pH level and microbiome balance & changes in inflammation in Long-Covid/ME?

Image generated with Midjourney by D. Troy Roach (28-02-2023)

pH level and microbiome balance & changes in inflammation in Long-Covid?    

Below is my theory which was originally published on May 28th, 2023. I think I might have found a major piece of the puzzle during day 4 of #TheNicotineTest. Is this the end of a long rabbit hole? I hope so!!! Details of the theory will be published in this Google Doc:

I am only at the beginning of this rabbit hole. I am still determining where it is going. All the things I am looking at might just be basic science that is boring for a microbiologist.

I might also be wrong on many levels! However, even if it is wrong, it might lead to a glimmer of insight somewhere in the search for answers? A piece of the puzzle?

Right now I just have a bunch of random points that seem connected but might not be...

Therefore, I will just list the points to see if anyone can help me make any connections:

1. My confusion over the presence of "Silent" Reflux (GERD) among many people with Long-Covid led me to this webpage which talks about LPR (

2. In LPR the "bad" guy is pepsin, not stomach acid per se.

3. PPIs are not an effective long-term solution for LPR.

4. Pepsin is calmed down at a pH higher than 6.5.

5. The easiest way is alkaline water with Baking Soda (pH8).

6. However, it is good for the stomach to be acidic (pH2)... so it is not as easy as just adding Baking Soda to water.

7. Gargaling Baking Soda might help the mouth and upper respiratory (above the Larynx), but that will not help from the larynx down to the top of the stomach (esophagus).

8. Some Japanese ENT is using Zinc scrubbing to reduce inflammation in the nasal cavity and throat of ME and LC patients, but that does not help the esophagus either. Seems to have some benefit, but painful and requires lots of visits... and my Spanish ENT thought it was interesting, but "odd" since she sees easier benefits with meds.

9. Some indirect benefits of fasting and IF might be the "rest time" that the biggest system gets to relax and repair itself and adjust pH levels in the different regions.

10. pH levels of the various regions of the Digestive System (DS) sections are very different.

11. Both antibiotics and fasting seem to benefit people with ME and LC. The wonderful researchers from the @remissionbiome project are going to get lots of data that will help improve our understanding of the antibiotic side... while letting us watch them do the research in real-time!

12. My first doubt: Are antibiotics beneficial to these diseases because they actively kill off "bad" microbes? Or might it have more to do with pH adjustment and regulation? BTW, Antibiotics do more, but that is not the point of this rabbit-hole rant😉.

13. Might Fasting, especially long fasts, arrive at similar results as antibiotics without the downsides?

14. My benefits (20% improvement) came from a 9-day fast while taking two antibiotics for Diverticulitis. What really helped me? The fast? The antibiotics? The fact that the digestive system could rest? The adjustment to the pH in my esophagus and intestines? A break from food that let the sphincter muscles of the Digestive System heal and work better at regulating pH? Maybe the reason is that a different pH helped the Vagus Nerve heal and to reduce the inflammatory/sympathetic signals from the brain?

15. Reading the experiments with Baking Soda lotions during the @remissionbiome project and the possible benefits to vagal tone seemed to be connected to this stream of thought, but I don't know how! A change in pH in any part of the Nervous System -- whether it be through the skin or through the intestines -- is beneficial for improving vagal tone.

16. Looking at which foods are alkaline (high pH) vs. acidic seems to correlate with most "healthy diet" recommendations for people with LC. Check out this list and graphic of food pH. Maybe these foods help keep the intestines (and the throat) alkaline, thus favouring a good microbiome?

17. This article gives an overview of how the pH changes through the digestive tract. It is interesting that my body seems to crave some peanut butter after eating. PB has a pH of about 6.5 and coats the mouth and throat on the way down. The mouth and throat have a pH of 6.8. Could the craving have something to do with the body balancing pH?

18. This website has articles on why pH is so important. It seems to be a wellness trend that people take too far towards alkaline by making the stomach too alkaline. It looks like they will be selling supplements, so we have to take what they say with a grain of salt! The key is to look for a natural balance. The stomach needs to be acidic and the intestines more alkaline. AND, anxiety (dysautonomia caused by Long Covid) can affect this balance! It is a two-way street in the gut-brain axis.

19. (added 24-03) When thinking of the microbiome people mostly think of the intestines. However, the mouth and bladder also have their own microbiome.

The Bladder:

Urogynaecologist, Professor Vik Khullar @vikkhullar1 should be a superstar in the world of #LongCovid!
In this video, he shows how great doctors work. Here is my TLDR of the main points.
1. He started to get an influx of patients with urinary issues.
2. Biopsies of bladders showed increased T-Cells (inflammation).
3. Patients had other issues so he connected the issues with MCAS, POTS, etc.
4. The inflammation is not caused by a persistent virus. It is an autoimmune problem 
that sees benefits from the treatment with H1 and H2 antihistamines.
5. Chronic inflammation damages the smooth epithelium layer of the bladder. 
6. This leaves a rough irregular surface, changing the environment of the microbiome drastically.
7. This environment increases the likelihood of infections.
8. This change in shown in a drastic change in types of bacteria. 
9. A rare bacteria that once was 3% of infections is now 60%. Proof of microbiome change.
10. First, reduce inflammation (H1 or H2). Then work on killing off bad bacteria.

My takeaway. The pH issue might also be a "rough texture" issue caused by inflammation.
Maybe this "texture" issue is the cause of so many gut problems? My acute Diverticulitis? 

LC is a complex issue that needs a holistic approach.

The Mouth:
Consultant Radiologist (
Dr. Graham Lloyd-Jones @DrGrahamLJ) is working on advancing the theory that the Mouth is a key player in Covid. Follow him on Twitter for details on how to take care of your oral microbiome!

Update 31/03/2023
I finished my 3-month long n=1 trial with PPI (Pantoprazole) a few weeks ago.
I now feel as though the PPI or the rebound from the PPI has affected my thyroid. I have never had thyroid issues in the past. I now feel "Hypo"...but I have never had Thyroid issues in the past. It is just a feeling. Hopefully, my thyroid levels will be fine and it is just my body reacting to the rebound.
There is some research on PPIs affecting the thyroid. This article found the same research that I did.
Rebound Symptoms from when I finished the PPI course for Silent Reflux.
1. From Day 1 to 5 I felt better than normal and stopped needing to get up once a night to urinate. Odd, but good.
2. Nightly bathroom breaks returned and increased acid levels caused GI discomfort and some indigestion (not common for me). Stomach acid change (the increase from the rebound) somehow is affecting my bladder muscles?, biome? In general, the issue with not-voiding completely seems to be better... thanks to the PPI rebound
3. Stomach Acid seemed to reach its peak at 10 to 15 days.
4. General feeling of being less hungry, more nervous energy (in the hypo sense, not the vagal sense), and very sensitive to caffeine. My two cups are now 1/2 a cup or 1 cup a day.
5. Slight weight loss, which is a good thing since I am trying to reduce visceral fat and gain it back in muscle mass... that is the plan. So far, the low-impact weight sessions are too few to make a huge difference--pacing while working and trying to recover is a high-wire balancing act.
6. Still pending a visit to the ENT to see if the PPI reduced the symptoms of silent reflux. My theory is that the benefit of PPIs comes from letting the esophagus rest while being subjected to less acid and pepsin. This helps reestablish pH levels above the stomach. Then the rebound helps increase stomach acid to good levels (I avoided antacids in the rebound). Higher acid levels help with digestion and help the signaling to the sphincter to stay closed and protect the esophagus. Better stomach digestion helps the intestines do their job better since the nutrients are more processed.

Update 25th of April 2023:
1. I seem to have recovered from my PPI rebound. My gust feels "normal" again and the "Hypo" feeling has passed.

2. Brandon Giles experimented with "probiotic enemas" that helped him recover to a high level. Unfortunately, his story did not have the happy ending we were all hoping for. 

3. A couple of researchers with Long-Covid have published a theory that is (in my opinion) similar to my pH theory. See Vicky van der Togt's feed for first-hand info! It seems to be based on abnormal lactate levels in #LongCovid, acidosis? and a low-acid diet. They found benefits from their theory and they want to test it on other patients.

4. Related to the lactate theory above is the current "fad" of #LongCovid patients to test lactate levels. It is tricky to test and devices and strips are not cheap. However, there is a device sold in the UK GlucoRX that is only 20 pounds! I do not know how reliable it is...time will tell. Testing lactate might be a great objective test to aid in pacing and recovery! This has led to another patient-led research project. Dr Naomi Harvey (PHD) is heading that up. That will be interesting to follow. Have access to a lactate monitor? Check out the protocol and add your n=1 to the data!
This article has great tips on being successful with your DIY lactate test. (See the article and tips in this tweet and the comments).
Update (august 2023): I bought the meter and did some tests, but it arrived after doing my second round of nicotine patches so the data did not show high lactate. I have switched gears to use the lactate meter as a way to test myself while doing exercises to safely get back into shape.

So, stepping back and looking at the big picture:

Might this be an issue that should be looked at by analyzing pH levels in different areas of the body and Vagal Tone? Is capillary lactate a good measure? It appears to correlate in this study.

Is there a correlation between disease severity and the pH levels in one area of the body? Maybe in the back of the throat or in one or more sections of the intestines?

Maybe a pill that directs sodium bicarbonate to an area of the intestines without stopping at the stomach would be as beneficial as antibiotics or fasting in some cases?

And, it might also be important to look at pH levels in the mouth, esophagus, upper airways, bladder, etc while looking for the best way to correct the pH to optimal levels.

Or maybe the "Double Antibiotic" therapy is beneficial because the "rough/damaged" surface needs extra strong flushing?

I currently think the digestive endothelium is damaged in many locations. Long-term Fasting, or fasting-mimicking is my bet for the best "cure" for LC. It lets the digestive system rest, heal, and reset. *

*Antibiotics may be needed as well to help kill off bad bacteria thriving in the small pockets left by the rough texture. My diverticulitis was just an acute infection in a "big pocket". 

** The Nicotine Patch Test is having great results so far. This could be due to a reduction in neuroinflammation that affects the pH balance in the gut and the neuroinflammation in the brain at the same time.

My rant for today is done! Any input or correction is welcome! Also...feel free to ignore me! 😂😂😂


"Take care of yourself, and if you can, take care of someone else too." Stephen Dubner

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