I have created a sharable collaborative workbook using data uploaded to http://microbiomeprescription.com/ . 

The data is ready for processing using Python/Panda, R or other packages. The datasets are available at

• * Symptoms Only: Explore which symptoms go together http://www.lassesen.com/ubiome/Symptoms.csv
• Symptoms and Metabolism: Explore how metabolism shifts impacts symptoms http://www.lassesen.com/ubiome/SymptomsMetabolism.csv
• Symptoms and Bacteria: Explore how bacteria impacts symptoms http://www.lassesen.com/ubiome/SymptomsTaxonomy.csv

The shared workbook is at:

• https://drive.google.com/file/d/1FYB0BapNxG5He_ZMIphsQ8P73XFPz5Yk/view?usp=sharing

Quick walkthru

When you open the link, you will see:

Click the [###] to execute the code and put into a cloud based virtual machine the data.

The next section shows some basic number. Again click the [###] to execute it.

The next section lists all of the columns in the dataset. There are many!

The next section shows how to test or put some science behind what you think may be associated. I do not intend to try teaching statistics to the brain fogged, just make the data easy to access for significant others and researchers.

Bottom Line

The data is now available to explore online using virtual machines and shared work books.

The data files will be updated once a week.

A reader wrote:

“Ken, I need to repopulate my microbiome. I have been treating candida overgrowth on my own and it is working but I think I need to take more or different probiotics. I have used a number over time in and effort to get a variety into my system but I can’t get rid of the candida to the point of normalcy. 

I can’t eat the anti candida diet due to gastroparesis. Is there a specific product or strain and what find of Dr might deal with this. None of the drs I see think it is a real thing. The 100lbs I have lost with the only change being natural anti fungals says otherwise. Thank you.”

There are actually two questions:

• Controlling candida
• Restoring a microbiome.

So today, I will review what we know from studies on PubMed on the first one. For the second, I suggest getting a ubiome done and then reviewing the suggestions (which will likely include probiotic suggestions).

Studies

• “Thirty Lactobacillus strains were isolated and evaluated for antimicrobial activity against in vitro C. albicans biofilms. L. paracasei 28.4, L. rhamnosus 5.2 and L. fermentum 20.4 isolates exhibited the most significant inhibitory activity against C. albicans” [2018]
• ” In conclusion, L. plantarum 59 and L. fermentum 137 were confirmed to have an anti-inflammatory effect against G. vaginalis and C. albicans and they were able to influence signalling in NF-κB pathway, making them interesting candidates as probiotics for the prevention or treatment of BV and VVC.” [2018]
• Lactobacillus paracasei 28.4 reduces in vitro hyphae formation of Candida albicans and prevents the filamentation in an experimental model of Caenorhabditis elegans [2018].
• Lactobacillus rhamnosus intake can prevent the development of Candidiasis.[2018]
• Antifungal defense of probiotic Lactobacillus rhamnosus GG is mediated by blocking adhesion and nutrient depletion. [2017]
• The In Vitro Effectiveness of Lactobacillus fermentum Against Different Candida Species Compared With Broadly Used Azoles. [2016] “The use of beneficial bacteria, especially lactobacilli, could be regarded as a good alternative for the prevention and treatment of Candida infections.”

Bottom Line

Three specific genus of Lactobacillus seem to be demonstrated to be effective.

• Lactobacillus paracasei [high potenancy, lowest $ per CFU: CustomProbiotics]
• Lactobacillus rhamnosus [high potenancy, lowest $ per CFU: CustomProbiotics]
• Lactobacillus fermentum [See this post  for sources]

Remember, we are likely talking therapeutic dosages.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

After my last post, a brain fogged reader asked about items she has available. She has ubiome results from 2018-02-12 for reference.

AGAIN: This is all theoretical using the best information available. The quality of the information could be objective to.

Process is simple: Go to http://microbiomeprescription.com/Library/GutModifiers

then search for each drug. After getting the full list, add &seq=###### to the address to get it refined for a specific ubiome result. In some cases, you may find two entries (due to how data was entered), so do both.

ciprofloxacin  – no impact (good or bad)

Oat Meal

No information found for:

1. Lorazepam

Bottom Line

This person has a MD that wishes to helpful (hence the wide range of antibiotics available to her) but does not know what to suggest.

The above analysis suggests that the following be reviewed and discussed with her MD

• Continued eating oatmeal
• Take Metronidazole (only one group with caution – more good than harm)
• Stop bacillus coagulans probiotics
• Azithromycin seems reasonable to include.
  Note: Protobacteria is increased in one study and decreased in a different study

This is an illustration of how the site can be used to review what you are taking against your microbiome.  In a few cases, things are complete cleared (everything lines up), but in most cases we have to weight the plus and minuses.

As always — review it with your medical professional. Many will see that the logic above many be better than picking random suggestions off the internet.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

I know many people whose autoimmune condition appear to have been triggered by mold or fungus exposure. Mold or mould is a fungus — so my focus will be fungus (which included the subset mold). I have not explore this area explicitly before.

From Wikipedia:

Toxic house mold

The common house mold, Trichoderma longibrachiatum, produces small toxic peptides containing amino acids not found in common proteins, like alpha-aminoisobutyric acid, called trilongins (up to 10% w/w). Their toxicity is due to absorption into cells and production of nano-channels that obstruct vital ion channels that ferry potassium and sodium ions across the cell membrane. This affects in the cells action potential profile, as seen in cardiomyocytes, pneumocytes and neurons leading to conduction defects. Trilongins are highly resistant to heat and antimicrobials making primary prevention the only management option.

Fungus Produced Toxins

• “toxins were identified with HPLC/ESI-MS/MS as trichorzianines, trilongins, trichostrigocins and trichostrigocin-like peptaibols.” [2018]
• “Buildings that have been flooded often have high concentrations of Trichoderma spores in the air while drying… inhalation of Trichoderma spores and mycelial fragments may result in exposure to membrane-disrupting peptaibols. This investigation contributes to a more comprehensive understanding of the biologically active natural products produced by fungi commonly found in damp buildings.” [2017]
• “Peptaibols are a family of antimicrobial peptides, which are synthesized by non-ribosomal peptide synthetases (NRPS) and contain high proportions of alpha-aminoisobytyric acid (Aib). Up to now, 317 peptaibols have been identified, and the majority of them are produced by Trichoderma strains.” [2011]

Clearly, mold can and does impact the microbiome. Eliminating the mold in the body (after verifying that it is there) is a first step. The second step is restoring the microbiome.

• “Dr. Brewer reports that chronic fatigue syndrome patients are much more likely than healthy people to have mold toxin in their urine…Brewer found that 94% of his CFS patients had at least one kind of mycotoxin detected in their urine.  ” [src] Discussion of the studies.
• The published studies are [2013] and [2014].
• A recover study:

  Reversal of Refractory Ulcerative Colitis and Severe Chronic Fatigue Syndrome Symptoms Arising from Immune Disturbance in an HLADR/DQ Genetically Susceptible Individual with Multiple Biotoxin Exposures [2016]

”

Antifungal and the Microbiome

Recently I added antifungals to the list of gut modifiers. These are listed at antifungal (prescription):

• amphotericin b (prescription)
• bifonazole (prescription)
• butenafine hydrochloride (prescription)
• butoconazole nitrate (prescription)
• chlorphensin carbamate (prescription)
• ciclopirox ethanolamine (prescription)
• clotrimazole (prescription)
• econazole nitrate (prescription)
• fluconazole (prescription)
• flucytosine (prescription)
• griseofulvin (prescription)
• haloprogin (prescription)
• isoconazole (prescription)
• itraconazole (prescription)
• ketoconazole (prescription)
• liranaftate (prescription)
• miconazole (prescription)
• naftifine hydrochloride (prescription)
• nystatine (prescription)
• oxiconazole nitrate (prescription)
• sertaconazole nitrate (prescription)
• sulconazole nitrate (prescription)
• terconazole (prescription)
• tiabendazole (prescription)
• tioconazole (prescription)
• tolnaftate (prescription)
• voriconazole (prescription)

The enhancement that I added recently, described in this post, Improved filtering of gut modifiers, allows the impact of various antifungals on your microbiome to be viewed.

The little trick to see the impact of prescription drugs on your ubiome

1. AFTER logging in to http://microbiomeprescription.azurewebsites.net
2. Click one of the above, for example  itraconazole (prescription)
3. You will see it’s address is:  http://microbiomeprescription.com/Library/Modifier?mid2=649
4. Simply add  “&seq=999999” (where 9999999 is your own sequence number) and you will see what this antifungal also impacts. An example (for a person with mold triggered CFS is used)

Finding a perfect fit is unlikely. The algorithm used on the site attempts to balance the pro-and-cons. Your medical professional can do your own tuning with the above. With prescription drugs there can be many factors involved for a specific patient.

For example, this one may be a better profile than above:

with this appearing to be the second choice

Bottom Line — review for other prescription drugs

With drugs, pharmacists know the term “contraindicated“. This means two drugs have undesired side-effects. Using the above technique, we can identify drugs that may be contraindicated for your current microbiome.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

A reader asks if it was possible for recommendations, such as shown below

If you click on an item, could it be filtered ONLY to the bacteria you have!!!

So instead of:

You get a shorter list:

Enhancement

Information about your ubiome is now displayed.  If it moved in the opposite direction to preference, a CAUTION is added.

Bottom Line

This modification should allow those with less cognitive impairment to determine which ones on the lists of suggestions/recommendations they may value most.