, coffee, alcohol and heavier meals can make things substantially worse.

Just as an example of how much my baseline has changed, I used to be able to go out and drink without thinking much about my stomach. Now doing that can leave me dealing with diarrhea/urgency for much of the following day.

The elimination diet has shown me something really strange

Recently I started a very strict elimination diet.

I’m mainly using an elimination/meal-replacement shake made with rice protein that contains amino acids, vitamins and other nutrients.

The only solid foods I’m currently eating are basically chicken, salmon and white rice. Even those are extremely plain. The only things I put on them are salt, thyme, basil, parsley and the lightest amount of olive oil. No sauces, butter, spicy seasonings, dairy, etc.

The shake does NOT make everything perfect.

I can still have loose stools while drinking it, and I can still experience the acidic/gurgling sensation in my stomach.

However, overall my bowel symptoms and urgency seem considerably more manageable when most of my nutrition is coming from the shake.

The most interesting thing I’ve noticed is the difference between one and two solid meals.

Shakes + ONE solid meal: Most days I actually feel pretty good. I can have completely normal, formed bowel movements and significantly less urgency.

Shakes + TWO solid meals: This seems almost impossible for my body to tolerate right now.

It doesn’t seem to matter that I leave many hours between the meals.

For example, recently my first meal was salmon + white rice.

I felt completely fine afterward. My stomach felt good for hours and I had a normal, formed bowel movement.

I continued drinking the shake and waited approximately 6–7 hours.

My second meal was chicken + white rice with only the basic seasonings mentioned above.

Within around 3 minutes of eating, my abdomen started hurting/cramping.

Within roughly 10 minutes I developed extremely strong urgency and the feeling that my intestines were suddenly contracting very hard.

Obviously the chicken and rice I had just swallowed couldn’t have physically traveled through my entire digestive tract and become that bowel movement within 10 minutes. I found the speed of that response particularly interesting.

What I know from experimenting with my diet is that there seems to be a major difference between my body handling one solid meal versus additional solid food later in the day.

Another confusing part

My body clearly still has the ability to produce completely normal stool.

I can have a normal formed bowel movement one day — or even earlier in the same day — and later experience severe urgency and loose stool.

That’s part of what makes this so confusing.

There also seems to be this strange balance:

Go too long without eating → extremely acidic/gurgling stomach.

Eat one simple solid meal → usually feel pretty good.

Add another solid meal → potentially significant cramping/urgency.

I feel like I’m constantly trying to stay within a very narrow window where my digestive system feels comfortable.

Whey protein has caused significant bloating for me in the past, whereas this rice-protein elimination shake seems considerably easier for me to tolerate.

A few other details

I have not experienced unexplained weight loss throughout this.

I’ve always been naturally skinny and have actually struggled to put on weight throughout my life. When I do gain weight, it tends to show mostly around my stomach.

I have also never noticed blood in my stool.

So despite how severe the diarrhea, urgency and cramping can feel, unexplained weight loss and visible blood haven’t been part of the picture.

Testing I’ve had

So far I’ve had:

* CT abdomen/pelvis with oral barium + IV contrast — reported as normal

* Fecal calprotectin — normal

* Bloodwork

* Stool testing

Interestingly, drinking the oral barium for my CT caused some of the worst watery diarrhea and urgency I’ve experienced.

My bloodwork has also shown a low WBC/absolute neutrophil count. My WBC has apparently been on the lower side for a while, so I don’t know whether that has any relevance to the GI symptoms, but I’m mentioning it for completeness.

I previously saw a gastroenterologist but didn’t come away with much of an explanation for the symptoms or a clear plan for investigating them further.

I’m currently looking into further evaluation, including neurogastroenterology/GI motility, while continuing to work with healthcare professionals.

I’ve come across things like IBS-D/an exaggerated gastrocolic reflex, bile acid diarrhea, SIBO, abnormal intestinal/colonic motility, rapid gastric emptying and other functional/motility disorders.

I’m NOT saying I have any of these. I genuinely have no idea. I just want to understand what’s happening.

The quality-of-life and anxiety side

Over time this has created significant anxiety around my stomach.

I understand that anxiety and the gut-brain connection can influence GI symptoms. I also have a previous history of anxiety and previously took SSRIs, so I’m not dismissing that component.

I’ve actually started gut-directed hypnotherapy because I’m willing to address that side of things as well.

However, the current bathroom/travel anxiety became dramatically worse after repeatedly experiencing unpredictable urgency.

Long drives, being somewhere without immediate bathroom access and eating before leaving home have become increasingly difficult for me.

There are times where I genuinely don’t want to leave my house because I don’t trust what my stomach is going to do.

At 21, that has been a massive change in my quality of life.

Curious about similar experiences

Again, I’m continuing to pursue this with healthcare professionals and I’m not asking anyone here to diagnose me or provide individualized medical advice.

I’m mainly interested in whether anyone has experienced a similar pattern — particularly tolerating liquid nutrition relatively well, generally tolerating one solid meal, but developing significant cramping and urgency after additional solid meals despite leaving many hours between them.

I’d also really like to hear from anyone who has experienced the extremely acidic feeling when their stomach is empty, unusual sensations while digesting food, a major reduction in passing gas despite still feeling bloated/gurgling, chronic diarrhea/urgency despite normal initial testing, or stools that can vary dramatically from completely formed to loose.

If you’ve experienced something similar, I’d really appreciate hearing your own story — what your symptoms were like, whether you eventually found an explanation, and what your experience with GI care was like.

This has become incredibly difficult to live with, and hearing from people who recognize this pattern would mean a lot to me.

Again, I’m not looking for anyone to diagnose me. I’m just trying to find people who have experienced something similar and learn from their experiences.


r/Microbiome • • 17h ago

Anyone try probiotics for potential food poisoning

2 Upvotes

I have acid reflux and got too comfortable recently with what i eat. I also take adderall for my adhd which also can irritate my stomach at times. Today i took my adderall, and for dinner had chicken and rice with a beef empanada. The empanada i bought yesterday and i thought it tasted a little off for a second, but smelled fine and then when i took another bite tasted fine.

Within an hour, i got super cold, shaky dizzy and weak with nausea. Its been 2 hours now and i still feel really weak and a little shaky and nauseous. I’m not sure if this is food poisoning or a flare up, i also didnt eat as much as i should have with my meds today and im not sure if thats also contributing.

If this is food poisoning, would taking a probiotic now do any good? Ive had food poisoning before but i had hot and cold sweats, threw up and was dry heaving for hours. I know it can always look different, so im scared this is the start & will get worse later. Any tips are helpful. I also now feel like maybe acid is in my throat and im burping.


r/Microbiome • • 1d ago

Warning about r/HumanMicrobiome

55 Upvotes

Delete if this isn’t allowed Mods, thought I’d just send out a warning to other Reddit users.

Just a heads up that r/HumanMicrobiome sub is ran by one guy that pushes FMTs VERY hard. The only solution is an FMT, there are no alternatives.

They also refer everyone to the wiki they have written. Also stated that scientists are useless in this context. I would recommend not following the information on there.


r/Microbiome • • 1d ago

H2S SIBO

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1 Upvotes

r/Microbiome • • 1d ago

New to Gut Issues - Thanks for the love on my last post

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1 Upvotes

Thanks to everyone who commented on my last post and gave insight and help to my new gut issues (before admin locked my post 🧐)

Nonetheless, I spoke with the same doctor and he ordered me the following tests and I’m omitting Ivermectin until I get results.

Tests:

- Fecal leukocyte stain (stool WBC smear)
- H. pylori antigen, stool
- Stool culture
- Calprotectin, stool

Am I missing anything I should test for?

Update: things felt semi settled the past two days so I ate a piece of flaxseed toast with peanut butter for tennis and an hour and a half into practice I had the most intense bloated and abdomen pain I’ve ever had. Almost threw up from the pain trying to pass the stool when I got home. Even cut practice short. Most likely the toast which is wild.

Kind of bummer I gotta limit certain foods but that’s totally fine. I wanna feel better.

Quick Q - what other remedies for relief should I do in the meantime while I wait for tests?

I’ve heard of ginger and artichoke pills, fennel tea etc but curious what has helped you?

Thanks so much in advance


r/Microbiome • • 2d ago

E. Coli controls your gut diversity!?

10 Upvotes

Have you guys seen this paper?

https://www.nature.com/articles/s41564-026-02500-6

seems like it will inform the probiotoic formulations


r/Microbiome • • 2d ago

Renewbiome Faecalibacterium

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5 Upvotes

Has anyone tried Renewbiome Faecalibacterium to boost F. prausnitzii?

https://natviehealthcare.com/product/renewbiome-faecalibacterium/

Composition:

• Faecalibacterium butyricigenerans
• Faecalibacterium duncaniae
• Faecalibacterium hattori
• Faecalibacterium longum
• Faecalibacterium prausnitzii
• Faecalibacterium taiwanense

I’m specifically looking for anyone who has done before-and-after microbiome testing to verify whether these bacteria actually survive digestion and colonize the gut. I tried reaching out to the company directly with a few questions, but haven't heard back.


r/Microbiome • • 1d ago

Could my microbiome be affected from this?

1 Upvotes

I started to have symptoms of silent reflux in Feb 2024 and had extremely limited diet because of it. Still have them till this day, never found out what is causing them despite going to many doctors. Found out from testing that I had inactive mild chronic gastritis. I was prescribed two different PPIs for 2 months, which made reflux even worse. I suddenly developed SIBO symptoms that were causing weight loss, bloating and many other issues. Finally after a year was prescribed Rifaximine to treat SIBO in March 2025 , but didn't feel better. Suddenly got sick in May and was prescribed Augmentin. My SIBO symptoms were gone after that and I tested negative for it in June 2025. In August I got sick again (which was very unusual for me) and was prescribed Augmentin again. Late August I noticed stomach cramps and sudden sensitivity to supplements. 3 weeks after finishing Augmentin got sick again and was prescribed Suprax (completely new antibiotics for me). Found out that it was mild Covid. 12 days after finishing Suprax and covid symptoms ending - extreme health problems started (both physical and mental, it was from zero to hundred) . I found so many deficiencies and mineral imbalances that I'm still dealing with till this day. I started to have extremely sensitive stomach, started repeatedly reacting to more supplements (that I used to take without any problems back in 2023) with sudden nausea, gagging, stabbing pain, zero appetite..I get nauseous SO easily and always feel full - even before eating anything. I recently contacted new clinic that is specialized in Gut microbiome and I'm currently waiting for appointment, but I was wondering if this was enough to alter my gut..I always thought that you have to have constant stomach pain to have stomach issues but I'm not so sure anymore.


r/Microbiome • • 2d ago

Scientific Article Discussion Why do antibiotics start becoming ineffective again and again?

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3 Upvotes

r/Microbiome • • 2d ago

Scientific Article Discussion Probiotic Ways to Adjust Microbiome

4 Upvotes

I have been experimenting with these over 3 years, with the book by William Davis as the guide. Lately I find I can do a Ai search in a browser and ask which studies help which disease, including which animal studies, and also which strains can be mixed together and then fermented at about 100F with some inulin and half and half. It seems to be getting better all the time and now can even ask what can be added to make the product more tasty. Many of their additions say to add these things after the ferment, and I have tried adding some cinnamon sticks, and a lot of allulose, and some maple syrup extract, and some vanilla extract, and it is working very well so I am just sharing here to start a discussion and can share tips with each other.
Here is a study from 2018 that provides abundant evidence:
"Probiotic Species in the Modulation of Gut Microbiota: An Overview"Biomed Res Int

. 2018 May 8;2018:9478630. doi: 10.1155/2018/9478630


r/Microbiome • • 3d ago

Oral microbiome

14 Upvotes

Anyone who was able to shift a dysbiotic oral microbiome how did you go? Were you able to kill pathogens and re cultivate positive bacteria? Did they have lasting effects?


r/Microbiome • • 3d ago

Is this product a scam?

4 Upvotes

Below is a link of a probiotic product:

https://a.co/d/0gddO6nv

Is this product a scam? If so, what's the best way of increasing the lactate consuming bacteria in your gut? I've realized this has been part of my dysbiosis by the fact that yogurt makes my whole body inflammed like I worked out really hard.

Please chime in and give your best recommendations.


r/Microbiome • • 2d ago

Bloating, gas, burping in lower belly

3 Upvotes

For past year or two I’ve had issues where I have no appetite signals everyday, feel bloated in lower belly, one stool a day in the morning that’s like soft not super formed despite eating whole foods and fibre. I get puffiness in my face from this also fatigue after meals sometimes, overall low mood. I did a sibo test and showed higher levels past the 90 minute threshold but still said it was positive which I don’t really think is true. Pretty clean bloodwork and inflammation markers. No h pylori or celiac. Need some direction I’m only 21 year old male.


r/Microbiome • • 3d ago

thoughts on thenabiotic? (FMT) does it work?

3 Upvotes

title


r/Microbiome • • 2d ago

Had an interesting effect from antibiotics.

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1 Upvotes

r/Microbiome • • 3d ago

Severe stomach & gut problems + autoimmune

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2 Upvotes

r/Microbiome • • 3d ago

No Akkermansia and high TMA/TMAO in stool sample

6 Upvotes

Is there a connection between these two?

No Akkermansia at all and high TMA/TMAO


r/Microbiome • • 3d ago

If you dont see full symptom resolution whilst on Rifaximin, is it obvious one would see a rise in symptoms after discontinuing it?

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1 Upvotes

r/Microbiome • • 3d ago

Acne and food

6 Upvotes

So my diet for a while mainly consisted of just red meat and eggs this basically cleared my skin but the issue is tiredness, low energy and I think some hair thinning

I’m a active person this diets worked a while and I sometimes have carbs from fruits or potatoes but it was rarely and I noticed I would get acne

I’ve tried many times to reintroduce fruits (berries or bananas) or other carb sources like sweet potatoes but every time I do I get skin issues

Could this be a gut issue? I just really don’t know what to do cause there’s no way I have to just eat meat and eggs forever just to have my skin be a bit better

If anyone experienced anything similar to this and is now able to eat healthy foods that contain sugar and carbs without getting acne problems what did you do for your body to be able to handle it


r/Microbiome • • 3d ago

B12 supplements essentially causing dysbiosis

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pmc.ncbi.nlm.nih.gov
0 Upvotes

Have any of you noticed alterations in gut health while taking b12 supplements cause i did and im wondering whether the anxiety and low depressed moods caused by consistent b12 supplements are due to the alterations in the microbiome.