This is from a person that have been using Microbiome Prescription for a while with significant success. He messaged me about a new sample and asked me to take a look. It was good timing because I have over the last week refactor forecast symptoms as well as allowing them to be used to generate suggestions. This gave me an opportunity to test the analysis and suggestions.

My impression is that they are both working well with better sensitivity than the older method. Prior posts include:

• A review of a ME/CFS Microbiome Jan 2021
• Evidence of ME/CFS improving using Microbiome Data May 2022
• Comparing 4 ME/CFS Samples with New Tool Jul 2022
• A Microbiome Trek Continues thru the land of ME/CFS. Feb 2023
• Biomesight vs Thorne Tests – Differences Mar 2023

Immediate Back Story

I had covid and an awful toothache a week after.

-PEM 
-Fatigue on and off specially in the morning. Lowest energy point 
-Some brain fog. If I take a binder my brain fog is much better. Guessing that could be related to mold/fungus issues?
-unrefreshing sleep
-hair shedding unless I take Lactoferrin 
-difficulty losing weight 

– Reader

Review of Test Results

I am skipping the sample comparison table because the forecast symptoms seem more useful for between samples comparisons.

Percentages of Percentiles

These are helpful overview to see if there are problems. At the top is a chi² value which a healthy person should have a value below 0.90 . All of his values were .99999…. indicating abnormal shifts.

Prior to 2023

2023, the impact of COVID in the latest sample is quite apparent.

Forecast Symptoms

What shocked (and delighted) me was how accurate the forecasts were, especially with the main issue, PEM being near the top on every sample. The percentage match ebbed and flowed with improvements and set backs (typically from COVID).

• 2023-11-02 – After recent COVID
  • 74.2 % match for Neurological: Cognitive/Sensory Overload on 31 taxa
  • 63.5 % match for Immune Manifestations: new food sensitivities on 52 taxa
  • 61.5 % match for Neuroendocrine Manifestations: cold extremities on 65 taxa
  • 60.9 % match for Neurological-Vision: Blurred Vision on 87 taxa
  • 59.6 % match for Condition: ME/CFS with IBS on 52 taxa
  • 58.3 % match for Post-exertional malaise: Worsening of symptoms after mild physical activity on 36 taxa
• 2023-07-07
  • 57.1 % match for Post-exertional malaise: Worsening of symptoms after mild physical activity on 42 taxa
  • 54.2 % match for Condition: ME/CFS with IBS on 59 taxa
  • 48.1 % match for Post-exertional malaise: Post-exertional malaise on 54 taxa
• 2023-05-10
  • 63.2 % match for Post-exertional malaise: Post-exertional malaise on 38 taxa
  • 59.3 % match for Post-exertional malaise: Muscle fatigue after mild physical activity on 59 taxa
  • 59.1 % match for Pain: Pain or aching in muscles on 44 taxa
  • 57.1 % match for Condition: ME/CFS with IBS on 42 taxa
• 2022-12-05
  • 82.4 % match for Official Diagnosis: Autoimmune Disease on 51 taxa
  • 81.9 % match for Comorbid: Histamine or Mast Cell issues on 83 taxa
  • 79.5 % match for Post-exertional malaise: Next-day soreness after everyday activities on 39 taxa
  • 71.8 % match for Post-exertional malaise: Physically tired after minimum exercise on 39 taxa
• 2022-10-29
  • 64.4 % match for Neurological-Sleep: Inability for deep (delta) sleep on 45 taxa
  • 62.7 % match for Official Diagnosis: Mast Cell Dysfunction on 75 taxa
  • 60.9 % match for Post-exertional malaise: Next-day soreness after everyday activities on 46 taxa
  • 60 % match for Condition: ME/CFS with IBS on 40 taxa
  • 55 % match for Post-exertional malaise: Muscle fatigue after mild physical activity on 60 taxa
  • 54.5 % match for Post-exertional malaise: Post-exertional malaise on 44 taxa
• 2022-03-23
  • 85.4 % match for Neurological-Sleep: Inability for deep (delta) sleep on 41 taxa
  • 82.1 % match for Immune Manifestations: Inflammation (General) on 67 taxa
  • 77.5 % match for Immune Manifestations: Inflammation of skin, eyes or joints on 111 taxa
  • 75 % match for Post-exertional malaise: Worsening of symptoms after mild physical activity on 32 taxa
  • 71.4 % match for Post-exertional malaise: Next-day soreness after everyday activities on 42 taxa

Drilling down on PEM

With the revised symptom-taxa association tool, I went to the 2022-12-05 sample because it had very high values for PEM in forecasting. I then went to [Special Studies] and selected all of the PEM items

Some 78 bacteria were selected with the following being the top suggestions:

While this is not his current sample, it is reasonable guidance for dealing with the bacteria associated with PEM.

Going Forward

I am going to do [Just give me suggestions] and then special studies selecting only PEM items that are shown. We thus ended up with 5 packages. Looking at the details we have high at 555 -> 277 for high threshold and -542 –> -271 for low threshold

• Antibiotics: the top 2 are used with ME/CFS
  • clarithromycin (antibiotic)s[CFS]
  • azithromycin,(antibiotic)s[CFS]
  • with an IBS antibiotic being close to the top: rifaximin (antibiotic)s
• Amino Acids
  • melatonin supplement
  • epicatechin
• Drugs (OTC etc)
  • acetaminophen,(prescription) Paracetamol in UK
• Flavonoids
  • resveratrol (grape seed/polyphenols/red wine)
  • quercetin,resveratrol
• Food
  • whey
  • Cranberry (just under… but seasonal)
• Herb Spices
  • aloe vera
  • garlic (allium sativum)
  • foeniculum vulgare,fennel
  • bacopa monnieri
  • cinnamomum tamala
  • cinnamomum zeylanicum
  • olea europaea,olive leaf
• Prebiotics
  • chitooligosaccharides (prebiotic)
• Probiotics
  • lactobacillus paracasei (probiotics)
• Sugars
  • saccharin
• Vitamins
  • Vitamin B1,thiamine hydrochloride
  • Vitamin B6,pyridoxine hydrochloride
  • vitamin B3,niacin
  • Vitamin B-12

In general, it looks very pro-forma ME/CFS. He may wish to check the PEM suggestions against the details and include anything that is positive.

Bottom Line

I have often used the analogy of going from the port of sickness to the port of health in a sailing ship along a rugged coast. There may be a long series of course corrections needed. While there are still ME/CFS taxa shifts seen in his samples, subjectively the only symptom left of concern is a PEM after playing basketball for a while.

This is a good illustration that taxa/bacteria does not rule — DNA and other factors are involved with symptoms and the ability to tolerate microbiome dysfunctions.

Questions and Answers

Q: I may do another Thorne test if they’re back in stock. Wondering how much aspergillus is holding back healing/gut shifts 

• Aspergillus usually impacts lungs and breathing [CDC] (thus ability to get oxygen in). An alternative mechanism for oxygen issues than with hypercoagulation.

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.

Part of this series of Technical Notes.

The following are bacteria that have very unusual statistical behaviors in uploaded samples. This hints that they may be connected to some disease or symptom state.

The common pattern seen with most bacteria is shown below. You can view each bacteria pattern by clicking on the chart icon after searching for a bacteria on https://microbiomeprescription.com/Library/Lookup

Prevotella oryzae

Phascolarctobacterium succinatutens

Bacteroides eggerthii

Paraprevotella clara

Phascolarctobacterium faecium

Paraprevotella

Preliminary evaluations have shown strong and accurate forecasting ability. I am working with a Ph.D. in Molecular Genetics and processing his microbiome sample the top forecasts were correct:

• He was a male
• He had no Health Issues
• He was blood type O-positive
• He snored
• He woke up early

This was not from a blood sample, but from a stool sample. The methodology is described in my earlier posts.

• Bacteria interacting with Bacteria
• Symptoms/Diagnosis association to Bacteria

The methodology is computing intensive. Unlike many contemporary artificial intelligence engines, it is easy to understand:

• In the entire population(n:10,000), a bacteria like unclassified Clostridiales has 10% of samples reported this bacteria with a mean of 0.3%.
• In the condition / sample population(n:1000) we find that 30% of the samples reported this bacteria with a mean of 4.8%

I used Chi² to determine significance because significance using means assumes a normal distribution which is a false assumption.

With this methodology it is good to get some indication of what sample sizes for conditions / symptoms is needed (assuming the control is at least the same size). A quick plot informs us that 200 looks like a minimum size with 300+ being desired.

One of the labs that I work with reports percentile ranking on their reports. This makes doing an exploration economical (i.e. cheap). Testing of the symptom/condition group is only needed because the control numbers are gifted you.

This also illustrates that the symptom is not with just one taxa, but the influence of many taxa working in unison to influence the symptom (or be influenced by the condition).

Samples of Symptoms / Conditions

The ones with the most predictors are below.

• Neurocognitive: Absent-mindedness or forgetfulness
• Neurological: Impairment of concentration
• Neurocognitive: Difficulty paying attention for a long period of time
• General: Fatigue
• Autonomic Manifestations: irritable bowel syndrome
• Official Diagnosis: COVID19 (Long Hauler)
• Sleep: Problems staying asleep
• Neurocognitive: Slowness of thought
• Neurological-Sleep: Insomnia
• Sleep: Daytime drowsiness
• Immune Manifestations: Bloating
• Neurocognitive: Problems remembering things

For blood types:

Only two were significant and we have the importance of sample size apparent.

Symptom Name	Sample N	Forecast Variables
Blood Type: O Positive	284	295
Blood Type: A Positive	126	3

For Age:

Symptom Name	Sample N	Forecast Variables
Age: 60-70	206	143
Age: 0-10	98	42
Age: 50-60	164	33
Age: 20-30	152	12
Age: 30-40	369	11
Age: 40-50	244	8

For Gender

Symptom Name	Sample N	Forecast Variable
Gender: Female	415	214
Gender: Male	554	200

Bottom Line

From the individual forecast variables, we can compute odds of a match. Consider a simplistic example of three factors

• Factor A uses 5%ile
• Factor B uses 10%ile
• Factor C uses 20%ile

With A,B,C all being true has a 99% chance of being a taxa match (1 – .05 * .1 * .2). This does not mean the person has it, it indicate a significant risk of having it (depending on other factors, DNA, age, gender etc).

Of course, the more forecasting variables, the better the estimate becomes and also the more tolerant the forecast is to variations in the microbiome.

A sibling is: Fungi: Clavicipitaceae / Hypocreales / Sordariomycetes

Fungi and the microbiome finally got on my radar. Apologies to some, but there is a lot of different items on the microbiome radar screen.

“Small intestinal fungal overgrowth (SIFO)… Two recent studies showed that 26 % (24/94) and 25.3 % (38/150) of a series of patients with unexplained GI symptoms had SIFO. …. but evidence for eradication is lacking.”Small intestinal fungal overgrowth [2015]

As I did with taxa years ago, I will be writing a blog on each one reviewing the literature. If there is sufficient data at the end, I may add it as a feature to Microbiome Prescription.

• CDC provides a list of known fungal diseases: Types of Fungal Diseases.
• For the current list of Fungi reviewed on this list, click Information of Different Types Of Fungi

One of my reader’s results motivated this choice. The data from a Thorne Microbiome Test. Almost 9 out of 10 people have less of it. The person also has a Crohn’s diagnosis.

Preventive for Fungi

The following are suggestions:

• Reduce and keep your living space humidity at 50% or lower (typically done by dehumidifiers). EPA recommends 30-50% [EPA]; we set our dehumidifiers for 35%.

Moisture parameters and fungal communities associated with gypsum drywall in buildings [2015]

• Use a HEPA filter appropriate to your space.
  Effectiveness of Airborne Fungi Removal by using a HEPA Air Purifier Fan in Houses [2018]
  Typically they are described as “Room Size: Up to 1500 sq.ft. maximum”. We are more aggressive and divide that by 4. For example we use 3 Austin Air HealthMate HEPA Air Purifier for our 900 sq.ft. living space.
• Check the north side of your building for mold. If found pressure wash it off and if possible, apply substances to inhibit them coming back.
• Check for mushrooms in lawns etc. If found, remove them and treat where you found them.

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] does not mention this fungi. Additionally, some spices are known to have Fungal Contamination of some Common Spices [2022] and Fungi and aflatoxins associated with spices in the Sultanate of Oman [2002] which included cloves (often deem an antifungal).

Basic Information

• Chaetomiaceae (Wikipedia)
• “The family contains several genera and species that have never been reported to cause human infection. ,,,  including eye and skin infections, a toe infection,  fungal peritonitis” Chaetomium-like fungi causing opportunistic infections in humans: a possible role for extremotolerance[2016] 
• Cited in Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome [2022]
• Fatal Cerebral Phaeohyphomycosis in an Immunocompetent Individual Due to Thielavia subthermophila^▿ [2011] – a member of this group.

Treatment

• From [2011], lower numbers are more effective
  • amphotericin B, 0.03 μg/ml;
  • fluconazole, 8 μg/ml;
  • itraconazole, 0.016 μg/ml;
  • voriconazole, 0.016 μg/ml;
  • posaconazole, 0.016 μg/ml;
  • isavuconazole, 0.016 μg/ml. 

Fungi and the microbiome finally got on my radar. Apologies to some, but there is a lot of different items on the microbiome radar screen.

“Small intestinal fungal overgrowth (SIFO)… Two recent studies showed that 26 % (24/94) and 25.3 % (38/150) of a series of patients with unexplained GI symptoms had SIFO. …. but evidence for eradication is lacking.”Small intestinal fungal overgrowth [2015]

As I did with taxa years ago, I will be writing a blog on each one reviewing the literature. If there is sufficient data at the end, I may add it as a feature to Microbiome Prescription.

• CDC provides a list of known fungal diseases: Types of Fungal Diseases.
• For the current list of Fungi reviewed on this list, click Information of Different Types Of Fungi

One of my reader’s results motivated this choice. The data from a Thorne Microbiome Test. Unlike other fungi, no ranges are provided — implies that it is a rare fungi. The person also has a Crohn’s diagnosis.

Preventive for Fungi

The following are suggestions:

• Reduce and keep your living space humidity at 50% or lower (typically done by dehumidifiers). EPA recommends 30-50% [EPA]; we set our dehumidifiers for 35%.

Moisture parameters and fungal communities associated with gypsum drywall in buildings [2015]

• Use a HEPA filter appropriate to your space.
  Effectiveness of Airborne Fungi Removal by using a HEPA Air Purifier Fan in Houses [2018]
  Typically they are described as “Room Size: Up to 1500 sq.ft. maximum”. We are more aggressive and divide that by 4. For example we use 3 Austin Air HealthMate HEPA Air Purifier for our 900 sq.ft. living space.
• Check the north side of your building for mold. If found pressure wash it off and if possible, apply substances to inhibit them coming back.
• Check for mushrooms in lawns etc. If found, remove them and treat where you found them.

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] does not mention this fungi. Additionally, some spices are known to have Fungal Contamination of some Common Spices [2022] and Fungi and aflatoxins associated with spices in the Sultanate of Oman [2002] which included cloves (often deem an antifungal).

Basic Information

• The Nectriaceae comprise a family of fungi in the order Hypocreales. It was circumscribed by brothers Charles and Louis René Tulasne in 1865.^[1] In 2020, an Outline of fungi was produced and listed 70 genera and about 1,336 species.^[2] [Wikipedia]
• Associated to Fungal Eye Infection [ScienceDirect]
• General Information: Nectriaceae [ScienceDirect]
• “This genus is also frequently involved in vertebrate infection.^6,7 Although the conditions in host tissues of plants and animals are very different, nearly all 24 taxa that have been described to occur in human infections as real cases” [2019]
• “Fusarium, a well-known plant pathogen, has emerged as an important cause of invasive or disseminated infection in immunocompromised patients. Fusarium species, which are considered as the second most frequent mold in fungal infection, cause a broad spectrum of infections including keratitis, onychomycosis, endophthalmitis, and skin infection….In the last few decades, as the number of people with diabetes increases, the case report of Fusarium infection associated with a diabetic patient is also increasing.” [2019]

Treatment

• Garlic does not work for this fungi. It causes Fusarium Basal Rot on garlic (i.e. feeds off garlic)
  • Also seen on Tomato and lemon basis [src], potato, melons, sweet corn [src]
• Multiresistant Fusarium Pathogens on Plants and Humans: Solutions in (from) the Antifungal Pipeline? [2019]
  • “Resistance has been observed for amphotericin B, itraconazole, fluconazole and echinocandins, but variable MIC results are recorded with the newer triazoles (posaconazole, voriconazole, and isavuconazole).”