Author: Research

Performance of Microbiome-Symptom Prediction Model

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.

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 NameSample NForecast Variables
Blood Type: O Positive284295
Blood Type: A Positive1263

For Age:

Symptom NameSample NForecast Variables
Age: 60-70206143
Age: 0-109842
Age: 50-6016433
Age: 20-3015212
Age: 30-4036911
Age: 40-502448

For Gender

Symptom NameSample NForecast Variable
Gender: Female415214
Gender: Male554200

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.

Fungi: Chaetomiaceae / Sordariales / Sordariomycetes

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.

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]

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

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: Saccharomycetaceae / Saccharomycetales / Saccharomycetes

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.

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

Also see it’s sibling: Fungi: Debaryomycetaceae / Saccharomycetales / Saccharomycetes

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]

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

A big group — some good and some bad.

Unfortunately, Thorne does not provide more detail.

Fungi: Trichosporonaceae / Trichosporonales / Tremellomycetes / Basidiomycota

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.

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]

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] . 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

  • “Basidiomycota is the second most species‐rich phylum of Fungi with nearly 32,000 described species” [2019]

Members of the Trichosporonaceae show a global distribution and have been recovered from a wide range of environments. Cutaneotrichosporon spp. are most frequently associated with a human host, and may represent opportunistic human pathogens. Trichosporon spp. form part of the natural microflora on human and animal skin and result in a non-serious mycosis of hair termed white piedra3. However, they have also been implicated in trichosporonosis, a collection of opportunistic infections caused by a number of species, including Trichosporon asahii, T. asteroides and T. ovoide

Genomic insights into the lifestyles, functional capacities and oleagenicity of members of the fungal family Trichosporonaceae [2020]
  • Trichosporonosis StatPearls [Internet].
    • “Invasive Trichosporon infections are common in immunosuppressed patients, such as those with hematological malignancies. Unfortunately, invasive trichosporonosis can be difficult to diagnose and treat, and the global incidence is increasing”
    • “In cases of central nervous system infection, the predominant symptoms are headache, nausea, vomiting, and fever.”
    • “Trichosporonosis has also been documented to cause peritonitis, pacemaker lead endocarditis, and pneumonia. Other rare manifestations include sinusitis in an immunocompetent patient, fungemia, and urinary tract infection in patients with diabetes mellitus, and nosocomial infection in patients with severe burns”
    • Treatment includes: itraconazole, voriconazole , fluconazole 
    • Most experts recommend combination therapy consisting of amphotericin and voriconazole/5-flucytosine.

Fungi: Synchytrium / Synchytriaceae / Synchytriales / Chytridiomycetes / Chytridiomycota

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.

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]

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] . 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

  • General Information: Synchytrium [ScienceDirect]
  • No information on disease in humans or other vertebrates could be located. One site implies it “few [Chytridiomycota] have any noticeable impact on humans, with the exception of a few that parasitize algae, cause potato wart (Synchytrium endoboticum), and those used in experimental research (e.g. Allomyces).” [Berkelely Univ] — unclear if this is the impact on food supply (potatoes) or humans.

Fungi: Nectriaceae Fusarium / 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.

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]

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

Fungi: Aspergillus \ Aspergillaceae \ Eurotiales

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.

One of my reader’s results motivated this choice. The data from a Thorne Microbiome Test. About 8 out of 10 people have less of it. The person also has a Crohn’s diagnosis (with SIBO and IBS earlier).

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]

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] does not mention all fungi that I am reviewing. 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

Aspergillus is available as a supplement, wakamoto (jp) / strong wakamoto w, containing aspergillus oryzae. So care need to be taken to avoid this supplement for at least one week before testing. It also implies that some species may be beneficial.

Aspergillosis is an infection caused by Aspergillus, a common mold (a type of fungus) that lives indoors and outdoors. Most people breathe in Aspergillus spores every day without getting sick. However, people with weakened immune systems or lung diseases are at a higher risk of developing health problems due to Aspergillus. The types of health problems caused by Aspergillus include allergic reactions, lung infections, and infections in other organs.

Center For Disease Control

Treatment

Fungi: Debaryomycetaceae / Saccharomycetales / Saccharomycetes

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.

One of my reader’s results motivated this choice. The data from a Thorne Microbiome Test. About 8 out of 10 people have less of it. The person also has a Crohn’s diagnosis (with SIBO and IBS earlier).

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]

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] does not mention all fungi that I am reviewing. 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

It’s a family with the lineage below: Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; CUG-Ser1 clade; Debaryomycetaceae

Bottom Line

Our ability to drill down further is limited because the results only report at the family level and sparse literature. Itraconazole, an antifungal that is the top choice for other fungi reviewed appears to work.

Fungi: Leotiomycetes / Ascomycota

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.

One of my reader’s results motivated this choice. The data from a Thorne Microbiome Test. About 8 out of 10 people have less of it. The person also has a Crohn’s diagnosis (with SIBO and IBS earlier).

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]

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] does not mention all fungi that I am reviewing. 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

Thorne only provided only class-level information unfortunately.

Bottom Line

This is a fungi that I would take no action on because it does not appear to produce any clear harm. If you have other fungi of concern, the treatment of those will likely reduce this one. Some of it’s children are reported sensitive to Itraconazole.

Fungi: Agaricales / Agaricomycetes

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.

One of my reader’s results motivated this choice. The data from a Thorne Microbiome Test. About 8 out of 10 people have less of it. The person also has a Crohn’s diagnosis (with SIBO and IBS earlier).

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]

Remember, all fungi are not the same. Antibacterial and Antifungal Activities of Spices [2017] does not mention all fungi that I am reviewing. 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

Thorne only provided only order-level information unfortunately.

Bottom Line

Our ability to drill down further is limited because the results only report at the family level. Itraconazole, an antifungal that is the top choice for other fungi reviewed appears to work. This order-level fungi has a significant risk of misidentification because it also contains common mushrooms that are consumed.