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 • • 20h ago

Living abroad changed my gut flora forever? Anyone has the same experience?

34 Upvotes

So I was born and raised in China. I never had any gut issues since 10 - I had the most ideal banana poop every single day. Then I moved to Ireland at 20 and lived there for two years, everything was fine too. The problem occurred when I moved back home. One month in, my gut became super sensitive to wind, cold, and even the slightest anxiety. I never got diagnosed but I suspected I had IBS. The symptoms appeased gradually in a year. Then I moved to Europe again and been living here for a few years.

And I feel like my gut is not as strong anymore. Whenever I have something fibre-rich, like kale, psyllium husk, or cabbage, my gut goes bananas, unless I tried to limit how much I eat. But I used to eat loads of vegetables without any issues, and I love them! And there was also a period of time when my gut just didn’t work well, although that was solved by the cheapest pro-biotic tablets in the drug store to my surprise.

Now after a course of antibiotic (Keflex), my gut has been the weakest it’s ever been. I had a slice of wholewheat bread and I exploded and I have no idea why lol. And waking up every morning wondering if I will have a solid or a loose stool is the worst feeling ever.

Rant ended ha


r/Microbiome • • 3h ago

hey, graduated a microbiology degree a few months back, been looking for entry level QA/QC roles by tailoring my resume accordingly and still being ghosted, so any advice on how to not get ghosted???/

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0 Upvotes

r/Microbiome • • 9h ago

Anyone start probiotics??

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2 Upvotes

r/Microbiome • • 8h ago

Use of antiviral drugs worsen SIBO?

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1 Upvotes

r/Microbiome • • 18h ago

SIBO and Anhedonia

5 Upvotes

Has anyone successfully treated SIBO with antibiotics like Rifaximin and also experienced an improvement or complete resolution of anhedonia?

I've been reading about the potential connection between gut health and mental health, and it seems like there could be a link between SIBO, gut microbiome imbalances, and anhedonia (the inability to feel pleasure or enjoy things).

I'm really curious to hear from people who have dealt with both issues. Did treating SIBO make a noticeable difference in your ability to feel pleasure, motivation, emotions, or enjoyment of life? If so, how long did it take to notice improvements, and did the benefits last?

I'd especially appreciate hearing from people who experienced significant or complete recovery from anhedonia after treating SIBO.

I know everyone's experience is different, and I'm not assuming there's a direct causal relationship, but I'd love to hear some real-life experiences. It seems like this connection deserves more attention.

Has anyone experienced this firsthand?


r/Microbiome • • 1d ago

Bloated 24 hours a day,

3 Upvotes

Hey guys,
I’ve had a bone infection and taken about 5 antibiotic courses over the last 5 month’s I never really had an issue until midway through my last course where I seemed to develop bloating that never goes away,

I’ve been finished the course for two weeks now and still nothing stops the bloating and dealing with constipation and feels like trapped gas all the time inside,

Been trying my best with good quality food and probiotics but nothing making a difference so far,

It’s now annoying me I’ve never bloated in my life till now am wondering if anyone has a had a similar experience and how long it took for them for bloating to stop,

Thanks!!


r/Microbiome • • 21h ago

Inulin seems to be the default fibre in supplements. Is that because it's best, or because it's cheap?

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2 Upvotes

r/Microbiome • • 1d ago

Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function

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3 Upvotes

r/Microbiome • • 1d ago

Pro athlete seeking advice🙏

1 Upvotes

Hey everyone! I am gonna try to keep it short and detailed, but I genuinely need advice as of now docs are of no significant help and if someone knows and has gone through something similar, please let me know.

Soo this February I had a viral infection that most likely turned into a bacterial one, because I was given antibiotics for a week.
My symptoms were razor-blade sore throat, very high fever for around 3-4 days and fatigue, no major coughing, but my chest x-ray said there was a problem there.

The big problem came 2 weeks after I finished the antibiotics and got a bit better from the acute symptoms.

One day while training my body acted so weird, I couldn’t imagine something like this before, never had such issues in my life prior to that.
My legs felt so strange and the lights were so overstimulating, like my brain flipped some sort of weird switch.

I don’t know if this is called DPDR or brain fog, although it is a full body thing for me. My memory and concentration are still okay, I just feel so strange and weird and when it gets bad it can become scary. I am desperately searching for answers and root causes of this thing, as I am completely sure this is not just anxiety, because I am not an anxious person to begin with and I feel happy even right now.

This just feels like a body state that you cannot outthink your way out of.

Weirdly enough when I got sick from a stomach bug in the summer, although I felt like shit from the bug, this feeling lifted.

I also have some history of IBS-D, which just happened randomly 4 years ago, again after some kind of virus and I have been suffering with chronic loose stools without pain since then.

Can my gut being disrupted or some inflammation there feed this body state of mine?


r/Microbiome • • 1d ago

Unpopular opinion: psyllium husk is great at one job and people treat it like a complete gut fix

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10 Upvotes

r/Microbiome • • 1d ago

Preserving Gut Health After Antibiotics

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2 Upvotes

r/Microbiome • • 2d ago

Does anyone else feel way more bloated after a light, healthy smoothie than a solid warm breakfast?

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3 Upvotes

r/Microbiome • • 3d ago

Allergies gone

130 Upvotes

I have type IV hypersensitivity allergic categorization. Drinking kefir completely removed my allergies to everything. I am now capable of existing in Europe where I was born. I can even breathe in sawdust without reaction or go mow our garden. I am fulfilled. This miracle cost me $5 without any side effects (the same cannot be said for pills). I am a forever skeptic when it comes to homeopaty.

But I am cured.


r/Microbiome • • 2d ago

What does the science actually tell us about DNA versus RNA microbiome testing?

6 Upvotes

I’ve spent nine months researching microbiome testing, particularly the differences between DNA-based analysis and RNA-based metatranscriptomics.
My interest is in what these technologies can actually measure, how reproducible their findings are, and whether the information has demonstrated clinical value.
For context, I’ve completed three rounds of Viome’s RNA-based testing alongside extensive conventional bloodwork and physician oversight. I’m now planning to explore Superpower’s DNA-based testing to better understand the differences between the two methodologies.

I’m not expecting identical findings. DNA and RNA analysis examine different aspects of microbial biology, and understanding those differences is precisely what interests me.

I recently came across a 2025 international consensus statement published in The Lancet Gastroenterology & Hepatology questioning the clinical usefulness of commercial microbiome testing.

https://pmc.ncbi.nlm.nih.gov/articles/PMC12343204/
That raises some important scientific questions.
How much variation in microbial DNA and RNA measurements is normal? How reproducible are these findings over time? And what independent evidence demonstrates that either approach provides information that improves clinical outcomes?

I’m particularly interested in the distinction between measuring microbial activity and demonstrating that those measurements can reliably guide clinical decisions.

For transparency, Viome provided my testing complimentary. I’m not being paid by either company, promoting testing services, requesting interpretation of personal results, or seeking medical advice.

I’m interested in the research and in sharing what I learn.
For anyone working in microbiome science, where does the evidence currently stand on the clinical utility of metagenomics versus metatranscriptomics
What would meaningful independent validation look like?


r/Microbiome • • 2d ago

Probiotic "bifidobacterium lactis hn019"

9 Upvotes

Has anybody had experience with this specific probiotic strain (hn019)? It is supposed to be the most effective at improving gut mobility and helping to relive constipation . There are conflicting research studies; some claiming 100% success and others saying no better than a placebo. What brands have you tried what was your experience.


r/Microbiome • • 2d ago

Please help me improve my diet

8 Upvotes

I've spent the past few years really dialing in my diet for my microbiome and I would love to get some suggestions for how to even further improve my intake. For reference, The listed breakfast is ~98% of my breakfasts. The listed lunch is ~75% of my lunches (I have a harder time being consistent here). I only eat 2 meals / day + a snack.

Also I have celiac so I can't add Gluten. I also have an oat allergy so GF oats can't be added :(

Breakfast:

2% Greek Yogurt (Fage Unsweetened) or Milk Kefir - I do Kefir 4x / week and Yogurt 3x

Almond Butter

Chia, Flax, and Hemp Seeds

Blackberries and Blueberries

Ceylon Cinnamon

Snack:

Kimchi <- everyday

Carrots and Humus

or

Popcorn (self popped w/ EVOO)

or

Eggs on sprouted corn tortillas

Lunch/Dinner

Brown Rice

Wild caught Sockeye Salmon or Chicken

EVOO

(All vegetables are raw)

Spinach, Kale, and Chard

Chopped Onion and Garlic

3 colors of Bell Peppers

Chia, Flax, Hemp, and Mustard Seeds

Sauerkraut

Random spices

Any advice would be great. I want to keep stepping up my microbiome game. I know I'm already doing fairly well but I want to keep improving!


r/Microbiome • • 2d ago

Visceral Hypersensitivity

4 Upvotes

I have made a few posts now about what is going on with my gut after a combination of Accutane and oral metronidazole. I still need to get tested for potential infections but if i don't have any of those, i'm highly suspecting that I have visceral hypersensitivity in my large intestine. Since getting off those medications 2 months ago, I have felt like I could feel my large intestine just sitting inside me 24/7, pressing up against my ribs and the sides of my abdomen causing me severe discomfort, especially when laying down. Most of my bloating has gone away and i'm wondering why that has improved but this hasn't. I think the combination of medicine really messed up the nerves in my gut and thats why i'm experiencing constant uncomfortable sensations along that part of my abdomen. It also flared up horribly this last week after my doctor gave me orthospore probiotic to try. Does it sound like I have visceral hypersensitivity and if so does anyone know any affective treatments or cures for it? Im literally terrified that this wont go away :(


r/Microbiome • • 2d ago

No idea what to do about my stomach post antibiotics

9 Upvotes

I took amoxicillin in march and haven't been the same since. I was perfectly healthy. Ive had persistent stomach issues like burping, some bloating, reflux (and silent reflux). Long story short, its been six months and I am not myself still. I have no idea what to do. Most probiotic foods I cannot eat due to acidity. I am afriad to eat certain foods now because of this. I was able to eat anything I want before. I was always healthy weight, healthy diet, no smoking no alcohol, not even caffiene. Those pills messed me up royally. Six years ago I was given cipro and flagyl and I was poisoned for a year and a half at least. But I didnt have stomach symptoms like this. I just had everything else under the sun. Also my mental health has been horrible. Probably due to both this whole situation and whatever those pills did to me. I dont know where to start. I eat clean and try to control my stress but I feel like theres more I should do. I tested negative for h pylori via breath test, had a test for candida albicans and it was in normal range via bloodwork, and had a big workup that showed I had low zinc and vitamin d (both I have been fixing and raised levels up since testing a few months ago). I feel like I need to be doing more for my gut. I dont know what to take for my stomach. I used to take garden of life probiotics but since have looked into probiotics and realized the difference between human and food sourced, plus how many brands (like garden of life) that dont have specific strains that have been studied. I dont have the money to just buy a ton of stuff and see what works. I also dont want to make myself worse. I also was given six weeks of a PPI which i definitely should not have taken. I havent taken any meds at all the past 9 weeks or so now. No pepcid, PPI, antibiotics, tums, nothing. I dont want to take anything else. Medication is what ruined me, so I doubt itll fix me. But I just want to be myself again. I get no guidance from doctors so I am turning here for some sort of advice.


r/Microbiome • • 2d ago

How to fix gut after harsh antibiotics

2 Upvotes

- been on multiple antibiotics the past year, I’ve had allergic reactions to two of them (not sure if this is gut related)

- just finished another course of them last week

- eczema widespread due to antibiotics, very itchy when eating anything except for home cooked foods

- on whole foods only diet now, paired with topical steriods itchyness calmed down

Cannot eat anything I used to be able to eat like two months ago without itching. Pls help me get my life and skin back. Even probiotics I’m taking rn are making me itch.


r/Microbiome • • 3d ago

What kills engineered cancer-fighting bacteria when they leave the lab

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2 Upvotes

r/Microbiome • • 3d ago

Permanent Colonization

11 Upvotes

Have any commercial probiotics strains been shown to permanently colonize the gut? I know most don’t but I can’t find a clear answer.


r/Microbiome • • 4d ago

Scientific Article Discussion The Relationship Between Depression, Poor Sleep, and the Microbiome

28 Upvotes

Has anyone here experienced the connection between depression, poor sleep, and the microbiome? What helped you turn things around—medications or dietary changes?

I had a colonoscopy and an upper endoscopy; the colonoscopy came back clear. But I have ileitis in the ileum and tissue fibrosis (my body has healed the underlying cause), and my calprotectin levels are normal. I don’t have Crohn’s disease, IBS, ulcers, or erosions.

I had Helicobacter pylori in my stomach, which was successfully eradicated.

I don’t experience any mental fogginess. However, I have a persistent state of low mood and depression accompanied by anhedonia.


r/Microbiome • • 3d ago

Would the data from a G.I. map allow me to accurately choose what what Kefir/yogurt and which bacteria strains that my body specifically needs, and so I don’t just buy ignorantly?

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1 Upvotes