Some answers to a reader’s questions on EndProducts Beta

First, I am NOT a medical professional. I am best described as a mathematician, a librarian and statistician.  I know how to shove numbers around, I know how to research, I know how to painfully logical. Anything on this site should be discussed with a medical professional before doing.

On my last post, a reader asked a stack of questions — these are my  thoughts on them.

Holy moly, I have so many questions! I have diagnosed RA and AS but none of the prescriptions they have ever given me over the years have done anything. This site has been much better at reducing symptoms and pain with suggestions.

Thank you for sharing that this site has benefited you.

Anyway, I’m currently taking Biotin, Kelp, Choline w Inositol (and two eggs and almonds everyday), 5HTP, Selenium, Zinc, GABA, Whey, Magnesium w B6, Quercetin w Resveratrol, Ashwaganda, Spezzata, COQ10, flaxseed… have been since March before this Ubiome in April. It’s now July. I’m wondering if I should stop taking some things? So many things here are extremely high! I just ordered N-Acetyl-D-glucosamine, now I’m thinking I better not take it?

The endProducts is just 1/2 of a balance: there are consumers and there are producers.  Low B12 production combined with Low B12 consumption may result in normal B12 levels. Think of a married couple with low earning but a frugal life style — they may have an excellent credit rating! Attempting to work on consumers is on my to-do list.

Perhaps I should add b-12 and pomegranate to the regimen? I’m not sure what 2,3-Butanediol and Formic acid is, or Phenylacetic acid. How would I or should I bother to try and raise those levels?

My thoughts comes from being the son of a farmer, you can have a good looking crop driving by in a car. You get the best crop when the soil has all of the nutrients needed by the crops. I view that having adequate levels of these end products will help to rebalance the microbiome — after all, how can some of the weak healthy bacteria retake your gut when it is starving or on low-rations?

Next, Wikipedia is your friend.

A second friend can be Cambridge University Botanic Garden. Doing a site search with google:
site:www.botanic.cam.ac.uk formic acid

find that Formic Acid is in Urtica dioica (stinging nettle). This may be purchased as a supplement.

Not being a medical professional, I cannot answer the question “Perhaps I should add b-12 and pomegranate to the regimen?“.  I can suggest that experiments are good if you keep good records. Experiments are better, when you share the results.

Is it good to have low Trimethylamine?

Again over to wikipedia as a starting point, Trimethylamine” In humans, it is synthesized exclusively by gut microbiota from dietary nutrients such as choline and carnitine” I could find no literature dealing with low levels, very high levels (usually associated with a DNA defect) is associated with fish odor syndrome.

What the heck is Propionate and Phloroglucinol and how would I ever lower that if that’s even needed to be lowered? A quick search shows some studies that say it’s beneficial to have high.

Again, to wikipedia: https://en.wikipedia.org/wiki/Propionate “Propionate is observed to be among the most common short-chain fatty acids produced by human gut microbiota in response to indigestible carbohydrates (fiber) in the diet.[2]” so to reduce, cut back carbohydrates seems reasonable.

https://en.wikipedia.org/wiki/Phloroglucinol  “The bacterium Pseudomonas fluorescens produces phloroglucinol, phloroglucinol carboxylic acid and diacetylphloroglucinol.[14]… It is also used as a treatment for gallstones, spasmodic pain and other related gastrointestinal disorders.[15][16]

So, the question arises, do you want to reduce it? If you  do, see this page on modifiers of pseudomonas.

My worst symptoms are brain fog of doom, lack of focus, concentration, and understanding words when spoken. Weird anger. Horrible fatigue. Bad depression. Swollen joints are the worst pain in my hands. Those are the main concerns and are a bit better than without these things but still debilitating.

My initial impression is that a SPECT scan has a 80% probability of showing hypoperfusion in the brain (i.e. low/slow penetration of blood into the brain tissue). There are multiple possible causes:

  • Build up of fibrin fragments — there are fibinolytics (fibrin disolvers)
  • Vascular constrictions — there are vascular dilators (my own usual is flushing niacin)
  • High blood viscosity — slow moving blood, think of oil versus water, I recall Alpha Lipoic Acid is one non-prescription supplement that can help with this.
  • Inflammation
  • etc

Again, by law, I can only suggestions/topics to discuss with your licensed medical professional.

Sorry about all the questions!! But I would love some answers!

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.

End Products Analysis is now in Beta

Bacteria produce end-products such as B12, Biotin, Butyrate etc. I have done a naive count of the number of bacteria in your ubiome that produces each and create a report from it. This is not perfect:

  • different bacteria are more or less efficient in production
  • this is based on available data. Some bacteria are hard to cultured and remain mysteries.
  • This is one side of the equation — if your are a low B12 producer AND low in bacteria consuming B12 then you may have normal B12 in lab results

This will work for uBiome and Thryve uploads. It is strictly experimental.

Some answers to readers questions are in this followup post.

Then you logon, you will see a new column on the sample page.

ep1

Clicking on this will take you to the new report. The Average was calculated from the 45 people that uploaded and reported no health issues. I will periodically recalculate these.

ep2

p3

Purely experimental

We see that this person may benefit from Vitamin B12 and Niacin, but does not need Riboflavin or Folate — A B-100 supplement may be a poor choice for them.

They are low in Acetylcholine — a neurotransmitter. This may account for some cognitive issues.

I will leave people to explore and add comments of any discoveries they make on this page! I would suggest focusing on the EXTREME values — there is a lot of natural variations.

Site again is: https://microbiomeprescription.azurewebsites.net

European MD suggestions on KyberKompakt Pro Results

A reader forwarded me results for this variation of KyberKompakt as well as their digestive European MD prescription.

kyber

European Digestive MD suggestions

The suggestions look like a standard cook book and definitely worth sharing.

What are the suggestions generated by the site

http://microbiomeprescription.com/Kyber/Recommendations/

Take:

I added a 🙂 after items that match the MD’s prescription above. The only item that did not match was resistant starch type 3, which was not listed. Two additional probiotics appear.

  • lupin seeds
  • broad beans
  • apple
  • low processed foods diet
  • high-level dietary fibre
  • inulin 🙂
  • enterococcus faecium sf 68 🙂
  • high-level dietary fibre
  • jerusalem artichoke
  • mediterranean diet
  • mutaflor 🙂  (E.Coli)
  • bacillus coagulans
  • high fiber diet
  • bifidobacterium longum bb536
  • lactobacillus acidophilus 🙂
  • resistant starch type 4
  • bifidobacterium animalis lactis 🙂

Avoid

  • omega 3 fatty acids
  • flaxseed
  • high fat diet
  • wheat
  • sorghum
  • garlic
  • walnuts
  • dates

Bottom Line

Apart from the Soil Based Organisms Probiotics (Prescript Assist, General Biotics Equilibrium) not being included in the game plan from the MD, I am very delighted with his plan.

 

 

Phages 101

A reader asked about phages and supplied a Youtube and a BBC program on it

http://www.bbc.co.uk/programmes/articles/yGJ6MtYrP2S0gjssltQBS2/could-viruses-called-bacteriophages-be-the-answer-to-the-antibiotic-crisis

As well as a shop selling them. http://bacteriophagepharmacy.com/shop/

Phage theraphy has been proposed for CFS and other conditions for at least 20 years. I am skeptical that it will be of significant help because my belief is that it is not a single bacteria responsible.

Phage Basics

A 2001 NCBI article does a nice background on it. I recommend strongly reading it BEFORE trying phages

“Bacteriophages or phages are bacterial viruses that invade bacterial cells and, in the case of lytic phages, disrupt bacterial metabolism and cause the bacterium to lyse[aka die]. ”

” In the 1940s, the Eli Lilly Company (Indianapolis, Ind.) produced seven phage products for human use, including preparations targeted against staphylococci, streptococci, Escherichia coli, and other bacterial pathogens…with the advent of antibiotics, commercial production of therapeutic phages ceased in most of the Western world. ”

Phages are far more specific than antibiotics — often effective against a single bacteria. 

“Very specific (i.e., usually affect only the targeted bacterial species); therefore, dysbiosis and chances of developing secondary infections are avoided… Because of the high specificity of phages, many negative results may have been obtained because of the failure to select phages lytic for the targeted bacterial species ”

Wait a minute, we are precise to a species!

So a phage for Bifidobacterium scardovii  will kill that one only and not any other bifidobacterium species. You may have a slackia overgrowth, using a phage may reduce Slackia isoflavoniconvertens, but the slackia overgrowth remains

FDA Workshops on Phage Theraphy

Bottom Line

So if you are targeting one specific species, a phage is ideal. It is “a smart bomb that take out a lance corporal in an army and leave the officers and soldiers untouched”. Antibiotics can be like atomic bombs — kills the soldiers, civilians etc.

If you have an overgrowth of the specific bacteria species that the phage is very targeted against, then it may be worth the experiment.

For example:

pio-amp-300x173

“a specific lysis of bacteria belonging to: Staphylococcus (S. aureus), Streptococcus (S.pyogenes, S. sanguis, S.salivarius, S. agalactiae), E.coli (Different types), Pseudomonas Aeruginosa, Proteus (Mirabilis and Vulgaris) spices. ”

We see from 300+ samples uploaded at http://microbiomeprescription.com/  that

So the odds of it being a match will typically be 1 in 60 patients.  Looking at the data, exactly two uploads are good matches for the above.

I will see about adding a phage recommendation page (using the products listed at http://bacteriophagepharmacy.com/shop/ this weekend. It should make the decision much easier for every one (i.e. don’t waste your money if you have nothing that the phage will kill!).

Beware of Products being hyped on Phages but wrong ones!

I did an earlier review of an inappropriate one,  Phage-Complete-A-Review/

Mutaflor Probiotic Feedback

I have written about E.Coli Nissle 1917 (“Mutaflor”) several times before, this week got two comments that I thought that I should share.

I should also note that Bifidobacterium longum infantis “failed to inhibit E. coli”. so may be taken with it. [2020], this may also be true for other Bifidobacterium.

Comment #1

“As you know I’ve been following your site and suggestions for several years now. I’ve seen some improvement lately with one major side effect and I’m hoping you have some thoughts.
I was recently able to find Mutaflor again. I’ve been able to get it occasionally over the last three years. The improvement each time I’ve dosed at full strength is profound and reliable. My pain almost disappears. When I’m in a flare of muscle pain and weakness, two Mutaflor is more effective than Advil. It also helps greatly with fatigue overtime as I continue to take more. One caveat is that it also results reliably in loose stools at best and pretty awful diarrhea at worst. This has happened every time in the past and is repeating again currently. Any suggestions on how to counteract this. Maybe taking some other probiotic alongside it?  

I can get Symbioflor (US Source, World Wide Source) more reliably, and while it does help, it’s not near what Mutaflor is. Also, it will cause loose and frequent stools at a high enough dose to effect positive change on pain, fatigue, etc.

Prior to my disabling CFS, I had IBS-D. But diarrhea is largely not a problem for me now and usually a rare symptom. And my IBS and once diagnosed Crohn’s have been reversed for nearly 10 years. However, all of my CFS like symptoms have continued to worsen over the last decade. “
– Email

Comment #2

“I have been in a mild UC flare for several weeks and just began taking Mutaflor along with my other excellent pribiotic, L-GG, and S. boulardii. (I dropped VSL#3, which I took for 6 months and never stopped causing gas. Maybe because I avoid dairy.) I noticed flu symptoms within a few hours of first taking 2 caps of Mutaflor. Symptoms worsened as I took 2 caps two more times the next day, then lightened up when I cut back drastically. Definitely detox, not the flu.

I’ve read a research abstract from 2013- 2014 that taking Mutaflor with two other strains of probiotics plus S. boulardii was very effective in getting UC into remission and keeping it there! My general probiotic by 1MD has both in it, I believe, but I’m using it up, regardless, with the Mutaflor and that probiotic yeast, which also helps with leaky gut. I need to seal my leaky gut before my colon can heal.

My UC became severe pancolitis 10 months ago, but I will not do any more steroids or drugs. My liver was being harmed, and this treatment should actually work better. After just 2 days, I see no blood or mucus and stools are normal again! (Just still too often and too urgent.)

The ECN 1917 kills a large quantity of bad bacteria that hinder colonizing by probiotic strains, even those with excellent adherence capability. ECN makes other probiotics many times more effective! Until I can get a full copy of the research mentioned above, however, I won’t know exactly how much to take of any of those studied together.

For now, I’m doing just two caps Mutaflor with one cap each of the other three. My detox or herx reaction should be easy enough to handle at that level.

Mutiflor was very easy to get thru Feel Good Natural in Canada. With shipping and a discount for buying 2 boxes, my net cost was only $10 US more than would cost if bought for me OTC in Canada. Shipping with ice packs was under $13 to VA.”

Comment on a prior post