Multiple Gut Insults — A mess!

Backstory

  • In September 2023 I suffered a series of gut insults (food poisoning, antibiotics and gastritis) in a very short period. This gave me unrelenting brain fog and cognitive issues, fatigue, tinnitus, sleep difficulties, and a slew of other issues.
  • In an attempt to recover from this I went hard on prebiotics and probiotics, and seemingly without reason these would trigger worsening of symptoms. Looking back at my November 2023 sample (closest after the insult) on your website, I can see some of the items that made me worse, like slippery elm, were at the top of the avoid list! I wish I had an understanding of the website back then...
  • I have undergone multiple killing phases with antimicrobials, which did nothing but make me worse. I now see that building up the good bugs and crowding out the bad is the better technique for my situation.
  • After getting enough of understanding of your website and suggestions I have made some objective improvements in my most recent sample and across the board symptom matches are down. Unfortunately, this hasn’t resulted in symptom improvements (yet).

Today

  • My worst symptoms remain brain fog (cognitive issues, fuzzy thinking, memory issues, etc), fatigue and tinnitus. I remain bedbound since the event in 2023.
  • I believe your approach of focusing on enzymes and compounds are more likely to result in improvements for me than just targeting bacteria changes.
    • Upon reviewing my enzyme and compound movements, pre and post 2023, there are some that are likely to be causing my cognitive issues and maybe fatigue (such as very low L-LDH, high H2S, etc). What do you think about this?
  • Based on the most recent sample suggestions I am using apple cider vinegar, BB536, cannabinoids and dandelion.

Preliminary Analysis

Using [Old Menu] / [Multiple Samples] is my usual start point when there are multiple sample.

I did a compare of the latest sample [2025-05-20] with [2025-03-25] and everything was better!

This person has a series of samples, so I am going to compare each against the prior to see the trend over time. The first sample marked with symptoms was 2023-11-30. Total is the count of distinct symptoms reported from prior and current sample.

SampleBetterWorseTotal
2024-02-02 7115
2024-09-0578078
2024-10-3007979
2025-02-200170
2025-03-251077
2025-05-2066066

There was a dramatic reversal in September 2024 which appears to be starting to correct itself in May 2025.

Going Forward

My approach is a three step approach.

  • Use the symptom patterns to identify the most likely bacteria involved. Then look for the best probiotics to address them
  • Use the symptom patterns to get a list of suggestions
  • Do a generic (not using symptoms) to get a 2nd set of suggestions

First step, using the symptoms to identify bacteria of interest and then get suggestions. We have a high rate of match for forecast symptoms and actual symptoms — which is a good indicator.

The result was just 6 bacteria identified as off.

BacteriaRankShift
DysgonomonadaceaefamilyLow
ErysipelotrichaceaefamilyHigh
ErysipelotrichalesorderHigh
ErysipelotrichiaclassHigh
HathewayagenusLow
NegativicoccusgenusHigh

For comparison, I did the same for the prior sample and instead of 6 bacteria, we had 18. Four are in common with the above.

Focus on Probiotics ONLY

We have the most information on probiotics. We have the following sets of data to work from:

  • Clinical Studies: Certain probiotics are heavily studies, others are not. Often reporting of changes is on a few bacteria. Studies populations are small resulting in only strong associations.
  • KEGG Data on Metabolites and Enzymes: Complete coverage of all probiotic bacteria. Ignores epigenetics and related issues, i.e. we assume everything is “turned on”. Yeasts (i.e. aspergillus oryzae, Saccharomyces) not included.
  • Taxa R2 Site : Complete coverage of all probiotic bacteria and full taxonomy. Yeasts (i.e. aspergillus oryzae, Saccharomyces) not included.

Our goal is determine the bacteria probiotics that every diverse methods agree upon. That is the “consensus” or conservative Monte Carlo Model.

Experiment R2 approach

I went to Microbiome Taxa R2 Site to see if there are any probiotics that would be suggested based on these. I have only listed those currently available (not pending)

Clinical Studies

I checked probiotics and found the top 2 were Bifidobacterium and thus should be avoided? Why do I trust R2 over clinical studies… simple — clinical studies are sparse for data. Just bits and pieces of the puzzle. R2 is far more complete.

Take items:

So we have three probiotics with a consensus and two yeast type probiotics

KEGG Bases

Probiotic computed from Kyoto Encyclopedia of Genes and Genomes compounds and  Probiotic computed from Kyoto Encyclopedia of Genes and Genomes Enzymes have the following with a positive value

And then Experimental Using Metabolites also had them on the take list. So we have the three key probiotics that are available retail with consensus for all of the above methods.

Other Suggestions

I am going to start with the Food Menu Planner. This look at some 111 nutrients identified and then at what various foods contain.

The site presents all recent results

The simplest way is to just click the “Quick” lists. It uses food nutrients databases from all over the world, so some items are likely not on your local cafĂ© menu.

Take Foods:

Picked for common foods:

Avoid Foods

Consensus View

We have some agreement with the above list

Avoids

Takes

My general impression is try to get a single course of each of the two specific antibiotics above (after each course, do probiotics, then the next course, followed by a different probiotic). I see that Rye is positive and wheat is negative… so we will likely be eating 100% rye bread likely with liver paste (that is one of my favorite foods by the way!) and Pizza (light on the cheese).

I would drop BB536 (Bifidobacterium) and keep to:

Remember these are suggestions — not a protocol. suggestions are items you should take a bit more of or a bit less of! The goal is to persuade the microbiome to shift in the right direction. I have only highlighted items of interest, a review of the details should always be done.

Looping back to Brain Fog — typically caused by excessive d-lactic acid. I have several past post on this issue:

Checking your microbiome tree, I see high levels of Veillonella but with a gotcha, Veillonella is mainly Veillonella montpellierensis (99%ile), a novel species. 1/6 of studies on pubmed has this species causing issues like Polymicrobial bacteremia with little known about it. It is not listed on R2 site for Veillonella.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

An overview of some issues trying to be addressed is described in this video.
https://www.youtube.com/watch?v=kUnHucfoxL0

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