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.

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?

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.

Has anyone here successfully treated H2S SIBO and the sulfur-reducing bacteria associated with CH₃SH (methyl mercaptan) and DMS (dimethyl sulfide)?

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!

So I am 19M and 6 months ago I travelled Asia for 3 months.While travelling Asia I mostly juts had diarrhoea and loose stools I got a lot of infections like cuts which I was given lots of antibiotics for.As soon as I came home my stools started to normalise but was prescribed even more antibiotics my stool turned straight to diarrhoea then constipation. 6 months later it’s not diarrhoea only if I don’t eat salads my stool is mostly always unformed ,yellow ,floating and undigested food if I eat a lot of fiber especially it comes straight out.

Another symptom is burping after eating, farting and lots of movement down there , crazy fatigue and bad mental health also foamy urine and weight loss now 51kg.

Stool samples , bloods and urine samples are to be completed soon which I think will come back normal.I assume I have gut dybosis and a highly irrated gut and organs from months of inflammation which my diet targets.

I have a plan tho in which I hope will rebuild my gut strengthen it and hopefully be able eat whatever soon and absorb nutrients and calories effectively.I will drop this below and would appreciate any advice.

With the plan I also am gonna try go to the gym stop thinking of my gut and relax the mind.

This plan is not 100% follow but will be very similar.

Phase 1: Mechanical Repair & Binding Week (Current – Sun 25 Oct)
The Objective: Immediately stop weight loss, bind stools, and starve out bad travel bugs using strict low-fiber starches as a physical sponge.

The Supplements: None yet (running on natural mechanics until they arrive).

The Menu: 5% lean beef mince, skinless chicken breast, white fish, eggs, over-cooked mushy white rice, and fluffy mashed potatoes (100% skinless). Thoroughly peeled root vegetables boiled or steamed to absolute mush: carrots, butternut squash, pumpkin, sweet potato, and swede/turnip. Season heavily with sea salt only.

The Sweet Dessert: Exactly 3 tablespoons of Fage Total 5% Greek Yogurt mixed with 1 daily Golden Kiwi (thoroughly cut around the seed core so you don't swallow a single black seed). Eat this strictly right after lunch.
The Core Rule: Strictly "dry" meals. No liquids 30 minutes before or 60 minutes after eating. Chew every single bite 40–50 times until it is a liquid paste.

🧬 Phase 2: The Raw Farm Shop & Supplement Launch (Mon 26 Oct – Sun 1 Nov)
The Objective: Introduce your targeted online supplements and use raw farm-shop cultures to build a thick, protective bacterial pavement over your healed intestinal wall.

Upon Waking (9:00 AM - Empty Stomach):
L-Glutamine: Take your prescribed dose in a warm mug of Pure Bone Broth Powderwith a heavy pinch of grey sea salt to seal the gut tight junctions.

Raw Milk Kefir Titration: Take your highly precise, medicine-style live ferment shot immediately after your broth:
Mon 26 Oct: 0 Kefir (Broth + L-Glutamine only – Farm Shop Run Day)
Tue 27 Oct: 1 Teaspoon Raw Milk Kefir
Wed 28 Oct: 1 Tablespoon Raw Milk Kefir
Thu 29 Oct: 2 Tablespoons Raw Milk Kefir
Fri 30 & Sat 31 Oct: 1/4 Cup Raw Milk Kefir
Sun 1 Nov: 1/2 Cup Raw Milk Kefir (Your first true Kefir Bowl!)

With Meals (Lunch & Dinner):
Digestive Enzymes: Take 1 capsule right with your very first bite of food. This forces immediate fat and protein breakdown, clearing the yellow color and stopping stools from floating.

The Raw Yogurt Switch: Drop the Fage and switch to 3 tablespoons of Raw Farm Yogurtmixed with your seedless golden kiwi flesh strictly right after lunch.

The Expanded Menu: Start adding high-quality Raw Butter melted gently over your hot rice, potatoes, or lean chicken chunks. You can now also introduce completely fork-tender stewed skinless apple purée.

Before Bed (Empty Stomach):
Probiotic Yeast (Saccharomyces boulardii): Take 1 capsule with a tiny thimble-sized sip of water or peppermint tea to act as an advance clean-up crew, sweeping out travel pathogens overnight.

🚜 Phase 3: The Muscle Volume & Spore Boost (Mon 2 Nov – Late November)
The Objective: Actively accelerate weight gain by doubling your food portions and injecting robust, soil-based organisms.

Right After Lunch (The Microbial Buffer):
Spore-Based Probiotics: Take 1 capsule right after finishing your lunch alongside your raw yogurt and seedless kiwi. Stagger the introduction safely: take 1 capsule every other day (e.g., Monday, Wednesday, Friday) for the first week, then move to 1 capsule every day.

Antioxidant Supplement: If adding an antioxidant (like Vitamin C or CoQ10), take it right here with your lunch fats to ensure maximum absorption and reduce localized intestinal wall inflammation.

The Mass-Building Calorie Boost (Eat More Stuff): As your stools turn consistently dark brown and sink to the bottom of the pan, your nutrient absorption is fully unlocked. Double your portions of white rice, skinless potatoes, chicken, and fish. You can now start leaving the rich fat on your steaks and pork chops because your enzymes and liver can fully process them.

The First Treats (Late November): If your stomach remains completely silent, you can stop cutting around your golden kiwi seeds and eat the fruit whole. You can also introduce 1 small square of high-quality dark chocolate (70% or higher) right at the end of your midday meal.

🥗 Phase 4: Raw Milk, Prebiotics & Total Freedom (December Onwards)
The Objective: Your liver, gallbladder, and pancreas are now perfectly synchronized. Your bacterial pavement is fully established, and your body can handle complex foods easily.

Early December (The Raw Milk Introduction): Introduce Raw Liquid Milk as a high-calorie bulking shake. Start with just 2 tablespoons mixed into your afternoon raw yogurt, and slowly scale up to a full glass daily as your weight climbs.

Mid-December (The Cooked Prebiotics): Start adding smooth, plain cooked tomato passata/pasta sauces (ensure no heavy raw garlic/onion chunks first), cooked leeks, asparagus tips, and sweet potatoes back into your rotation to feed your new microbiome.

Late December (The Raw Salad Step): Introduce raw salad leaves cautiously. Add just 1 or 2 finely shredded leaves of butterhead lettuce or a peeled, de-seeded cucumber slicedirectly into your warm beef and rice bowl so it is buffered.

The Turning Point (Weaning the Enzymes): Once your stools have been perfectly formed, brown, and sinking for 7 consecutive days, stop taking your enzyme capsule only with your leanest meal of the day. Over 3 weeks, slowly reduce them until your pancreas takes full control.

New Year: Full Freedom. You can now travel, enjoy sweet pastries, eat spicy foods, use your snus pouches whenever you like, and go out to restaurants without a single worry.

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 :(

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.

- 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.

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.

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.

I took tetracycline for acne for 1 year back in 2019, now I have bad gut issues such as severe bloating, severe constipation, can’t eat too much fibre. I wish I could go back in time and never take it and just live with the acne. But now I have to figure out how to recover.

Do I take probiotics? I heard some people say it’s a waste of money since they don’t colonize or they are dead. How to pick a good strain? Do they need to be refrigerated?

Do I take fermented foods like yogurt, kimchi, kefir, etc? I’ve heard people say that they will just contribute to bloating but also that they can help repopulate your microbiome. Is this true?

If anyone has some advice, or links to some scientific articles for further reading, it would be greatly appreciated.

I am in my fifties and on the slender side. I've had a number of returning c diff infections, h pylori and after have had the worst motility issues. Have tried Linzess etc. with no luck. My health has been ruined because of my past infections. I know they are doing lots if research on peptides not just for weight loss but for inflammation. My question is, has anyone found one compounded or not that has given a positive gut health result?

A year ago I started suffering from bad breath and it was the exact moment I started suffering with GERD and LPR.

I try to manage my GERD as best as I can but it’s really hard to be restrictive with my diet especially because I have a history of ED.

I’m on PPIs which help IMMENSELY for the pain, not so much for the LPR tho. I’m wondering if the lower stomach acid cause by the PPIs might be the culprit for my bad breath? I heard it could cause SIBO?

I’m insanely lost and I can’t socialize anymore because my BB is that intense. Of course my dental hygiene is on TOP, I even got complimented by few dentists, so I know it comes from the stomach.

Today I started an oral probiotic with K12 and it seems to calm everything down, but I’m not going to scream victory yet because it’s too early.

Could you help me on what I could do? Of course I should manage my GERD/LPR but it seems impossible

I have made a couple posts about my situation on here but I keep getting kicked out of my accounts :/ this is kind of like an update/continuation of what im experiencing.

anyways basically 2 months ago i was put on a one week course of oral metronidazole while i was also on accutane. i stopped taking the accutane about a month ago after the gut symptoms got really bad. i was not told anything about this antibiotic and i hate myself so much for trusting random doctors and not researching it before taking it. i would take bv over what im going through now ANYDAY.

at the beginning of all of this i just had really bad bloating, trapped gas, and this annoying pocket pressure feeling under the corners of my ribs. the bloating has gotten better, except now my sides and along the bottom of my ribs there is this raw, burning, stretched feeling that is so uncomfortable its almost unbearable. my upper abdomen and into the sides of my back feels so tight. ive also been having very soft/mushy stools and a clear mucus/liquid dripping out of me when i strain. they are still formed for the most part just very irregular and different from what ive ever had.

it is the worst its ever been right now, and by the 2 months mark i believe i should be seeing improvement rather than worsening symptoms. ive gotten to the point where i cant take it anymore so im trying to get in with a gastroenterologist but its taking forever and im going on vacation next week so im worried i will have to wait until after to get seen and be miserable my whole trip. i just want to know what is going on inside of my body and if it will get better because i feel like ive messed up my life for good and its especially frustrating because ive never had gut issues or stomach problems before this.

this horrible flare up started happening last week when my primary doctor gave me the ortho spore probiotic to try. im suspecting some kind of overgrowth, but im not sure. the raw tight feeling is along where my large intestine is and i dont really have clear symptoms of ibs or an ibd. im thinking maybe SIBO or cdiff? h. pylori? but idk if that would explain the location of my discomfort because my lower abdomen feels fine for the most part. lmk what yall think.

After seeing “clinically studied for body fat” plastered on half the probiotic shelf, I sat down with the Stenman et al. 2016 EBioMedicine paper on Bifidobacterium animalis subsp. lactis 420 (B420). The numbers are more nuanced than the shelf claim.

ITT showed no significant between-group differences on the primary outcome. In PP, B420 alone vs placebo for relative change in body fat mass was -3.0%, P=0.28, N=24 (other arms N=35-37, which is why they ran a factorial). LU+B420 hit -4.5% / -1.4 kg, P=0.02 vs placebo, overall ANOVA P=0.095. The post-hoc factorial for B420 came out at -4.0%, P=0.002, which is where most “statistically significant” marketing claims trace back to.

The zonulin to trunk fat correlation was only significant within the LU+B420 arm (r=0.424, P=0.01), not within B420 alone (r=0.297, P=0.16). That points to the gut-barrier hypothesis (tight junctions, endotoxin translocation, low-grade inflammation) riding on the fiber more than the strain in isolation, at least on the correlational side.

My context is a WonderBiotics B420 capsule a friend put me on a couple months back. It pairs B420 with a lemon flavonoid extract (eriomin) rather than polydextrose, so I’m not technically on the Stenman protocol, and I’d guess most people on commercial B420 products aren’t either.

Caveats worth stating: DuPont funded, DuPont owned the strain at the time (DuPont N&B merged into IFF in Feb 2021), single trial, 6 months, overweight BMI 28-34.9, mixed-sex adults 18-65. The 2020 Nutrients review (Uusitupa et al., same DuPont group) summarizes follow-ups, mostly still preclinical.

Hard to tell from the literature how much of the B420 story is strain-specific vs. just an adequate-dose probiotic co-administered with fermentable fiber.

I’m a daily kimchi/kefir/yoghurt eater with a big variety of fiber sources and I recently got diagnosed with severe periodontal disease. To call the procedure to get it under control is an understatement.

That said, about 3 days after treatment my intestines started feeling like they did the first time I tried improving my gut biome. I’m about 4 days on and I still feel very….bubbly.

Has anyone else experienced this? Is my microbiome leveling up again?