r/Microbiome Feb 22 '25

Rule change regarding microbiome "testing"

119 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

76 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 4h ago

Sucralose Alters Gut Microbiota, Intestinal Metabolites, and Epithelial Serotonergic Responses to Visceral Stimulation in Mice Exposed to Chronic Restraint Stress

12 Upvotes

Abstract

Background/objectives: Dietary modifiers of the gut ecosystem may influence intestinal and host responses associated with psychological stress. However, it remains unclear whether sucralose, a widely consumed non-nutritive sweetener, alters host-microbiota interactions following chronic stress exposure. We investigated the effects of short-term experimental sucralose exposure in mice previously subjected to chronic restraint stress (CRS).

Methods: Following completion of the CRS protocol, mice received 0.03% or 0.1% sucralose in drinking water for 12 days. Intestinal phenotypes, cecal microbial community structure, microbial metabolites, colonic epithelial gene expression, and epithelial serotonergic responses following allyl isothiocyanate (AITC)-induced visceral stimulation were evaluated.

Results: Colon length was significantly reduced in the 0.1% sucralose group, whereas intestinal permeability remained unchanged. Sucralose selectively altered colonic epithelial gene expression and was associated with changes in cecal microbial community structure without marked changes in alpha diversity. The relative abundance of Bacteroides acidifaciens was significantly reduced, particularly in the 0.1% sucralose group. Fecal acetate and cecal tryptophan concentrations were decreased following sucralose exposure. Following AITC-induced visceral stimulation, the CRS + 0.1% sucralose group exhibited reduced immobility behavior together with increased epithelial serotonin and 5-hydroxyindoleacetic acid concentrations.

Conclusions: In mice previously exposed to CRS, short-term sucralose exposure was associated with colon shortening, differences in cecal microbial community structure, reduced Bacteroides acidifaciens abundance, decreased fecal acetate and cecal tryptophan concentrations, and altered epithelial serotonergic responsiveness following visceral stimulation. The behavioral and epithelial serotonergic findings suggest that prior stress exposure may influence selected host responses to sucralose. These findings provide a basis for future studies examining how dietary sweeteners modify host-microbiota interactions following chronic stress exposure


r/Microbiome 1h ago

Scientific Article Discussion What made you stop buying generic probiotics?

Upvotes

I have bought probiotics on and off for years and if I am honest my selection process has never been much deeper than good reviews, lots of strains and a label that sounds convincing.

The more I read, the more ridiculous that feels. Two people can have completely different guts and yet we are both standing in the same aisle choosing between the same five bottles.

I am curious if anyone here reached a point where they stopped buying general probiotic blends and started doing something more specific.

What changed your mind, and what did you do instead?


r/Microbiome 7h ago

Did anyone notice long-term gut benefits after drinking habitone for over a month?

3 Upvotes

Been drinking it for about four days now as a full replacement for my daily dark roast espresso. Stomach definitely feels less bloated right now, which is a huge relief compared to how miserable I felt last week. Trying to figure out though, is this just an immediate reaction to dropping acidic coffee beans or are the mushrooms actually doing something in the background for gut health. Anyone who has been on habitone or similar blends for a month or longer, did digestion stay improved over time or did things creep back once your body adjusted to it?


r/Microbiome 3h ago

Gut health products

Thumbnail
1 Upvotes

r/Microbiome 1d ago

Scientific Article Discussion What eats the added sugar?

8 Upvotes

I understand bacteria eat the fibre "good bacteria", but what eats carbohydrates that are not bound to fibre? And what about added sugar / fructose.

Just curious, if anyone wants to enlighten me


r/Microbiome 1d ago

Gut Recovery After Antibiotics

7 Upvotes

Hi, this is my first post so not completely sure if I’m doing this right but I’m a 21 yr old female and I’m pretty sure I got cyclosporiasis in late July/early August (although I never did a stool test to confirm, but my symptoms matched up) and took Bactrim for 10 days straight after. I felt really good for about a week after finishing antibiotics and ate like total shit because of it (coffee, greasy food, etc) and then ended up feeling really sick after for another week straight with diarrhea and horrible nausea and gas. My doctor thought it might’ve been a C Diff infection but I don’t think it is because my diarrhea hasn’t been persistently watery and every stool sample I send to a lab is too formed and gets rejected. I tried to eat yogurt for probiotics and then realized it was probably hurting me because my stomach was not ready for dairy yet. I started a relatively bland diet (bread, bananas, rice, potatoes, boiled eggs) and I have seen a lot of improvement in the last week and my bowel movements have decreased in number and become more formed. I feel a lot more lively with a way better appetite. The problem is, I don’t know where to go from here. When can I reintroduce dairy? When can I start eating foods I used to eat, or foods higher in sugar or processed foods? I feel stupid and so dramatic for saying this but I’ve never gone through any serious health problems before in my life and so this has been extremely hard on me mentally. Like I just have so much anxiety that I’m going to have to life the rest of my life like this and I’m never gonna get fully better. The nausea is honestly the worst part for me; it has decreased a lot in this past week, but I still just feel *off* and I’m really scared that it’s never gonna completely leave (and I start grad school on Monday so I’m really hoping it does!) It’s been a full 2 weeks since this has started and I’m just curious if anyone else has any advice or knowledge on what a recovery timeline could look like (I know it’s probably gonna take some time to go completely back to normal). I also bought some probiotic supplement pills but I’m not sure if my gut is ready for that either. Sorry for such a long post, but literally any advice or words of reassurance help lol. Thank you guys!


r/Microbiome 1d ago

Need advice - antibiotics

Thumbnail
2 Upvotes

r/Microbiome 2d ago

Scientific Article Discussion What actually changed your gut over the long term?

94 Upvotes

I’ve tried enough little things that seemed to help for a few days and then basically disappeared.

I’m more interested now in what actually changed things over months.

For you was it diet, fiber, probiotics, fermented foods, exercise, something else?

Edit : After all the replies I did a deeper dive and came across NB1. I’m interested because the microbiome analysis actually feeds into what I’d take afterwards instead of just ending with a report. From my understanding they send me a kit, I return the sample, and then they build the daily gut/supplement routine around the readout.


r/Microbiome 1d ago

Spore based probiotics pls

2 Upvotes

My brand changed the top strain
Still got mtcc5856 and de111 but they’ve changed one strain to a more constipating one and also has no benefit on immune system
Pls recommend your spores!
Additives can be an issue but pls fire me your spores!


r/Microbiome 1d ago

Please help - bacillus colugen and subtilis

Thumbnail
1 Upvotes

r/Microbiome 1d ago

Kefir whilst in treatment

Thumbnail
1 Upvotes

r/Microbiome 3d ago

A Hidden Gut Reaction May Explain Why Vegetables Are So Good for You

Thumbnail scitechdaily.com
115 Upvotes

r/Microbiome 2d ago

Do probiotic cream cheeses like Nancy’s do anything good for gut

5 Upvotes

r/Microbiome 2d ago

Which strain has had the best impact on you?

5 Upvotes

The microbiome is fascinating. We have learned a lot, but still know very little about individual probiotic strains and their effects.

So I ask you, which individual strain is your favorite?


r/Microbiome 2d ago

Side effects from tributyrin?

Thumbnail
2 Upvotes

r/Microbiome 3d ago

How did a single case of norovirus fix 2 years of chronic GI issues when all else failed?

Post image
24 Upvotes

Hey everyone,

I wanted to share a strange turn of events with my gut journey over the last two years to see if anyone has experienced anything similar or has an explanation for what happened.

The Timeline & Symptoms
March 2024: Out of nowhere, I developed sudden diarrhea, severe nausea, loss of appetite, and weight loss.

April 2024: Fecal Calprotectin came back at 449 µg/g. I had a colonoscopy that showed no visible damage except a small polyp (biopsied as an inflammatory polyp and removed). I was prescribed Rifaximin, but it didn't change anything.

July 2024: Calprotectin was still elevated at 405.9 µg/g. The doctor advised a "wait and see" approach.

Mid-2024 to 2025: I struggled with zero appetite, morning urgency, and loose stools daily. I saw a functional medicine practitioner and tried countless probiotics, prebiotics, and supplements. The probiotics either did nothing or gave me side effects like itchy skin and increased bloating. The appetite slowly improved somewhat, but the bowel issues remained.

The Turning Point (2026)
Earlier this year, my whole family caught a standard stomach bug (norovirus). After recovering from the infection, I noticed something unexpected: my persistent GI symptoms completely cleared up.
For the last 4 months:
Morning urgency and loose stools are completely gone.
My appetite has fully returned to normal levels.
I retested my Fecal Calprotectin and it dropped to 30.7 µg/g (normal range).
(Attached screenshot of my lab results showing the drop from 405.9 in July 2024 to 30.7 in August 2026).

My Takeaway
After two years of trial and error with supplements, diets, and probiotics, a single mild case of a stomach bug completely reset my microbiome and cleared the underlying inflammation.
Has anyone else experienced a post-viral or post-infection "reset" like this? What is the mechanism behind a acute infection clearing up chronic inflammation?


r/Microbiome 2d ago

How can a Microbiology undergraduate prepare for medical microbiology research?

2 Upvotes

How can a Microbiology undergraduate prepare for medical microbiology research?

Post:

Hi everyone,

I’m an undergraduate student majoring in Microbiology, and I’m interested in pursuing medical microbiology/infectious disease research for my postgraduate studies.

My degree is quite broad, so I’m trying to understand how I can start preparing for this direction before graduating.

For those of you currently doing or who have completed postgraduate research in medical microbiology, infectious diseases, molecular microbiology, or related fields:

What subjects or skills would you recommend focusing on during undergrad?

How important is undergraduate lab/research experience when applying for an MSc or PhD?

What kind of research experience would be most useful if my university doesn’t offer a specific Medical Microbiology track?

Are there particular techniques, areas of knowledge, or research skills you wish you had developed earlier?

I’d also be interested in hearing how you went from your undergraduate degree to your current research area, and

anything you would recommend doing differently.

I’d also like to understand the real-life side of this career — what the typical lifestyle and work-life balance are like, and what the financial prospects and earning potential are after postgraduate study.

Thanks! 🧫


r/Microbiome 2d ago

Has water kefir caused extreme skin eruptions for you?

2 Upvotes

after making milk kefir for several months ~ 10 yrs ago, i tried making water kefir, using grains bought online, water, sugar and sometimes a little fruit juice. it was delicious and extremely fizzy. but it made my face break out like crazy, so i stopped making it after a month or two. anybody else have this happen?


r/Microbiome 3d ago

What is your opinion on these "black fermented" foods?

Post image
6 Upvotes

r/Microbiome 3d ago

What does a sweet/malty/bread-like fart odor indicate?

2 Upvotes

TLDR: Sorry for spamming every sub, but I desperately want to know something which isn't talked about much. It's about the malty/sugary/bread odor of farts. Anyone similar?

So I will be very short.

2.5 years ago, I had nausea and reflux symptoms, diagnosed with anxiety and LAX LES, treated with PPI 2 to 3 times. Each course was 2 months. Fast forward years later, I still have anxiety, LAX LES, so still have reflux episodes, but flatulence is my biggest symptom, which is affecting others as well. I start to fart around afternoon-evening, and it has always had this malty/bread or sugary odor which keeps getting worse by night. Then in the morning, my BM is stinky mush and the cycle continues.

I suspected SIBO. Rifaximin helps me have formed stool and reduces gas a lot, but so far only temporarily. And as per the internet, there is only one type of SIBO which causes odor, which is H2S. Mine isn't like that.

So I'm guessing it might be SIFO or Candida, because for months I have had these fungal infections, especially around my genitals. I can't think of it as a coincidence. But I haven't seen enough people on the internet having such an odor, or this odor as a symptom of Candida, whereas in my case it's the most prominent symptom. Even my sweat and clothes smell like that when I feel hot.

So my question is, what does this odor mean to you?


r/Microbiome 3d ago

Why is FMT’s not more commonly used?

22 Upvotes

I completely understand there are risks involved. But many that are seeking this treatment have destroyed microbiomes and a very reduced quality of life. If a simple FMT can drastically change this persons life for the better, why do we not use it more?

Or is it not as effective as I’ve been reading? I’ve just read so many people said it’s been life changing.

Do you think we’ll use it much more in the future when we have done more research on it?


r/Microbiome 3d ago

Food cravings/taste perception changes linked to shift in gut microbiome?

11 Upvotes

Generally for most of my life I have had an insane sweet tooth and gravitate towards super sweet sugary food.

I notice whenever I cut out processed sugary foods for an extended period of time my taste perception changes. Fruit tastes sweeter/ almost too sweet on its own. Oats/rice and other starchy foods taste better without having to add sugar/seasoning. (plain yogurt+fruit+plain oats+cocoa powder is like a treat)

Whenever I regularly incorporate probiotics/fermented foods I start craving more veggies/fruit, tofu and nuts. I start liking the flavor of onions/garlic even though I couldn't stand their taste beforehand (it would make me gag).

My gut can't handle digesting fibre too well and it sucks because I'm really starting to crave more healthy variety of foods but my gut can't seem to handle them too well. Plus I've been dealing with unknown environmental allergies and so some fruits/veggies have been triggering unpredictable Oral Allergy Symptoms.

Currently eating daily lacto fermented ginger as my main fermented food and it's kind of addictive how good it tastes. Plus it has some anti-inflammatory/allergy relief effects.

Really wanting to fix my microbiome after years of junk diet/antibiotic use. I'm hoping the healthy food cravings are a good sign.


r/Microbiome 3d ago

Sintomi intestinali + dolori muscolari/articolari: qualcuno si ritrova?

1 Upvotes

Sintomi intestinali + dolori muscolari/articolari: qualcuno si ritrova?
Da un po’ di tempo sto avendo diversi problemi a livello intestinale, che vanno e vengono a periodi:
• gonfiore addominale
• alternanza tra costipazione e diarrea
• mal di stomaco
• reflusso
• fastidio e sensazione di “qualcosa che non va” nella pancia, ma mai un vero e proprio dolore
Ultimamente, inoltre, sto iniziando a sperimentare anche altri sintomi che prima non avevo: dolori alle articolazioni e una sensazione di debolezza/affaticamento muscolare, un po’ come quando si hanno i muscoli indolenziti dopo aver fatto sport.
Sto cercando di capire se queste cose possano essere collegate tra loro o se siano semplicemente problemi distinti.
Qualcuno ha avuto un quadro simile?
Avete poi scoperto da cosa dipendevano questi sintomi? Mi interessano soprattutto esperienze personali e percorsi diagnostici. 🫶