Back Story

In 2021, at age 28, I developed an upper respiratory infection while working in a hospital (tested negative for Covid repeatedly). The URI persisted for over a week so I was prescribed a course of Augmentin thinking it might be a sinus infection. On day two of antibiotics, brain fog, headache, orthostatic intolerance, and fatigue began and never went away. I would go on to develop PEM and sleep disturbances and I was eventually diagnosed with ME in 2023. 

I have two tests that have been uploaded. The first is from 2023, at which point I was Mild/moderate and still had some bfido/lacto left but was also dealing with a dysbiosis. The second is from 2024 and am now very severe. Probably unsurprisingly, I have had a decrease in levels of desired bacteria and also changes in the dysbiosis. 

There seems to be conflicting suggestions between new UI and the cross validated items to add. If I was considering an antibiotic for example, the new IU weights specific floroquinolones highly and lists macrolides as items to aovid, while the cross validated suggestions say to add specific macrolides. Diet styles and some specific supplements also seem to conflict. What do you recommend when there are conflicting suggestions between the two?

Additionally, within the new UIs suggestions,

 the individual probiotics in items to add list list don’t always match the recommended probiotic products. (Ex. L. Sakei and L. Hellveticus are listed under to avoid/decrease column, but are also listed in the commercial probiotics section with a relatively high weight.)

I am wondering if you can help me better understand the specific bacteria that have changed as my ME had gotten worse, how to potentially optimize them, which suggestions to follow, and how I might apply all that to Dr. Jadin’s protocol? 

I apologize for my lack of understanding and for all that you’ve already explained and that I’ve missed. I’ve spent a lot a time on your site but am very limited in what I can do and process at the moment and want to make sure I’m approaching this the right way. 

You have my permission to use the above information for a blog post. 

Review of Concerns

Microbiome Prescription does best efforts and without dedicated staff to do checking — a variety of errors can occur. I depend on people like the above person to ask questions.

Conflicting Suggestions

Above there is the subjective report of getting worse, this is objectively seen with predictive symptoms where the number exploded and the agreement with self-reported was significant

2023-01-23	2024-11-23

The first question is which methods were used in both the simple UI and the old UI. Different choices result in different suggestions. Suggestions are based on which bacteria were selected to be significant and the type of modifiers. You can get some items flipping from take to avoid with different choices. No one knows the right way to select which bacteria and their significance. Microbiome Prescription tries to give a variety of choices (so people can follow their beliefs on what is significant).

For the New UI suggestions, I will use: Beginner-Symptoms: Select bacteria connected with symptoms . Despite the large number of symptoms, we ended up selecting only 24 taxa, with 12 genus being significant:

The suggestions are below

Old UI

The old UI gives many different ways of getting suggestions. These choices allow users to follow their beliefs for better or worse. A few choices are below

I tried Critical Bacteria Associated to Symptoms. This seems to be the closest equivalent to the Simple UI. We got just 16 bacteria selected with only 4 genus. 1/3 of what we got above. Why? When I wrote the Simple UI, I incorporated a different way of weighting and filtering bacteria as a result of more recent research and observations. Also, I also incorporate multiple algorithms in the Simple UI (which is why it takes much longer to get suggestions).

I checked the top few items from the Simple UI and they were on this to take list, just with a lower value. The additional bacteria shifted the order.

Q: Why did I not revise to make them agree?

• Answer: I do not know which is the best. I intentionally avoid changing algorithms that have been in use for any time (unless there is a gross error). When I did that in the past, I got a flood of email asking for explanations. The Simple UI captures my best current thinking when I added it.

Probiotics Question

From the Beginner-Symptoms: Select bacteria connected with symptoms we have

Looking at the KEGG computations on the Simple UI we have those on the KEGG Compound / Enzymes Lists Suggestions

• aor / probiotic-3 at 45 / 107
• bioflorin (deu) / bioflorin at 41 / 86
• mwsb / candida yeast support at 44 / 105
• Pendulum / Pendulum Glucose Control at 40.6 / 90.6
• miyarisan (jp) / miyarisan at 46 / 115

We have apparent good agreement.

Looking at Critical Bacteria Associated to Symptoms suggestions, we see a short list

Looking at the KEGG computations on the Simple UI we have those on the KEGG Compound / Enzymes Lists Suggestions

• Maple Life Science™ / Bacillus clausii – 50 /122
• Maple Life Science™ / Bifidobacterium infantis – 38 //75
• o’donnell / flora-balance – 45 / 105

Bottom Line for Probiotics

I do not see either L. Sakei and L. Helvetius in the above list, so I will assume that a different filter was used to get them.

Antibiotic Question

Unlike probiotics, we do not have 2 additional scales to evaluate suggestions (i.e. KEGG Compounds and KEGG Enzymes)

Simple Suggestions

The — numbers below are from the OLD UI

• Floxacin family
  • norfloxacin — 0.056
  • ciprofloxacin [CFS] — 0.053
  • ofloxacin — 0.034
  • sparfloxacin (antibiotic) — 0.023
• metronidazole [CFS]
• ornidazole
• benzylpenicillin sodium (antibiotic)

So, what we see is that with the smaller genus count, antibiotics are of a much lower value. When the other genus are added, they become more important.

Bottom Line

I wish that I was omniscient on the microbiome and how to adjust it. I am not. I have listened to people on what they believe is the right way and implemented it. For the Simple UI, I did my best attempt to compute suggestions. With the suggestions computed from PubMed studies and the suggestions computed from KEGG’s data being in general agreement (at least for the top items), I fell confident that they are reasonable. The same core algorithm was used for Suggestions Cross Validation using PubMed where we had an average of 86% agreement.

Post Script

I went and used Strict PubMed Cross Validated Suggestions, with  Inflammatory Bowel Disease and Chronic Fatigue Syndrome. This uses a different approach to filtering and thus different suggestions are expected.

The Genus flagged were the 8 below (midway between the 4 and 12 above):

• Bacteroides – genus : High
• Bifidobacterium – genus : Low
• Clostridium – genus : Low 
• Faecalibacterium – genus : Low
• Haemophilus – genus : Low
• Lachnospira – genus : Low
• Prevotella – genus : Low
• Streptococcus – genus : Low
   

With the suggestions below (remember ONLY items showing positive effects in studies are included, items not reported in studies are excluded):

The “best” would be to use what all methods agree on. If there are conflicts, omit the items. Usually, there will be a significant list of items in agreement.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Backstory

I have been suffering from various health problems almost all of my life (49 years old) starting at around age 7 with digestive issues, eczema, acne and multiple sensitivities. These issues have only escalated in the last 15 years causing me to have to resign from my position as a data analyst 6 years ago due to my health issues which are food sensitivities to gluten, dairy, soy, corn, sugar, MCAS, multiple chemical sensitivities and in the last 5 years electromagnetic sensitivities so that i have had to remove all sources of wireless and cell phones in my home. I have installed ethernet for my PCs and have had to resort to basically becoming a shut in because i cannot go out in public or drive for more than a few minutes before experiences various health problems like heart palpitations, shortness of breath, dizziness, etc. luckily i have been eating pretty healthy since 2010 (no gluten, dairy, soy, sugar, corn) and am able to at least survive in my home but it would be fantastic if i could get some guidance as to what seems to be causing these issues. I have had tests for mold and lyme and both have tested positive and i am so sensitive that i am unable to tolerate any supplements. This has obviously made it extremely difficult to make much progress. I have transferred my Biomesight report to MicrobiomePrescription If you could please find the time to help me with my biomesight report and feel free to use it anonymously for a blog post it would be greatly appreciated 

Analysis

I am not a health professional, I have built an academic model that generates suggestions that are expected to typically reduce symptoms; in some cases, I have gotten reports of full remission. All of the suggestions should be reviewed by a knowledgeable professional.

Looking at entered symptoms, we see a high agreement between forecast and reported symptoms.

This allows us to focus on the bacteria that are likely to be involved with this person’s symptoms.

I usually do a multiple step approach because there are no “correct” way to do analysis and get suggestions. The ways are:

• Beginner Symptoms
• Probiotics:
  • From KEGG Enzymes
  • From KEGG Metabolites
• Browse through the Consensus

Beginner Symptoms

We have 20 bacteria identified:

The “kitchen sink” suggestions are below

With a “skinny” list (no prescription items) below. Remember, many people with do the take suggestions and skip the avoids …. and then wonder why progress is slow…..

KEGG Based Probiotics

The top probiotics that are relatively easy to get are (Metabolite / Enzymes) With ** being positive on consenus, and *** being very positive.

• Bifidobacterium longum subsp. longum (45.1, 47.55)
• Limosilactobacillus fermentum (42.5, 49.4)
• Lactiplantibacillus plantarum (40.95, 55) **
• Enterococcus faecium (40.65, 58.45) **
• Bifidobacterium longum subsp. infantis (40.3, 46.5)
• Lacticaseibacillus rhamnosus (39.45, 60.5) **
• Bacillus subtilis (37, 61.6)
• bacillus subtilis natto {B.natto} ( 32.75 ,60.65 ) ***
• L. Casei (33.75, 55.2 )***
• L. Gasseri (16.5, 37.5 ) ***

With B. natto being the highest I would start there — unfortunately, the main source is a Japanese food called Natto — a bit of an acquired taste and unfortunately soy.

The secondary way is using Nattokinase supplements. If the natto food causes problems, then go to Nattokinase.

Given the number of allergies, I would only suggests from these sources. Your reactions may be partially caused by additives,

• Custom Probiotics :they list all of their strains — many are researched on the above list. No other ingredients just the bacteria.
• Maple Life Science™: No strains yet, but shipments usually have manufactured date within 4 weeks of arrival (i.e. FRESH). Contains FOS
• Bulk Probiotics: US based Newbie — but has some species not available at the other two sites. No other ingredients just the bacteria.

I would experiment with the following three (different genus) probiotics to see if any are tolerable after reviewing Probiotics – General Advice

• Bacillus subtilis
• Bifidobacterium longum subsp. longum
• Limosilactobacillus fermentum
  

The rest, given your allergies and sensitivities, are likely having to do trial and errors on the suggestions to see what you react to.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Back Story

I got COVID on 2022. Then my symptoms started like 6 months after the infection.

Pain at the base of the skull and nausea (I went to a neurologist who ordered an MRI and everything was normal).
One day, I was sitting at work when my heart started to race for no apparent reason, about 180 bpm, lasting for 5 hours. Since I thought I was having a heart attack, I went to the emergency room, where they performed an ECG and enzyme tests, all of which came back normal. I was prescribed medication for colitis.
Tingling in my arms and hands.
Metallic taste in my mouth during moments of alertness or high stress (e.g., when about to crash in a car).
Exaggerated reaction to situations that were previously normal, such as involuntary hand muscle shaking when I was about to start an F1 race. Feeling like I was going to faint after a huge emotion, like after my team scored a goal while I was in the stadium. Rapid heartbeats, shortness of breath, and rigid hands during a traffic jam (it would usually improve by drinking electrolyte solution). Rapid heartbeats when speaking in public (this didn’t happen before).
Afterward, I saw an internist, and he said my symptoms were due to vagus nerve irritation, prescribing Esomeprazole, Lunarium, and Cinitaprida. At that time, I didn’t have any symptoms of acid reflux or heartburn, but he suggested it might be silent reflux. I was on this treatment for 2 months, but the other symptoms didn’t improve. They did improve a little by taking Vitamin B complex and magnesium.

Subsequent symptoms:

• When it’s very cold or hot, I start feeling disoriented and a little nauseous.
• Burning sensation on the outer part of my left arm.
• Shortness of breath with exertion.
• Cold hands.
• Epigastric bloating (I feel this is what causes me to not be able to breathe deeply). It has gotten so bad that when I breathe deeply, I hear a crackling sound in my sternum.
• Nasal passages closing.
• Acid reflux.
• Pain in the center of my back, related to reflux.
• After exertion, disorientation, weakness, a little dizziness (it was worse before, but not as much now).
• Brain fog (this has improved over time, I feel more mentally clear).
• If I skip a meal, I feel extremely bad, I get nauseous, and feel very disoriented.
• Constipation (I used to go 3 times a day with normal consistency, now it’s only 2, with very variable consistency).
• Slurring words when speaking (this doesn’t happen much anymore, but it was common at one point).
• Belching (in the morning and during/after exertion).
• Very fast heartbeat after eating, feeling dizzy while eating.

Recent symptoms that concerned me:

On a camping trip, we went to … for work, and after walking approximately 10,000 steps uphill and downhill according to my app, I started feeling short of breath and my epigastrium was very bloated. I was also burping a lot and regurgitating some food. My heart rate was extremely fast, way too rapid, and I felt weak. I started feeling disoriented. My extremities were freezing. I didn’t have dizziness, chest pain, or nausea, but it felt like I was about to faint at any moment. It was time for lunch, and I had no appetite, but I ate anyway. My pulse regulated about an hour later. Then my blood pressure was taken, and it was 138/80. Normally it’s around 110/70, I’ve checked it in the mornings, and it’s always close to that value. After that, the rest of the day, when walking, I felt short of breath easily. The next day I still felt very fatigued, maybe due to my lack of physical activity. On Saturday, I went to a wedding, and since we were running a bit late, I started feeling short of breath. I danced for about an hour, then sat down as my heart rate started accelerating. I felt disoriented for a few moments, but then my heart rate slowly regulated. The next day, I felt fine. Then, while driving, I had a lot of acid reflux, so I took TUMS. About two weekd after , after 10 minutes of walking, I started feeling very weak, so I checked my blood pressure, and it was around 90/60. Then it went up. This happened for about two weeks, and then stopped.

When I clon Ed stairs, about 3 flights at a normal pace, when I reach the top, I feel short of breath, I burp, and feel disoriented. Normally, it takes about 1 hour for me to feel okay again. When I’m worried about something, I feel like I’m about to faint.

Today, I am bedbound and can hardly think. I cannot walk more than 3 minutes. I would like your help to improve, thank you, god bless you. 

Analysis

Looking at forecasted versus entered symptoms, we see many matches. We will use this as one of our collection of suggestions. The other two are Cross Validated for Long Covid and KEGG Enzymes/Metabolites. No one knows the perfect solution, I look to where we have the greatest agreement as the best pathway forward,

From the above, we get just 25 critical bacteria. The top suggestions are very familiar from other analysis:

• Inulin
• Wheat Bran
• Wheat
• Dietary Fiber
• Barley
• Maize
  

The list is below

The top probiotics appear to be Limosilactobacillus reuteri {L. Reuteri}, bacillus licheniformis {b. licheniformis},Saccharomyces cerevisiae var boulardii {S. boulardii} and L. Gasseri . Unlike most people with Long COVID, only a single antibiotics appears in the top list.

Going to Cross Validated Suggestions, we see a smaller number of bacteria flagged as significant.

With the suggestions having some overlap with the above:

• minocycline
• Propolis {Bee glue}
• ß-glucan {Beta-Glucan} i.e. Barley etc

In general. these same items often appear further down the list on the consensus list. The list above lacks priority.

KEGG Enzymes and Metabolites

The top suggestions are:

Probiotic	Compound	Enzymes	Consensus
Lactiplantibacillus plantarum	41.65	33.85	292.7
Escherichia coli (Mutaflor)	38.65	51.65	63.2
Limosilactobacillus fermentum	36.6	30.95	314.8
Bacillus subtilis	36.5	49.5	80.6
Limosilactobacillus reuteri	34.85	34	492
bacillus licheniform	33.95	48.6	422
L. Gasseri	17.6	15.85	74.6
Saccharomyces cerevisiae	—	—	366

My suggestion for probiotics to be used in rotation (1-2 weeks of each and then move to the next) are:

• L. fermentum
• L. plantarum
• L. Reuteri
• Bacillus subtilis
• Mutaflor

See Probiotics – General Advice for more information.

My recommendation for a regular breakfast is porridge (Barley, Oats) as well as a high fiber diet (see How much fiber is best/ideal? ).

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Back Story

Back story: I have probably been infected by Covid since Nov 2021 and developed post Covid. In mid 2022 I got many urinary tract infections and took many antibiotics including ciprofloxacin. After another infection in End of 2022, I developed MECFS in early 2023 and was diagnosed with viral myocarditis in 2024. I have had problems with medication intolerances (bile issues: losartan, clopidogrel; pain, breathing: prednisolon, ketotifen, LDN) since 2023 and develop biliary pain every time I take them, which has persisted since the first time I took clopidogrel and is made worse again by the abovementioned medications. Everything has been checked many times with ultrasound, bloodwork, faecal examination, MRI and the like, including the pancreas. Nevertheless, the potential medical condition worries me. Can I counteract it?

It has been confirmed that I am dealing with chronic myopericarditis. Additionally, I have been suffering from constant gastritis since July 2024, which has caused ongoing issues. In the first half of 2024, I tried new medications. Ivabradine works well for me, and I continue to take it. However, I could not tolerate Prednisolone and Losartan due to side effects. Losartan, like Clopidogrel previously, caused biliary pain. Prednisolone led to severe muscle and joint pain, likely due to FQAD (following Ciprofloxacin use), which has had long-term effects on me.

Currently, my main symptoms are:

• Chronic gastritis, likely triggered by Pentoxifylline, turmeric, or possibly diet.
• Persistent biliary pain, worsened by fatty meals (extensively checked by gastroenterologists with examinations including bloodwork, MRI, ultrasound, and tests for the pancreas and gallbladder – all results were normal).
• Severe fatigue and lack of energy.
• Muscle pain. (feels like lactic acid. Tested after a lot of sugar/carbs on christmas)
• Persistent tiredness.
• Anxiety and nervous system overstimulation.
• Medication reactions (possibly MCAS).
• Reactions to carbohydrates/sugar, resulting in heart palpitations and autonomic nervous system overstimulation.
• Concentration difficulties.
• Angina Pectoris symptoms.

I am currently housebound and feel that I need to rebuild my stomach health to heal the gastritis and regain energy. Unfortunately, I had to take Pantoprazole, Gaviscon, and slippery elm for a long time due to the gastritis.

I have already purchased all the probiotics from your list and created a 4-week plan (attached) based on your PDF. However, I recently read your December 2024 post about the potential dangers of Lactobacillus, which has left me feeling uncertain.

Analysis

First, the lactobacillus probiotics issue is mainly a caution. There are lactobacillus probiotics that will produce significant amount of d-lactic acid that will worsen brain fogs etc. This is compounded by both species mis-identification issues on retail probiotics and that different strains of the same species may produce different compound. Avoiding lactobacillus is the safest (simplest) course for many.

Chronic myopericarditis has no explicit literature on microbiome shifts. I suspect Heart Failure is the closest match for what I have gathered data on. My expertise is assembling “the facts” from studies on the microbiome and the mathematical application of these facts. So proceeding with my skill sets and available data, let us look at your data.

Quick Health Review

• Low bacteria leak from the Oral Cavity
• General Health Predictors has no concerns
• Mold ratio is higher – 82%ile than ideal (See Associations of observed home dampness and mold with the fungal and bacterial dust microbiomes .)
• MHI-A Ratio is very high – 96%ile. This is an indicator of post-antibiotic dysbiosis — which is very much in agreement with your back story.
• No medical conditions pattern matched your microbiome
• Two bacteria are of possible concern: Faecalibacterium and Bacteroides uniformis

Most of the other measures are questionable in their usefulness given your back story.

Predicted Symptoms that matches back story

A few of the clear matches are below.

• General: Fatigue – [88.5%]
• Neurocognitive: Brain Fog – [88.2%]
• Official Diagnosis: COVID19 (Long Hauler) – [87.6%]
• Comorbid: Histamine or Mast Cell issues – [86.9%]
• DePaul University Fatigue Questionnaire : Anxiety/tension – [86.5%]
• Comorbid: High Anxiety – [86.2%]
• Immune: Sensitivity to smell/food/medication/chemicals – [86%]
• DePaul University Fatigue Questionnaire : Abdomen pain – [86%]
• Autonomic Manifestations: palpitations – [85.9%]

These are checked and use to generate suggestions. Because of the existing use of prescription drugs, those are included in the suggestions.

Some 66 bacteria were picked from the matching patterns

Checking substances tried or taking (where we have information). The goal is to see what helps or hurts the microbiome. I have switched to % of highest or lowest value below

• ciprofloxacinm, LDN, around 61 ( -20%)
• losartan, clopidogrel, ketotifen, clopidogrel, Ivabradine, Prednisolone, Losartan, Gaviscon, Pantoprazole – no listed (i.e. no effect on microbiome or balanced effect)

Alternatives to clopidogrel likely include:

• aspirin, resveratrol:  -30% which are likely worse choices.
• slippery elm: -30%
• Ginkgo biloba {Ginkgo}: +80%

So no major hurt and no apparent better with the exception of these antibiotics that are round +30% positive (lincosamide, kanamycin, paromomycin, ofloxacin) and a potential discussion point with your MD.

Prescription items high on benefits are:

• proton-pump inhibitors (prescription): +100%
• metformin (prescription): +85%
  

Cross-Validated Suggestions

I went to the old UI to see what shows up with cross validation.

The algorithm is slightly different (no one knows the right answer — and I have implemented multiple “reasonable” approaches across the site. We see that with this alternative algorithm, the slightly negative for LDN above is now positive. Similarly with Prednisolone.

The preferred pattern is to always discuss with your MD, try items in isolation (i.e. one new item a week) and taking notes for response.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Backstory

• 25 Year Old Female 
• 2016: Experienced a concussion.
• 2018: Diagnosed with chronic Lyme disease.
• 2019: Dealt with chronic mold exposure 
  • all of the above diagnoses/symptoms improved by 2020.
• 2022: Food poisoning led to IBS-D (Irritable Bowel Syndrome with Diarrhea).
• 2024: Contracted COVID, resulting in hives, joint pain, and fatigue.
• 2024: Chronic UTIs managed with Hiprex.
• Current Symptoms:
  • Persistent diarrhea and stomach cramps.
  • Constant fatigue.
  • Occasional joint pain.

Analysis

First Thoughts

The constant UTI infection cause a knee-jerk suggestion for the following two probiotics:

• Lactobacillus Johnsonii {Lactobacillus Johnsonii} [store] [store]
• Lactobacillus Jensenii [store] – suggestions are neutral for this

Details

The reader does not appear to have added their symptoms, but the top current symptoms is cited under Current Symptoms. In fact, there are 245 symptoms forecasts at 80% or higher…

• Lyme at 84%
• COVID at 90.1%
• Diarrhea at 90.7%
• Joint pain at 87.9

I am just going to do  Novice: Just tell me what to take or avoid, to start. We have 43 bacteria identified as being too high or too low. The top suggestions are shown below

Typically I look at Probiotics first — mainly because of the common belief that they should be “cure all” In this case we have the following being usually available, I added some online stores after a few of them:

• Limosilactobacillus reuteri {L. Reuteri} [store] [store] KEGG:30/67
• Clostridium butyricum MIYAIRI 588 (CBM 588) {Miyarisan} [store] KEGG: 50 /121
• Streptococcus salivarius subsp. thermophilus {S. thermophilus} [store] KEGG: 22 /46
• Levilactobacillus brevis {L.brevis} [store] KEGG:32 /76
• Lactobacillus Johnsonii {Lactobacillus Johnsonii} [store] [store] KEGG: 22 / 47
• Enterococcus faecium {E. faecium} [store] KEGG: 29 /75
• Heyndrickxia coagulans {B. coagulans} [store] KEGG: 52 / 139
  

My usual suggestion is to do one at a time starting with a low dosage and then increase (double every second day) until you are at known effective dosages listed here. Keep at the maximum dosage for a week (or bottle is empty), and then proceed to the next Take notes on any changes seen (stool shape, farts, moods, etc). Some will have dramatic positive effects, others little.

The above were computed based on the complex interactions across the microbiome using literature from the US National Library of Medicine. An alternative approach for probiotic selection is using KEGG data to supplement with enzymes and metabolites that you appear to be low in.

Typical for Lyme, Long COVID and ME/CFS, Escherichia coli is the top choice (Mutaflor and Symbioflor2) at 109/293. With this method, {B. coagulans} and Clostridium butyricum would be the next choices.

Other Items

• Vitamin B-3 (explicit, not a B-Complex). B1 and B2 are to be avoided.
• Vitamin K
• {Tryptophan}
• {Taxifolin}
•  {Fisetin}
• magnolia bark {magnolia bark}
• eugenol {Eugenic acid}
•  {Inulin}, {Chicory},s {jerusalem artichoke}
•  {Ribose} – known to help ME/CFS and Lyme often

There were no strong diet suggestions to take, but avoid high carbohydrate diet and ketogenic diet. Foods to avoid are atypical items (cranberry bean flour, cranberry bean flour, {black currant},lychee fruit etc). Also to avoid: {Ginkgo}, a-Gluco-oligosaccharides {GOS}, Carrageenans {Carrageenan}, {Stevia}.

Cross Validated for Long COVID

This is a more restricted identification of bacteria to shift. The changes found that agreed with literature is shown below.

The suggestions are shorter and includes antibiotics.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

• Terrain-related data
• Signs of low stomach acid, pancreatic function, bile production, etc.
• Detailed health history
• Specific symptom characteristics (e.g., type and location of bloating)
• Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
• Individual susceptibility to specific probiotics
• Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
• Possible histamine issues
• Colon acidity levels
• SCFA production and acidification needs

Backstory

I’m writing today to get your guidance.  I recently got back my 5th microbiome sample and I haven’t made significant progress.  I suspect it’s because of the food I eat, and I’m hoping you can help advise me of what to eat.

Earlier post: Another ME/CFS person has gone to Firmicutes! [Jan 2023]

My hypothesis as to why i’m not getting better results is that I haven’t followed the dietary recommendations very closely.

The recommendations are to basically eat a carnivore diet.  My main diet… Fruit, Oats, Rice, Potatoes, Nuts, Wheat and cheese are all hugely negative.  Thus, I think this is what’s holding me back.  It’s nice to identify the problem, but the solution isn’t easy.  

The only thing for me to eat on the recommendation list is Meat.  Even vegetables are mostly disallowed because I’m supposed to eat low fiber.  

Is that your understanding as well from the recommendations – that I should be nearly 100% meat (and possibly eggs), with some low fiber vegetables?  It’s hard for me because i prefer to be vegan.  But i’ll do whatever I need to fix my gut.

Note: 4 months ago I completely eliminated wheat and cheese and I started eating beef once a day.  That helped but it doesn’t seem to be enough, which is why I’m reaching out to inquire what to eat. 

 I  think I can withdraw my question.  I didn’t know what I would eat when meat showed up on my Suggestions list as basically the only option.  But I’m having miso or bone broth soup for breakfast, eggs for lunch, and meat for dinner… and that feels sustainable for me.  So far I think it’s working.  Time will tell.

Over the last 18 months i’ve had some good days and even a good week here and there, which has given me hope that your approach holds the solution i’ve dedicated a lot of my life to over the last 15 years.  However I always gravitate back to my baseline of feeling crummy.

I thought that taking all the top suggested pills, and cutting out the foods with very negative Priority score would be enough, but I now believe that my diet of mostly oatmeal, nuts, beans, (and previously wheat) has been holding me back.  All those items have a negative Priority scores, and my recommendation list very clearly points to red meat, low fiber, low carb.

First Step: Compare Last to First Sample

This immediately ran into issues with sample quality. One sample produced 723 bacteria versus 434, i.e. 66% more. It makes comparing the numbers very difficult.

Criteria	Current Sample	Old Sample
Lab Read Quality	11.8	4.3
Outside Kaltoft-Moldrup	220	86
Bacteria Reported By Lab	723	435
Bacteria Over 85%ile	84	66
Bacteria Under 15%ile	268	58
Lab: Thryve
Pathogens	33	20
Condition Est. Over 85%ile	2	10
Kegg Compounds Low	238	331
Kegg Compounds High	196	309
Kegg Enzymes Low	83	479
Kegg Enzymes High	322	237

A second approach is to compare forecast symptoms

Current Sample	First Sample

The surprising thing is how close both sets of forecasts are to each other, often with less than 1% difference. The reader’s “I haven’t made significant progress” appears to be right on. This is the first repeat analysis that there was not objective improvement all. The expert system is not perfect.

Going Forward — let us try getting religious on suggestions!

I am going to do three approaches to try helping this person:

• Stock suggestions from the Expert System using the simplified UI. This used only studies on PubMed to try to shift the microbiome.
• Using the Food Site – This use the nutrients identified as significant and tries to map them to a wide variety of foods (infer from nutrients to food)
• Probiotics using KEGG – this uses no explicit studies, rather identify what substances that the microbiome may be starving for, then identify any probiotics that produces those substances. The reasoning is that the starvation contributes to the dysfunction.

Remember, everything are estimates of likely to help (or hurt). Estimates can be wrong. In some cases, it may be worthwhile to do a short term trial to see if there are any immediate changes. This applies especially to anything that is a mixture because the good may overpower the bad (or the reverse).

Simplify UI

We get 137 (out of 723, i.e. ) or 19%. The top diet types are shown below

We see high values for:

• diosmin polyphenols at 340
• high red meat at 423
• Crataegus {Hawthorn} Herb at 320
• Carrageenans {Carrageenan}
• With inulin, the basic form is a big -1040, while oligofructose-enriched inulin is a positive but different forms of oligofructose are all negatives — so would definitely avoid all inulin
• probiotics are low in ranking
• Biotin {Vitamin B7} is the top suggestion

I had the same takeaway about inulin!  The basic form was super negative but the oligofructose enriched was very positive.  Not going to risk touching it.  

Similar thing with “low-fat high-complex carbohydrate” diet, which has a positive Priority score of 237.  However,  “Slow digestible carbohydrates” are negative 634  AND a “restricted-fiber diet” is hugely positive.   It would seem to me that eating low-fat high complex carbs is way too risky  🙂

Reader Feedback

The hard part – AVOIDS

The list contain many items that are often seen as to take.

Over to Food Helper

The food site, Microbiome Prescription Food And Nutrients is designed to bridge the gap between some nutrient tested in studies and foods it is found in. The food are often not tried in studies – so this is an inference because of sparse data. It should always be used with a grain of sodium chloride (salt).

The quick take list suggests:

• American cranberry (a good seasonal food)
• Seal, Whale, Beluga, Canada Goose and then ham sausage!!!
  • Bột cá (Fish Meal)
• Beet root, peeled, boiled, drained (without salt)
• Okra stew, (Thelele lobala lokupa)
• Onion, fresh, boiled (without salt), drained
• Turmeric, dried, ground

The suggested nutrients are shown below

Take translates to American cranberry, raw black olives, a variety of fish

And these are the to avoid

Avoids translates to Vinegar, Almond, Red wine, chocolate

I will leave it to the reader to dig more on the food site. It may reveal what may have gone wrong.

KEGG Probiotics

This is an alternative way to determine probiotics working off compounds and enzymes produced (or not produced) compare to an estimated norm.

The results are shown below (first compounds and then enzymes). Suggestions are similar with the exception of the E.Coli probiotics. I would suggest these two:

• Bacillus clausii (linked to source)
• Bacillus mesentericus

Note: Prices include shipping anywhere in the world. These are typically manufactured weeks before shipping (have manufactured date) and thus alive. If you double the number of capsules, the costs usually go up by 20% only (see example below) and the price is awesome!!

$.29 per capsule	$.20 per capsule	$.15 per capsule

I just ordered the bacillus clausii and the bacillus mesentericus you recommended.  Thanks for making it so easy and linking it to an eBay seller!..

[Update] I just cancelled the bacillus mesentericus and the bacillus clausil you linked to.  They both contain fructooligosaccharids, which are a negative 193.

Question: Why did I skip Mutaflor?

• Items that are on both list are more likely (better odds) of having a positive impact. I am an odds-person (i.e. a statistician).
• Also, Mutaflor has a large number of additives: The other ingredients include maltodextrin, talc, methacrylic acid-methylmethacrylate copolymer, macrogol, triethyl citrate, glycerol, titanium dioxide, iron(III)-oxide, white beeswax, carnauba wax, shellac, and purified water

Probiotics Solutions when additives are a problems

There are two providers with no declared additives that I know of:

• Custom Probiotics :they list all of their strains — many are researched on the above list. No other ingredients just the bacteria.
• Bulk Probiotics: US based Newbie — but has some species not available at the other two sites. No other ingredients just the bacteria.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

My back story –

I’m now 35. As a child I contracted a bacterial gut infection from water that had cow poop in it (broken pipe through a field), and was unable to eat sugar without being sick. As a teenager I had relatively bad insomnia, acne and eczema. I was prescribed months of antibiotics as treatment and put on a contraceptive to address the acne. I also had a spinal injury that I was prescribed painkillers including ibuprofen and codeine, and a painkiller that’s no longer approved for distribution that I forget the name of. By the time I was 19 I was in a high stress job, sleeping well, but taking guarana and caffeine pills on top of coffee to stay functional due to fatigue. 

Doctors took blood tests, and everything was in the normal range so no diagnosis. 

At 22 I had sever food poisoning in the Netherlands. 

At 25, in 2016, I took a trip to California – I’m from New Zealand – and contracted giardia, during a heatwave, and ended up in hospital in hypovolemic shock. I was prescribed fluids which where intravenous and an anti-psychotic, which as a New Zealander I didn’t take. My sister flew over to help me get home. Once back in NZ, I was found to have irregular heartbeat, giardia, and neck injury from severe vomiting. I had an allergic reaction to the first antibiotic to treat giardia, was given a course of prednisone then a different antibiotic which killed off the giardia. 

During this time, I had extreme fatigue, brain fog, heart palpitations, insomnia, panic attacks, tension headache and the worst, internal vibrations or tremors that could not be seen. I developed a dependency on sleeping pills, which quickly stopped working all together. Doctors couldn’t find anything physically wrong with me, and eventually one decided to try b12 injections. This, along with osteopathy and rest, resolved most symptoms, leaving only tinnitus. I have had b12 injections 1-3 monthly ever since, and this mostly controls the vibrations. I resolved my dependence on sleeping pills by using natural sleep aids and pushing through several sleepless nights. I was left with an inability to eat gluten and dairy.

By 2021 I was in good health – able to regularly exercise and hold down a high pressure job. I had my first Covid vaccine no issues, the second vaccine I became violently ill for 48 hours with fevers, fatigue, and body aches. I took the recommendation to get the third shot, still Pfizer, and was bedbound for 2 days with fevers, rigours, vomiting, headache, weakness and fatigue. In December 2022 I contracted Covid. My symptoms included sore throat, swollen lymph nodes, vomiting, fevers, rigours, fatigue, elevated heart rate. By day 7 I was weak but recovering. On day 8, internal vibrations started with severity, followed by blurred and double vision (I required a new prescription following this), breathlessness walking across a room, heart palpitations, tension headache, brain fog, PEMS and extreme fatigue. I was diagnosed after 3 months with long Covid. 

I tried every treatment suggested by the internet and then some, from HBOT to magnesium floats to ozone sauna, thousands of dollars of supplements, osteopathy, massage, and more. After almost 2 years I’m working full time again, and most symptoms are managed enough to wake up, work, clean up a bit, and sleep again. However they are not fully resolved – I can’t exercise without an extreme energy crash, and I have to continually practise meditation and other calm down methods to regulate. It’s certainly not a life lived well, and one in constant fear of catching so much as a cold.

I am hesitant to accept a ‘long Covid’ diagnosis, despite it being the only thing on offer. This is because I experienced the same set of symptoms I after having giardia and dehydration, neither of which are viral so not a “post viral syndrome”. My lifelong battle with fatigue indicates to me that serious illness triggers a specific set of symptoms, and my Biomesight results strongly indicates a gut issue. I have tried various diets, each resulting in my becoming more fatigued – keto, Mediterranean, low carb, vegetarian, carnivore, low formal, and high protein. 

I find the microbiome prescription results a little overwhelming and difficult to sort through, so your advice would be so appreciate

Analysis

First, about “overwhelming”. I agree! Just like “No man can serve two masters”, “No site can server all users”. My primary focus has been correctness, depth of coverage and other technical (nerd) aspects. This came out of seeing failure after failure of simplified and naïve approaches. The “new UI” has been an attempt to simplify the process while maintaining a reasonable level of accuracy.

You have had a long history of microbiome insults causing dysbiosis. Some are known to cause ME/CFS, see IBS/CFS/Long Covid Insight from Bergen’s Giardia Infection [2018]. Rather than retracing past events, let us focus on your current state and go forward.

Looking at predicted symptoms versus reported symptoms, we see a high number of matches.

This usually indicate that “Beginner-Symptoms: Select bacteria connected with symptoms” is likely the best start, This will focus on the probable bacteria that are causing most of the symptoms (and ideally ignore bacteria shifts that are likely just noise).

Usually the number of bacteria identified is a fraction of the symptoms. In this case we have 63 bacteria identified for 55 symptoms. The suggestions are shown below. I usually suggest keeping to those above 50% of the highest weight (1706 x 50% =853) and avoiding to those below 50% of lowest value (-1375 x 50% = -865). The reason is that the higher (or lower) the weight, the more probable it will have an impact).

I retried checking all types of microbiome modifiers (usually overwhelming). Mainly to see if antibiotics often used for ME/CFS rank high. Going to the Consensus Report and filtering to antibiotics we see that none made it over the threshold – which means that they are likely to be really helpful.

At this point, I typically decompose suggestions into types, first with probiotics. VSL#3 is rarely a clean choice because there were changes in the formula and other issues.

I would go for the following probiotics (two weeks of one at a high dosage – 50-150 BCFU) and then rotate to the next. Given that you are “down under” , I would suggest getting them from my favorite Indian Manufacturer (usually manufactured just weeks before shipping and best prices) – I linked to the sight below. Note that doubling the capsules in a bottle often costs just 20% more and a lot cheaper than ordering two bottles!!

• Lactobacillus gasseri {L.gasseri}
• Bifidobacterium breve {B. breve}
• Limosilactobacillus reuteri {L. Reuteri}

P.S. spirulina was a coding error – just fixed it.

Your inability to handle gluten or diary means that some suggestions must be excluded. I would be tempted to try an experiment with oats flakes, then barley flakes, then 100% rye bread — mainly to see if it is wheat gluten that is the issue (there are many types of gluten).

A handful of almonds and walnuts everyday is an obvious item. Do not do a B-Complex — some B vitamins will help and other hurt. Keep to Vitamin B7, B2. Hopefully you can tolerate dark chocolate (Cacao). Lime is suggested (as is Vitamin C).

The avoids should be pretty clear.

Alternative Paths

At this point, we branch into two additional paths — one by using Kyoto Encyclopedia of Genes and Genomes (KEGG) data on compound being produce and consumed by your microbiome. With KEGG we look for probiotics that can provide enzymes etc that you are deficient in. Why these alternative paths? Simple, there is not enough data available so we use inference.

The second path is going to the food site to identify foods rich in suggested nutrients. The foods may not have been used in studies, but the dominant nutrients in the foods may have been studied.

KEGG

The top suggestions are below. #1 item is common for ME/CFS, Mutaflor is available in Australia, I warn people that it may cause a major die-off / herx reaction. Symbioflor 2 is the same probiotic species but at ~ 1/100 of the BCFU and unlikely to cause die off. To the above list I would add these two

• Maple Life Science™ / Bacillus mesentericus [Link]
• Maple Life Science™ / Lactobacillus plantarum [Link]

Foods

We see that you may be eating a lot of beans – they appear to be providing some of the nutrients that caused wheat to be suggested above.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes. outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

• Terrain-related data
• Signs of low stomach acid, pancreatic function, bile production, etc.
• Detailed health history
• Specific symptom characteristics (e.g., type and location of bloating)
• Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
• Individual susceptibility to specific probiotics
• Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
• Possible histamine issues
• Colon acidity levels
• SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.