/r/Microbiome

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Welcome to r/Microbiome :)

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The Microbiome Reddit

Microbiome - an "ecological community of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. A microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host. The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.

The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genomic characteristics, sometimes collectively referred to as a holobiont.

Wikipedia: microbiome


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/r/Microbiome

127,928 Subscribers

1

Can I open the florestor probiotic? Trouble swallowing it

I need to take a probiotic because I am recovering from food poising and it was recommended by my doctor.

I don’t usually have a problem with pills but for some reason I can’t swallow this one at all. Can I open it and sprinkle it over some type of food or water? Thanks

1 Comment
2025/02/01
13:23 UTC

1

CAMPYLOBACTER Bacterial infection

I recently just got diagnosed with Campylobacter due to food poisoning and its impacted my mental health like hell. Tomorrow would be just x3 weeks in total that I’ve had issues. My GP (doctors) did a stool test and found CAMPYLOBACTER, they said it will take time for it to clear up as my immune system should clear it without the need of antibiotics. However after reading other peoples experiences i feel its not best to wait that long and get anti biotic’s to clear it up before it leads to anything serious. At the moment i feel better in general however i still notice my stomach makes more noises in general, my stools are forming quite solidly, no vomiting or diarrhoea. BUT i have noticed a few chest pains more than normal and if i introduce some of the meals or foods i used to eat, then it wont sit well and my stomach will hurt leading up to me going to the bathroom, but after I’ve been toilet then i’m fine again. Any suggestions or advice would be greatly appreciated

My questions are:

How long generally does this take to fully clear from the system if so, Are there any chances this would come back randomly?

Can this leads to any other serious underlying health conditions such as Chrons or IBD?

Should i take the antibiotics even though its been x3 weeks in total since I’ve been having these

9 Comments
2025/02/01
10:48 UTC

1

Enteropathogenic ecoli question

I’m not asking for medical advice, I’m just curious about why would someone test positive on a biofire stool test for a month? How does this strain stay in someone’s body for this long?

0 Comments
2025/02/01
05:22 UTC

1

But, how???

How do i know that my gut health is good and doesnt need some Change?

1 Comment
2025/02/01
04:54 UTC

0

Help with market research

I’m in the middle of doing market research for an online program to help busy moms eliminate bloating and IBS-like symptoms. If you feel like you resonate and can help me by sparing 30 min for a quick chat can you please respond in the comments or send me a message? TIA!

0 Comments
2025/02/01
02:59 UTC

4

Hey all! Why won’t my GI run a GI map test or gut intelligence test?

I keep asking for more specific testing, but they say they can’t offer anything beyond standard stool and blood work. Instead, they pushed me toward a biologic even though I still had concerns. I’ve seen others with detailed microbiome data, how can I get that information to show my GI? Or would it be better to find a new specialist altogether?

18 Comments
2025/01/31
22:53 UTC

0

Microbiota-friendly home production

Here is my "microbiota-friendly" production of the week: bone broths, unpasteurized yogurt, unpasteurized cheese, whey, beet brine, and fermented orange-carrot pickles.

0 Comments
2025/01/31
21:52 UTC

2

Years of antibiotics off and on and opioids due to a recent surgery.

Hi all. I’ve been on numerous antibiotics for years due to issues with my tonsils. I got them removed recently and had to be on opioids due to the surgery. This being said, I’m dealing with a lot of bloating and constipation especially recently. I eat fairly healthy but I’m willing to do an entire health change if it means fixing this issue and feeling better. Any advice would be appreciated. Thank you 💗

0 Comments
2025/01/31
20:49 UTC

1

Am I stupid for buying this Elemis Digestive System Support?

https://www.timetospa.com/elemis-renew-21-day-digestive-support-system.html

I was sold this on a cruise ship to try to fix my history of constipation and infrequent bowel movements (once every other day, sometimes less). Do the ingredients make any sense?

Should I try and return it?

2 Comments
2025/01/31
17:34 UTC

0

Bloodwork, panicking

I’m panicking really hard. Bloodwork

Really woried for blood test results,

Lupus anticoagulant, LA-AUTO being positive means I’m at very high risk?

Male 23. 105kg, 6’4.

•	Calcium total (serum): 2.51 mmol/L (high)
•	Magnesium: 0.9 mmol/L (normal)
•	Serum iron: 12.7 µmol/L (normal)
•	Cyanocobalamin (Vitamin B12): 186 pg/mL (low)
•	Ferritin: 150 ng/mL (normal)
•	Folic acid (serum): 5.24 ng/mL (normal)
•	Vitamin D (25-hydroxyvitamin D, 25-(OH)D): 15.3 ng/mL (low)
•	Erythrocyte sedimentation rate (ESR): 2 mm/h (normal)
•	White blood cells (WBC): 6.58 ×10⁹/L (normal)
•	Red blood cells (RBC): 5.46 ×10¹²/L (high)
•	Hemoglobin (HGB): 166 g/L (high)
•	Hematocrit (HCT): 48.3% (normal)
•	Mean Corpuscular Volume (MCV): 88.5 fl (normal)
•	Mean Corpuscular Hemoglobin (MCH): 30.4 pg (normal)
•	Mean Corpuscular Hemoglobin Concentration (MCHC): 34.4 g/dL (normal)
•	Platelets (PLT): 282 ×10⁹/L (normal)
•	Red Blood Cell Distribution Width (RDW-SD): 38 fl (normal)
•	Red Blood Cell Distribution Width (RDW-CV): 11.8% (low)
•	Platelet Distribution Width (PDW): 9.4 fl (low)
•	Mean Platelet Volume (MPV): 9.2 fl (normal)
•	Platelet Crit (PCT): 0.26% (normal)
•	Neutrophils (per 100 leukocytes): 49.4% (normal)
•	Neutrophils (abs.): 3.26 ×10⁹/L (normal)
•	Lymphocytes (per 100 leukocytes): 36.2% (normal)
•	Lymphocytes (abs.): 2.38 ×10⁹/L (normal)
•	Monocytes (per 100 leukocytes): 9% (normal)
•	Monocytes (abs.): 0.59 ×10⁹/L (normal)
•	Eosinophils (per 100 leukocytes): 3.8% (normal)
•	Eosinophils (abs.): 0.25 ×10⁹/L (normal)
•	Basophils (per 100 leukocytes): 1.4% (high)
•	Basophils (abs.): 0.09 ×10⁹/L (high)
•	Immature granulocytes (per 100 leukocytes): 0.2% (normal)
•	Immature granulocytes (abs.): 0.01 ×10⁹/L (normal)
•	Prothrombin time (PT): 11.1 sec (normal)
•	Prothrombin by Quick: 124.8% (normal)
•	International normalized ratio (INR): 0.9 (normal)
•	Activated Partial Thromboplastin Time (APTT): 22 sec (low)
•	Thrombin time (TT): 18.9 sec (normal)
•	Fibrinogen: 2.85 g/L (normal)
•	Lupus anticoagulant screening test: 50.8 sec (high)
•	Lupus anticoagulant confirmatory test: 32.6 sec (normal)
•	LA-AUTO: 1.56 (moderate risk)
•	C-reactive protein (CRP): 1.09 mg/L (normal)
•	Thyroid stimulating hormone (TSH): 1.3 µIU/mL (normal)
•	Free Thyroxine (T4 free): 1.05 ng/dL (normal)
•	Thyroid peroxidase, antibodies (ATPO): 12.4 IU/mL (normal)
•	Glycated hemoglobin (HbA1c): 5.08% (normal)
•	Homocysteine: 16.8 µmol/L (high)
•	Parathyroid hormone (PTH 1-84): 25.8 pg/mL (normal)

•	HCV Antibodies: 0.13 (Negative)
•	HBsAg: 0.172 (Negative)
•	HBcorAg Antibodies: 2.39 (Positive)
•	Cholesterol: 5.03 mmol/L (Slightly High)
•	Triglycerides: 1.96 mmol/L (High)
•	HDL-C: 1.08 mmol/L (Normal)
•	LDL-C: 3.25 mmol/L (Slightly High)
•	VLDL: 0.7 mmol/L (Normal)
•	Atherogenic Coefficient: 3.66 (High)
•	ALT: <5 U/L (Low)
•	AST: 27 U/L (Normal)
•	GGT: 30 U/L (Normal)
•	ALP: 100 U/L (Normal)
•	Total Bilirubin: 7.33 µmol/L (Normal)
•	Direct Bilirubin: 2.55 µmol/L (Normal)
•	Indirect Bilirubin: 4.78 µmol/L (Normal)
•	Total Protein: 69.6 g/L (Normal)
•	Albumin: 47.9 g/L (Normal)
•	Creatinine: 109 µmol/L (Slightly High)
•	Urea: 4.26 mmol/L (Normal)
•	Uric Acid: 544 µmol/L (High)
•	Total PSA: 0.424 ng/mL (Normal)
•	Free PSA: 0.219 ng/mL (Normal)
•	Free PSA/Total PSA Ratio: 51.651% (Normal)
•	Total Testosterone: 18.5 nmol/L (Normal)

The last part. I think it confirmed this dangerous auto immune disease? I’m panicking very hard right now. I have history of bad depression and substance abuse. Help me understand what’s happening please

1 Comment
2025/01/31
16:52 UTC

1

What does it mean if PPI caused issue like oral thrush

Does this mean my microbiome is compromised or that I have low stomach acid now? Ever since I took Pantoprazole my tongue is white and I burp all the time. Can anyone please help me

1 Comment
2025/01/31
16:32 UTC

2

probiotics & antibiotics. When?

Probiotics & antibiotics. When?

Doxycycline + Probiotic Schedule:

•	9:00 AM – Take Doxycycline (empty stomach or with a light snack if needed).

•	12:00 PM – Take Probiotic (at least 3 hours after Doxycycline).

•	9:00 PM – Take Doxycycline (12 hours after the morning dose).

•	12:00 AM – Take Probiotic (at least 3 hours after Doxycycline).

Is this schedule ok? My dr told me to take a probiotic first on an empty stomach but I just realised I am taking it after my antibiotic… which is the correct way?

7 Comments
2025/01/31
13:09 UTC

2

PPI question and advice needed

Background: early 30s, got rid of hpylori which was a very tough and excruciating battle last year. Felt better for months then got a lot of nausea, pushed for an endoscopy and they found a little gastritis, inflammation in my throat and a small segment of BE, no dysplasia. I had a hill grade 2 which my GI said was my LES and it’s normal. This was a big surprise to me since I never felt reflux in the past, only silent reflux after getting hpylori. GI said to take omeprazole 20mg till I felt better then take it every other day or Pepcid as needed. They didn’t seem worried at all even though the BE sent me into a healthy anxiety scare I’m still battling today.

I went on omeprazole 20mg, felt better for months, went every other day and things got worse as life got more stressful.

Currently I switched from omeprazole to 15mg of lansoprazole about 2 weeks ago due to dissociation and anxiety from omeprazole which I’ve had issues with on omeprazole and even worse on pantoprazole (really wish I didn’t have as many side effects on them). Overall I feel was more like myself on lansoprazole, but I still feel depressed and anxious/ not like myself at times. I don’t have any stomach issues, just silent reflux and a sore throat with triggers. I’m wondering if I need to up the dose to 30mg or add Pepcid at night.

I’m also waiting on a SIBO test but really doubt I have it since I would have bloating most likely. I think I have messed with my vagus nerve and still need to health my throat. I’m eating very clean and GERD friendly diet, take a strong multivitamin, fish oil, magnesium at night, Gaviscon advance or reflux gourmet before I sleep, sleep on an incline.

Wondering if there’s any other tests to ask the GI for or what I can do to solve my LPR issue? I feel like PPIs really don’t agree with me and I still feel sad and not like myself. Appreciate this community and everyone’s help!

0 Comments
2025/01/31
02:10 UTC

411

Anyone seen anything like this? Painful spasms in my intestines for the past 5 months. What should I do?

344 Comments
2025/01/31
01:26 UTC

0

Has anyone taken the Jona Gut Health Test?

wondering what you guys thought compared to viome etc

0 Comments
2025/01/31
00:18 UTC

1

Loads of gas, any tips? What helped you? Over a year post treatment h pylori. Epigastric gas ball

0 Comments
2025/01/30
23:58 UTC

4

High stomach acid & gerd

Been to the doctor and have been suffering with excessive saliva in my mouth, which when swallowed causes gas, bloating and severe gurgling noises.

I've been on peptac & omeprazole, but no relief from the excess saliva.

I've tried taking Kefir, increasing fruits and eating sprouts, but no joy. I've also tried ginger tea, which only gave temporary relief.

Is there any prebiotics I can take or if someone has suffered a similar problem?

6 Comments
2025/01/30
21:41 UTC

3

I really need some advice. Suddenly developed chronic constipation over a year ago.

Male 28, I’ve never had any GI issues until last November. I’ve eaten an extremely clean and strict diet most of my life but even more so in recent years. No history of any GI issues save for an occasional stomach bug. Last November I had a respiratory illness and was put on azithromycin. I’ve been on multiple antibiotics over the years and have never had any issues, I eat extra fermented foods/take probiotics a couple hours away from the antibiotics during the times I’m on them and, more recently, I started taking digestive enzymes.

About a week after the Azithromycin, I was put on Bactrim. I had yet another respiratory illness and had coughed up some bloody phlegm. I could not tolerate the Bactrim and it made me feel horrible so the doctor switched me to doxycycline and I felt better.

However, one day I had noticed “thats weird I haven’t pooped in 24 hours…” which had never happened to me before in my life. And about 12 hours later I had a brick like stool pass. I could quite literally see a line in the stool where it went from 27 years of healthy to completely compacted and constipated. It was also tan colored.

Since that day my GI system has been altered. I’ve seen specialists, tried any and every supplement, dietary change, OTC constipation remedy, had a HIDA scan, stool sample, Colonoscopy, CT scan, ETC. there doesn’t seem to be any rhyme or reason to my change and getting any doctor to hear me or help me is nearly impossible. They suggest fiber and miralax which I am already on daily. Now I’m having significant abdominal pain daily due to it being this chronic. One doctor suggested recently it’s a motility issue due to the nerves not working properly but even he said he was spitballing.

I also have found that more recently the stools themselves might even be soft due to the supplements/prunes/miralax I take but it will sit in my gut for days. When I’ve had CT scans they always come back that my GI system is backed up.

I should also mention that certain foods have become completely off limits: last year when this started I was unable to consume anything with nuts or seeds, any sort of chocolate or coffee and any sort of cheese. I mean that if I had a single chocolate chip, a single almond my system would shut down. Not just that it would get slightly worse, that it would immediately shut down. At some point this past fall I started being able to have chocolate again for some reason without issue.

I also found that taking digestive enzymes, any sort of organ supplement, and NAC caused my issue to get much worse.

I know this is very complex and weird but any sort of help or advice would be appreciated.

I just want to figure out what is wrong

35 Comments
2025/01/30
17:26 UTC

5

Gluten sensitivity but not celiac or allergy. I’ve done a celiac test and I’ve come back not celiac, I’ve sent off for blood allergy and intolerance test, come back as to having no sensitivity for gluten/ grains. But when I eat gluten I get a burning sensation in my stomach. Any ideas?

11 Comments
2025/01/30
17:14 UTC

10

Is it true? (New here sorry)

Is it true or have any of you experienced this? Do antibiotics, and ppis like nexium actually ruin your gut health to the point it can cause anxiety and mental disorders?

I’m starting to wonder if this is part of my problem. I take probiotics now. But I had a lot of times over the years with antibiotics and long term ppi use whether it was nexium Prilosec or pantoprozole .

feel free to share your experience or knowledge on this! I’m thinking of stopping nexium completely apparently even my bp pill might have caused anxiety

33 Comments
2025/01/30
16:25 UTC

4

Antibiotics messed me up.

In the last 3 years I have taken brad spectrum antibiotics once a year. And I finally noticed, after taking antibiotics by symptoms such as reflux, cold fingers after eating, loss of facial volume and overall thinning gets worse. I have read that since antibiotics caused major dysbiosis, it caused low stomach acid, gut inflammation because of excess pathogens and possibly also SIBO if there is an overgrowth of pathogens in the small intestine. In the past I have test positive for SIBO hydrogen and also GI stool test showed dysbiosis. I took antibiotics a month ago due to some chest infection, which I should not have. My current protocol is taking HCL with meals and also ginger-artichoke for motility.

Now moving forward I am not sure what to do.

  1. Should I do a SIBO test and a GI map stool test ? And then focus on getting rid of SIBO first
  2. Or Should I just do a GI stool test and try to focus on building specific low gut keystone bacteria ?
14 Comments
2025/01/30
16:06 UTC

0

Low stomach acid

I got blood work done and took it to a functional medicine doc. I have low stomach acid. I went through a bottle of HCI and never felt any discomfort. I have moved on to ACV and it’s only been a few days. I was curious and did the baking soda test this morning and it’s been 15 mins and I still haven’t burped. Any other ideas for me? Or do I stick with ACV for now?

23 Comments
2025/01/30
14:01 UTC

126

The Gut-Brain Connection: How Diet Can Influence Mental Health

The connection between the gut and brain is stronger than many people realize. Research shows that an imbalanced gut microbiome, often caused by poor diet or stress, can lead to systemic inflammation, which is strongly linked to depression (Jacka F., et al., 2017). On the other hand, maintaining a healthy gut through probiotics, such as those found in fermented foods like yogurt, kimchi, and sauerkraut, can support neurotransmitter production and reduce depressive symptoms (Li X., et al., 2022).

Anti-inflammatory diets, like the ketogenic diet, have also shown promise for improving mental health. By shifting the body’s energy source to ketones, this diet helps reduce inflammation and stabilize mood-regulating neurotransmitters, such as serotonin and GABA (Dietch D., et al., 2023). Additionally, cutting sugar and processed foods can help restore gut balance, further benefiting emotional well-being (Jacka F., et al., 2017).

Making small changes to your diet, such as introducing probiotics, reducing sugar intake, or exploring keto, could make a difference in how you feel mentally and emotionally (Dietch D., et al., 2023).

If you're curious about this topic or want to learn more, I can send you links to scientific articles.

30 Comments
2025/01/30
12:58 UTC

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