The importance of functional testing?

[Keyhole]

Some of you probably know that I study nutritional therapy. My course content is geared toward functional medicine, so I have been lucky enough to learn quite a lot about how to read various tests from one of my lecturers. On top of that, throughout the past few months I have spent significant amounts of my own time attempting to understand the biochemistry that underlies the various markers involved in these tests. I will be honest and say that it is NOT easy and it is certainly not for everyone, but it has been totally worth it - so much so that I have decided to enrol in professional training in functional medicine in October 2018.

Just a quick definition of what I am talking about: Medical diagnostic testing is performed by biomedical labs for doctors and measures specific biomarkers which can be used to diagnose a specific pathological condition. On the other hand, functional testing is not necessarily used to diagnose pathology, but is instead designed to assess imbalances in physiological function, and basically measure how well things function. Regular doctors are not trained in reading these tests unless they have specifically undergone training in functional medicine.

I started this post to demonstrate how guess-work with supplementation can sometimes be a waste of time and a waste of money in a complex case. I have learnt this through my own experience.

A brief history of my health problems:

-Up until I was 18yo, I was in fairly good health. No major digestive issues and nothing else that was too concerning.
-I went backpacking through India for 9 months at age 18, and experienced several bouts of gut infection and diarrhoea.
- Since returning back, I developed severe IBS characterised mainly by diarrhoea and abdominal pain, the onset of dandruff, bloating, fatigue etc. Low libido also set in.
- I tried various dietary approaches: Paleo, Ketosis, Elimination type diets, lower-fat etc
- I spent probably at least £2000 on supplements, and saw only moderate benefits.

In March 2017, I decided to invest the money on a GI Effects functional test by Genova Diagnostics. This is NOT a medical test, and medical doctors do not know how to read or interpret such tests.

Here were my results:

Without explaining ALL of the markers, I will just go into the points of concern:

- Protein breakdown & fat digestion were good. A later result for pancreatic elastase (pacreatic enzyme function) came up OK. This answered questions I had about my ability to breakdown food--- it was good.
- IBD was very unlikely, due to low Calprotectin etc.

MAIN IMPORTANT POINTS:
-Elevated fecal secretory IgA: This is an immunoglobulin which is produced by the mucosal cells in the gut. If it is too low, or too high (like in my case), it suggests the gut is trying very hard to fight off some pathogen or other irritating substance.
-Highly elevated Betaglucuronidase!: To excrete certain waste products, toxins, and estrogens, the liver undergoes the process of "glucuronidation". This is part of phase 2 liver detoxification. It functions by attaching a glucuronic acid to a substance it wants to get rid of, and carries this complex into the intestines. Normally, this can then be excreted into the faeces.
However, as part of normal bacterial metabolism, certain gram-negative bacteria produce this enzyme called "Beta glucuronidase". This enzyme detaches the glucuronic acid from the substance to "free it up" in the intestine. The result is that the toxin is reabsorbed and needs to be processed again.
Key insights derived from this finding are: I had some sort of dybsiosis involving betaglucuronidase producing bacteria. Secondly, my liver was being put under stress. Finally, I was overburdened with estrogen because I could not detoxify it properly.

This is showing the levels of "commensal bacteria", which basically refers to ordinary species of bacteria which populate the gut. This is testing via a method called PCR whereby they measure the DNA of various species. It is a fairly new technology and seems to be the best out there so far.
In contrast with many other tests I have seen, I had very high levels of bacteria. There are some who have LOW levels, and some who have practically zero on the test. Mine was the opposite as you can see above.

Important points worth noting
See the "H" next to various species - this means I had higher than normal levels of bacteria in the colon. Just to note, this is NOT a common finding from what I understand. I believe it suggests that my immune system has a hard time at regulating the levels - as is reflected in my secretory IgA levels.

The above are traditional stool cultures. As you can see, no parasites were picked up on the stool culture, and no major gut infects either. No major candida either surprisingly.

Key insights from the whole test in general :
1. My gut immunity was being stressed by something
2. I had dysbiosis in the colon, as reflected in the high levels of bacteria of most species
3. My liver was being placed under stress because phase 2 detoxification was being reversed as soon as it entered the gut because of those pesky critters!

My suspicions: Due to symptoms coupled with the test results, I suspected SIBO. This test does not measure the upper intestine, so it is difficult to diagnose SIBO from these results alone. However, all things considered I embarked on a SIBO protocol.

Protocol: It involved various botanicals, anti microbials/fungals and biofilm disruptors etc. I undertook the treatment for around 2-3 months without stopping. In the first month, the results were AMAZING. My stool consistency normalised, I maintained very good motility (going 2-3 times per day at the same time each day), gas/bloating practically dissapeared, and I finally felt that I had conquered this thing.

Unfortunately, after finishing the first month protocol, the symptoms gradually came back. So to 'nip it in the bud', I devised a different protocol and continued for a further 2 months. This consisted of different botanicals etc. This time, I did not see any real benefits. Overall, I spent around £600 on these supplements (they were top of the range). Additionally, I spend £290 on the test. So overall, it was very expensive. In the end, I decided that the reason for my failure in this regard was because I did not have enough data to work with.

So... I was back to studying.

My reading led me to H.pylori. I tested that privately and unfortunately it came back negative. This was disconcerting for me, because I wanted answers!

In my search for more data, I learned of the Great Plains laboratory test and immediately fell in love with it.

Quite frankly, I now believe it is one of THE most useful tests in gaining an objective picture of "where you are at" physiologically speaking. I have learned a LOT since then. It has taken me a long time... hours of reading articles, papers, and maybe 30+ hours of webinars and lectures on the interpretation of this - but boy am I thankful - and I cant wait to start using it with my clients in practice. The next post will explain exactly why I am so fascinated with this test, and how it can help to investigate both physical and psychological issues many of us deal with. I now think it is indispensable for anyone dealing with anxiety, OCD, aggression, IBS, fatigue, methylation issues, obesity... the list goes on!

 

[Keyhole]

Re: The importance of functional testing!

Let me share with you my recent test results from the Organic acids panel. In short: I finally have some answers with regard to specifics, which I am over the moon about! Below are the results and I have annotated them to help people understand what the important markers signify.

For readers: This post will contain some biochemistry. I will try to keep it simple, but honestly when you learn how certain critters can affect your brain function - I believe you will want to know how it works, especially in light of the discussions taking place on recent session thread (October 2017) about brain chemistry and "learning about your machine". Try not to become overwhelmed... If you are not a health practitioner you do not need to know how to read the whole test. If your not interested in the details, just pay attention to the bold parts.

What is an organic acids test?
Organic acids testing is a urinary test which measures a variety of metabolites - substances involved in biochemical reactions/ or products of biochemical reactions which take place. It can help us to assess the efficiency of specific functions such as mitochondrial energy production (carb and fat oxidation), protein metabolism, methylation, the quantity/utilisation of vitamins, antioxidant status, neurotransmitter status (dopamine, noradrenaline, adrenaline, serotonin), yeast & fungal presence, bacterial presence, oxalate toxicity, clostridia bacteria, ammonia clearance, and detoxification capacity!

For the money, this test is practically unrivalled in its ability to measure the health of ones metabolism and provide insight for practitioners.

Page 1

FYI I will not attempt to explain all of the markers. I will only focus here on the ones which are related to my results. Later I will post the various study material for those of who you seek to understand how to interpret this test.

1. Yeast & Fungal markers
This measures biochemical products produced by yeast and fungi inhabiting the GI tract. If there are elevations, this means there is an overgrowth of these species.

Point of interest on this section: Marker 7) Mild elevation in Arabinose . Arabinose is a metabolite of candida. This means that I have a slight overgrowth of candida, which is not surprising since my gut immunity is working overtime anyway (high secretory IgA). Not a major concern for me right now.

2. Bacterial markers
Similar to the gut test, this measures gut bacteria. But instead of actually measuring DNA or culturing, this measure the metabolites produced by the bacteria themselves.

Two major concerns in this section (which are in agreement with my stool testing):
1. HIGH elevation of Hippuric acid -

A bacterial product of phenylalanine metabolism. Most hippuric acid in urine is derived from microbial breakdown of chlorogenic acid, a common substance found in beverages and in many fruits and vegetables. Higher levels indicate GI bacterial overgrowth that can be reduced with natural antibacterial agents and/or high-potency, multi-strain probiotics.

Abnormalities of urinary benzoate and hippurate may reveal clinically significant detoxification or dysbiosis issues. High benzoate indicates poor detoxification via phase II glycine conjugation. Interpretations of other scenarios are collected in Table 1. The organic solvent toluene is metabolized by oxidation to benzoic acid and excreted as hippurate.

Hippuric acid may be elevated for a couple of reasons. It can be excess bacteria, poor phase 2 detoxification, or excess polyphenol/coffee consumption. For me, I have all of those things... so it is no wonder this marker came back high. Anyway, this is not too much of a concern.

2. HIGH elevation of DHPPA (3,5-Dihydroxyphenylpropionoic acid).

DHPPA in urine indicates intake of chlorogenic acid, a common substance in beverages and many fruits and vegetables. Harmless or beneficial bacteria such as Lactobacilli, Bifidobacteria, and E. coli increase the breakdown of chlorogenic acid to DHPPA, so high values are mainly associated with increased amounts of these species in the GI tract.

The meaning of DHPPA is debated. Some laboratories claim it is a marker indicating clostridia overgrowth and see it as pathological. Whereas Dr William Shaw disproved this, and showed that DHPPA is an antioxidant substance which can be released via healthy microbial metabolism. Nonetheless, mine is high which reflects an overgrowth of GI bacteria (which we already knew about), and the DHPPA is potentially protecting against that.

3. Clostridia (maybe the most important, must read section!)

Very important finding - elevated HPHPA! This means I have Clostridia living in my gut at potentially pathological levels. (This was NOT picked up on the GI testing)

So, now is time to dive into some of the physiology behind this so I can demonstrate why this one finding is so fundamentally important.

The dysbiosis marker 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), the predominant dihydroxyphenylpropionic acid isomer in urine, is also measured in the Organic Acids Test offered by The Great Plains Laboratory. This marker was proven by Dr. William Shaw to be due to a combination of human metabolism and the metabolism by a group of Clostridia species, including but not limited to C. difficile.

HPHPA has been one of the most useful clinical markers in recent medical history. Treatment with metronidazole, vancomycin, or high doses of probiotics of individuals with high urinary values has led to significant clinical improvements or remissions of psychosis.

The biochemical role of Clostridia in altering brain neurotransmitters is due to the fact that Clostridia metabolites inactivate dopamine beta-hydroxylase, leading to an excess production of brain dopamine and reduced levels of the neurotransmitter norepinephrine. Excess dopamine is associated with abnormal or psychotic behavior. This imbalance can be demonstrated in the Organic Acids Urine Test by observing the ratio of the major dopamine metabolite, homovanillic acid (HVA), to that of the major norepinephrine metabolite, vanillylmandelic acid (VMA) when the Clostridia marker HPHPA is elevated. After treatment with metronidazole or vancomycin, HPHPA values return to normal along with normal ratios of HVA/VMA and normal behavior.

The highest value of HPHPA was measured in the urine of a young woman with first onset of schizophrenia. Treatment of Clostridia bacteria resulted in loss of auditory hallucinations. In autism, children with gastrointestinal Clostridia commonly exhibit aggressive behavior, agitation, obsessive compulsive behavior, and irritability. They may have very foul stools with diarrhea with mucus in the stools although some individuals may be constipated. Stool testing for Clostridia is usually of limited usefulness since most Clostridia species are considered probiotics or beneficial. There are about 100 species of Clostridia that are commonly found in the gastrointestinal tract. Only seven of these species are producers of HPHPA including C. sporogenes, C.botulinum, C. caloritolerans, C. angenoti, C. ghoni, C.bifermentans, C. difficile, and C. sordellii while C. tetani,C. sticklandii, C. lituseburense, C. subterminale, C.putifaciens, C. propionicum, C. malenomenatum, C.limosum, C. lentoputrescens, C. tetanomorphum, C.coclearium, C. histolyticum, C. aminovalericum, and C.sporospheroides do not produce compounds that are converted to HPHPA.

The same article by Dr. Shaw indicates that 3,4-dihydroxyphenylpropionic acid (DHPPA) is a marker for beneficial bacteria in the gastrointestinal tract such as Lactobacilli, Bifidobacteria, and E. coli. The exception is one species of Clostridia orbiscindens that can convert the flavanoids luteolin and eriodictyol, that occur only in a relatively small food group that includes parsley, thyme, celery, and sweet red pepper to 3,4-dihydroxyphenylpropionic acid. The quantity of C. orbiscindens in the gastrointestinal tract is negligible (approximately 0.1% of the total bacteria) compared to the predominant flora of Lactobacilli, Bifidobacteria, and E. coli (7). DHPPA is an antioxidant that lowers cholesterol, reduces proinflammatory cytokines, and protects against pathogenic bacteria. 2,3-Dihydroxyphenypropionic acid, a different isomer has been claimed to be a metabolite of Pseudomonas species but the literature indicates that this compound is formed by the in vitro action of these species on quinoline, a component of coal tar, a substance missing from the diet of virtually all humans.

Simplified:
1. Certain strains of clostridia bacteria produce a metabolite (phenolic compound) called HPHPA. HPHPA has a very similar molecular configuration to dopamine.
2. HPHPA inhibits the enzyme which allows the brain to detoxify dopamine by converting it to noradrenaline (norepinephrine) & adrenaline (epinephrine).
3. The excess dopamine is neurotoxic and pro-oxidant. It can lead to brain inflammation and alter behaviour- aggression, OCD, anxiety, neurological symptoms, thrill-seeking behaviours, "intense" persona etc etc.
4. Is VERY common in autism, schizophrenia, depression, anxiety disorders, bipolar, IBS, IBD, chronic inflammatory conditions.

HPHPA, 4-cresol, 4-hydroxyphenylacetic acid, and 3-Indoleacetic acid are all Clostridia metabolites capable of inhibiting dopamine beta-hydroxylase activity.

Ontop of that, they also have proinflammatory effects, can initiate cytokine production and competes with aromatic amino acids (tyrosine, phenylalanine, and tryptophan) for entry into the body via the intestinal tract.

In humans, phenylalanine and/or tyrosine from dietary proteins or amino acid supplements are absorbed into blood from the intestinal tract where these amino acids cross the blood-brain barrier and enter the brain. Phenylalanine in the brain is converted to tyrosine by phenylalanine hydroxylase. The ring of tyrosine is then hydroxylated to dihydroxyphenylalanine (DOPA) by tyrosine hydroxylase. DOPA is then converted to dopamine by DOPA decarboxylase which requires a vitamin B6 cofactor. The fate of further dopamine metabolism depends on the neuron type. In dopamine-secreting neurons, dopamine is the final product. In these neurons, dopamine is metabolized into homovanillic acid which can be measured in the urine organic acid test. In norepinephrine-containing brain neurons, neurons in the peripheral central nervous system, and in the adrenal gland, dopamine is converted to norepinephrine by dopamine-beta-hydroxylase. Dopamine-beta-hydroxylase requires ascorbic acid and copper as cofactors. In the adrenal gland, norepinephrine is further converted to epinephrine. Both epinephrine and norepinephrine may then be metabolized into vanillylmandelic acid (VMA).

In the species of Clostridia bacteria mentioned at the beginning of the article, phenylalanine is converted to HPHPA by a pathway that requires both human and bacterial enzymes. If Clostridia difficile is present, tyrosine is largely converted to 4-cresol. These byproducts are then absorbed into the body through the intestinal tract where they have the ability to inhibit dopamine-beta-hydroxylase. These byproducts covalently bind to the enzyme active site, irreversibly inhibiting conversion of dopamine to norepinephrine.

The resulting excess of dopamine becomes neurotoxic via the following pathway:

Basically, excess dopamine places a strain on the antioxidant (glutathione) system. It is NOT good.

So, all this time I have been testing with supplements, protocols and other stuff with no luck - because I had clostridia all along. Did it have any effect on my neurotransmitter system? Lets jump to the section on neurochemicals:

Let me explain what the above section means.

The first marker is "Homovallinic acid" (HVA). HVA is the product of the breakdown of dopamine:

As you can see, MAOA (monamineoxidase A) and COMT (catechol o-methyltransferase) are the enzymes responsible for this breakdown. (side note: theoretically, if someone has genetic polymorphisms in these genes (I do in both), then this could alter the effectiveness of this process)

The important thing to know here is that high HVA means high dopamine.

Normally what happens to dopamine is that some is broken down to HVA, and the other portion is converted to adrenaline and noradrenaline. Ideally, there should be some sort of "homeostasis" between these three markers. After dopamine has been converted to adrenaline/noradrenaline, they are then converted into "Vanilylmandelic acid" (VMA). You can see below:

To recap: High HVA means high dopamine, and high VMA means high noradrenaline/adrenaline. Great plains lab generously provide a "HVA/VMA" ratio. This ratio can help us to assess how well we are converting dopamine, and give us precious insight into the enzymatic efficiency of dopamine beta-hydroxylase.

An elevated ratio is often the result of a decreased conversion of dopamine to norepinephrine by the
enzyme, dopamine beta-hydroxylase. Inhibition of this enzyme is commonly caused by Clostridia byproducts,
including HPHPA, 4-cresol, and 4-hydroxyphenylacetic acid.

So when we examine my results, we see ordinary HVA (dopamine). However, we also see quite low VMA (adrenaline/noradrenaline).

Remember that HPHPA (elevated in my results) inhibits the function of D-B-Hydroxylase enzyme, the one responsible for converting HVA to VMA. So although my dopamine was "normal" on that day at that specific time, I clearly have some issues with this conversion. This test is only a snapshot in time, so I suspect that on another day, my dopamine marker may have been elevated. This would help to explain some of my characteristics eg giving the impression of being 'intense', some obsessive tendencies, addictive behaviours etc.

It is no doubt that this pesky clostridia has been messing with my brain for god knows how long now!

Secondly, the 5-hydroxyindoleacetic acid marker is a measure of serotonin in the brain and nervous system. Notice that mine was low! Why might I have lowish serotonin? See above that clostridia metabolites compete for gut absorption with tryptophan.




The above section shows mitochondrial intermediates and other metabolites involved with metabolism of glucose.

Overall, my mitochondria are functioning fairly well. There are no real concerns at the moment.

Oxalic acid is a measure for oxalates, and it is slightly elevated. But this can be related to dysbiosis. There are a few other markers slightly elevated, but they are related to protein metabolism and a lot of this stuff can be related to the chronic clostridia infection.

Ultimately, looking at different mitochondrial metabolites can be extraordinarily useful in fixing mitochondrial function. For example, elevated levels of "Succinic" are often related to toxicity. Citrate elevations can be due to several factors, but most notable excess ROS production and oxidative stress.
2-oxoglutaric acid (aka alphaketoglutarate) is commonly due to deficiencies of B1, but may be B5 and others etc.



The top section her examines folate metabolism. FYI anyone who is interested in learning whether their "MTHFR" is really negatively impacting their folate metabolism should do this test. A high Uracil typically means that folate is not being used in adequate quantities.

Interestingly enough, I have 3 SNPs on the MTHFR gene, yet my methylation seems to be relatively OK. Slight elevations in Uracil means I could do with adding a little bit extra methylfolate I think.

Fatty acid oxidation is OK. These ketone markers are commonly elevated with the consumption of high fat diets and MCT oils (which I consume).

The lower fatty acid markers could indicate carnitine deficit. Mine seem alright, but I could probably do with a little carnitine just to help things along.

Below that are the "functional vitamin markers". Methylmalonic acid is a marker for B12 (in its active form ie how much participates in methylation - very different to serum B12). All look relatively OK, apart from the vitamin C.

Vitamin C could quite easily be elevated due to the oxidative stress and damage caused by the chronic infection in my gut. Also smoking possibly affects this, so I know i need to up the vitamin C intake.

Finally, the last page of the test is below:



This provides us with insight into how well detoxification is taking place. You can see my 2-hydroxy butyric is elevated, indicating a stressed glutathione system (which we already deduced).

Orotic acid is a good marker for measuring efficiency of the urea cycle and bacterial ammonia production. Thankfully, i don't have any bacteria which are dumping ammonia into my bloodstream.

Finally 2-hydroxyhippuric elevation can be due to several factors, although I believe in my case it is related to dysbiosis.

Moral of the story and reason I have done this mega long post

Having this test provided me with information that I could not have gotten elsewhere. I have learned what is wrong with me, and now I can target it appropriately. This has saved me money in the long-run, and it was a fairly cheap investment. It has not been easy to learn, and I am still getting to grips with it, but from what I have seen so far, it is an invaluable tool for those living with chronic conditions who try lots of different things and come up against a brick wall. Therefore, I would totally recommend it.

My plan from here:
Devise a cyclical protocol specific to clostridia, having 2-days off and 1-day on for around 12 weeks to deal with spore formation etc. I will retest 1 week prior to finishing the protocol to make sure the critter is gone.

Hope this helped!

 

[Keyhole]

Re: The importance of functional testing!

List of video lectures for practitioners or people who want to delve into learning the details

https://vimeo.com/185542318

https://vimeo.com/239647033

https://vimeo.com/227799627

https://vimeo.com/230514398

https://vimeo.com/221340427

https://vimeo.com/208558838

https://vimeo.com/195043468

https://vimeo.com/187877405

https://vimeo.com/179473389

https://vimeo.com/41993293

https://youtu.be/zVab1OLDbmo

https://youtu.be/C2WuzTuYYUE

https://youtu.be/BJ1mxfrCs1Q

https://youtu.be/Xz8sUXVt7Ac

https://youtu.be/kwJxovcVza8

 

[aragorn]

Re: The importance of functional testing!

Thanks, Keyohole, very interesting!

What kind of protocol are you going to follow?

The notion of clostridia having a connection to mental disorders is intriguing; I wonder how many individuals with various disorders like ADHD etc. actually have a 'clostridia-problem'.

Sorry to digress a bit, but two people I know quite closely have recently been diagnosed with Alzheimer's – have you come across any information regarding a possible connection between dysbiosis (Clostridia etc.) and Alzheimer's?

 

[Gaby]

Re: The importance of functional testing!

Evil critters!! I don't know how frequent this is, but it could partly explain why people felt better on metronidazol in the autoimmune protocol. For some, metro had an anti-anxiety effect.

Thank you for distilling this information. I'm very happy for you too

 

[Keyhole]

Re: The importance of functional testing!

The notion of clostridia having a connection to mental disorders is intriguing; I wonder how many individuals with various disorders like ADHD etc. actually have a 'clostridia-problem'.

Yeah either clostridia, candida, or oxalates are apparently found in the majority of tests when running them on children with behavioural/developmental disorders. Also very high pyroglutamic acid, which indicates very heavy glutathione stress, probably due to metals and other oxidative stress.

I tend to think this is due to the several factors which disrupt the gut flora in early years- glyphosate, vaccinations, and the heavy metals which decimate the gut's immune function. This subsequently allows for these pathogenic clostridia, candida (etc) to set up camp and begin messing with the kid's neurochemistry. Dr William Shaw has come out and said that he believes the excess of dopamine is the primary mediator of behavioural and physiological defects in these kids. Apparently, the clostridia markers are very common in the lab results they see.

Sorry to digress a bit, but two people I know quite closely have recently been diagnosed with Alzheimer's – have you come across any information regarding a possible connection between dysbiosis (Clostridia etc.) and Alzheimer's?

Not sure about clostridia. There is definitely a connection with spirochetes/Lyme type illnesses, heavy metals, methylation defects, PUFA excess, lack of B1, etc.

Two supplements I would say are a "must" for alzheimers are Methyl-B12 and phospotidyl choline.

What kind of protocol are you going to follow?

I will use a product called biocidin, activated charcoal/propylite clay, perhaps another product called "olivirex" and specific species of probiotics, along with some liver support like dandellion root, milk thistle, and NAC. That is not the whole protocol, but that has been shown to be sufficient for clearing out the clostridia.

It will be biocidin 3X/day for 2 weeks. Next it will be 3X/day every third day to allow for spores etc. The activated charcoal will be used to clear the residues etc. I have not decided on the rest yet. It will probably involve various things like colostrum, glutamine, etc. I haven't thought too much about it yet.

After around 12 weeks, I will gradually try to "repair" ie

 

[Jenn]

Re: The importance of functional testing!

I also had relatively normal health when I was on the SBD (standard British diet ). Then it all went abit wrong when I went travelling with Keyhole. While I was there I contracted numerous stomach bugs and also salmonella which made it's way into the blood stream and was treated with antibiotics. After returning home I had repeated digestive issues which fluctuated between diarrhoea, bloating and fatigue, dietary changes seemed to aggravate these symptoms.

In 2016 I had two bouts of diarrhoea which both lasted about 2 weeks and were about 6 months apart. Medical tests came back inconclusive and I was advised to take antidiarrheal medicine, which I did not take and symptoms cleared up by themselves. Then in January 2017 I developed erythema nodosum on my shins, although this has gone now I recently was referred to a GI specialist and had a "camera capsule test" which is similar to an endoscopy, reportedly there is a link between erythema nodosum and gut health. Long story short, my digestion is still up and down and medical testing has been unpleasant and a complete waste of time.

So, I took the GI effects test and the results are pretty interesting... Not only do I have a parasite living down there, I have candida, poor fat digestion, low bacterial species, possible inflammation (elevated secretary IgA) and high beta-glucuronidase. I have ordered an Organic Acids Test from the same lab mentioned by keyhole and with his help will hopefully put together more of the pieces of the puzzle.

Overall I am pretty happy that I have a better understanding of what's going on. For a while I was starting to think it was something to do with my psychology, or because of dietary changes my body was just "sensitive" now. Had I settled for the medical model I would be absolutely no closer to understanding what was going on with my body and would probably end up with some nasty autoimmune condition in a couple of years!

 

[Gaby]

Re: The importance of functional testing!

I tend to think this is due to the several factors which disrupt the gut flora in early years- glyphosate, vaccinations, and the heavy metals which decimate the gut's immune function. This subsequently allows for these pathogenic clostridia, candida (etc) to set up camp and begin messing with the kid's neurochemistry.

I think Dr. Cate Shanahan's thesis on this subject is also very important to take into account. She basically blames metabolites of oxidized PUFAs as the main culprit that ruins the host, which then is more susceptible to environmental pollutants, microbes and poor digestive health.

Rancid fats not only mutate DNA directly, they also make DNA more susceptible to mutations induced by other environmental pollutants (glyphosate, mercury, aluminum, etc). Vegetable-oil derived toxic products cause a breakdown in the systems for accurately duplicating genes, a process that if gone wrong, leads to instability in our genetic material and also to de novo (new) gene mutations. In this sense, Dr. Shanahan describes how vegetable oils may possibly be the primary culprits behind the increase in Autism Spectrum Disorders and many other common diseases, describing at least three PUFA-derived compounds which bind to DNA and create new, de novo mutations. As she explains in Deep Nutrition (2017), "Nearly every day a new study comes out that further consolidates the consensus among scientists that autism is commonly a genetic disorder. The latest research is focusing on de novo mutations, meaning mutations neither parent had themselves but that arose spontaneously in their egg, sperm, or during fertilization. These mutations may affect single genes, or they may manifest as copy number variations, in which entire stretches of DNA containing multiple genes are deleted or duplicated..." This highlights the importance of discussing the toxicity of vegetable oils in our diet and their role in inducing mutations in our DNA which leaves us vulnerable to environmental pollutants.

In this sense, transfats and vegetable oils have an explosive (TNT-like) effect in our DNA and cells, affecting the health and resilience of the terrain (host).

 

[Divide by Zero]

Re: The importance of functional testing!

Keyhole, wow, so much info!

I have occasional digestion issues and was curious to do the test through great plains. Is the organic acid test the one that you found to help the most?

Unfortunately it seems for the USA, it's complicated though and not in NY state!

https://healthlinkpartners.com/testingkits/
"For all domestic orders, the test requisition form (included in test kit) must be signed by a medical practitioner and accompany all specimens sent to the Great Plains Laboratory. Alternatively, practitioners can submit signed kit requests to our lab via fax or through our online test requisition form. The Great Plains Laboratory does not offer testing in the state of New York."

I wonder if there is an alternative source for those of us in the USA, and New York State?

 

[Keyhole]

Re: The importance of functional testing!

Here is a comprehensive paper by Dr William Shaw on clostridia and autism, but really this may relate to everyone with any psychiatric condition.

Inhibition of dopamine conversion to norepinephrine by Clostridia metabolites appears to be a (the) major cause of autism, schizophrenia, and other neuropsychiatric disorders. All of these factors can now be monitored in The Great Plains Laboratory organic acid test.


By Dr William Shaw, PhD

Concentrations of the dopamine metabolite homovanillic acid, or HVA, have been reported to be much higher in the urine of children with autism compared to controls. In the same study severity of autism symptoms was directly related to the concentration of HVA. There was a relation between the urinary HVA concentration and increased agitation, stereotypical behaviors, and reduced spontaneous behavior. Furthermore, vitamin B6 which has been shown to decrease autistic symptoms decreases urinary HVA concentrations. Excess dopamine has been implicated in the etiology of psychotic behavior and schizophrenia for over 40 years. Drugs that inhibit dopamine binding to dopaminergic receptors have been some of the most widely used pharmaceuticals used as antipsychotic drugs and have been widely used in the treatment of autism. Recent evidence reviewed below indicates that dopamine in high concentrations may be toxic to the brain.

Dopamine is a very reactive molecule compared with other neurotransmitters, and dopamine degradation naturally produces oxidative species Figure 1.) More than 90% of dopamine in dopaminergic neurons is stored in abundant terminal vesicles and is protected from degradation. However, a small fraction of dopamine is cytosolic, and it is the major source of dopamine metabolism and presumed toxicity. Cytosolic dopamine (Figure 1) undergoes degradation to form 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA) via the monoamine oxidase pathway. Alternatively, dopamine undergoes oxidation in the presence of excess iron or copper (common in autism and schizophrenia) to form dopamine cyclized o-quinone, which is then converted to dopamine cyclized o-semiquinone, depleting NADPH in the process. Dopamine cyclized o-semiquinone then reacts with molecular oxygen to form oxygen superoxide free radical, an extremely toxic oxidizing agent. In the process dopamine cyclized oquinone is reformed, resulting in a vicious cycle extremely toxic to tissues producing dopamine, including the brain, peripheral nerves, and the adrenal gland.

It is estimated that each molecule of dopamine cyclized o-quinone produces thousands of molecules of oxygen superoxide free radical in addition to depleting NADPH. The o-quinone also reacts with cysteine residues on glutathione or proteins to form cysteinyl-dopamine conjugates (Figure 1). One of these dopamine conjugates is converted to N-acetylcysteinyl dopamine thioether which causes apoptosis (programmed cell death) of dopaminergic cells. These biochemical abnormalities cause severe neurodegeneration in pathways that utilize dopamine as a neurotransmitter. Neurodegeneration is due to depletion of brain glutathione and NADPH as well as the overproduction of oxygen superoxide free radicals and neurotoxic N-acetylcysteinyl dopamine thioether. In addition, the depletion of NADPH also results in a diminished ability to convert oxidized glutathione back to its reduced form.

What is the likely cause of elevated dopamine in autism? A significant number of studies have documented increased incidence of stool cultures positive for certain species of Clostridia bacteria in the intestine in children with autism using culture and PCR techniques. All of these studies have indicated a disproportionate increase in various Clostridia species in stool samples compared to normal controls. In addition, metabolic testing has identified the metabolites 3-(3-hydroxyphenl)-3-hydroxypropionic acid (HPHPA) and 4-cresol from Clostridia bacteria at significantly higher concentrations in the urine samples of children with autism and in schizophrenia.

Treatment with antibiotics against Clostridia species, such as metronidazole and vancomycin, eliminates these urinary metabolites with reported concomitant improvement in autistic symptoms. In addition, I had noticed a correlation between elevated HPHPA and elevated urine HVA. The probable mechanism for this correlation is that certain Clostridia metabolites have the ability to inactivate dopamine betahydroxylase which is needed for the conversion of dopamine to norepinephrine (Figure 2).

Such metabolites are not found at only trace levels. The concentration of the Clostridia metabolite HPHPA in children with autism may sometimes exceed the urinary concentration of the norepinephrine metabolite VMA by a thousand fold on a molar basis and may be the major organic acid in urine in those with severe gastrointestinal Clostridia overgrowth, and even exceed the concentration of all the other organic acids combined. Dopamine beta hydroxylase that converts dopamine to norepinephrine in serum of severely retarded children with autism was much lower than in those who were higher functioning. Decreased urine output of the major norepinephrine metabolite meta-hydroxyphenolglycol (MHPG) was decreased in urine samples of children with autism, consistent with inhibition of dopamine beta hydroxylase.

Many physicians treating children with autism have noted that the severity of autistic symptoms is related to the concentration of the Clostridia marker 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) in urine. These are probably the children with autism with severe and even psychotic behavior treated with Risperdal® and other anti-psychotic drugs which block the activation of dopamine receptors by excess dopamine. I have identified a number of species of Clostridia species that produce HPHPA including C. sporogenes, C.botulinum, C. caloritolerans, C. mangenoti, C. ghoni, C.bifermentans, C. difficile, and C. sordellii. All species of Clostridia are spore formers and thus may persist for long periods of time in the gastrointestinal tracts even after antibiotic treatment with oral vancomycin and metronidazole.

How do the changes in brain neurotransmitters caused by Clostridia metabolites alter behavior? The increase in phenolic Clostridia metabolites common in autism significantly decreases brain dopamine beta hydroxylase activity leading to overproduction of brain dopamine and reduced concentrations of brain norepinephrine, leading to obsessive, compulsive, stereotypical behaviors associated with brain dopamine excess and reduced exploratory behavior and learning in novel environments that are associated with brain norepinephrine deficiency. Such increases in dopamine in autism have been verified by finding marked increases in the major dopamine metabolite homovanillic acid (HVA) in urine. The increased concentrations of HVA in urine samples of children with autism are directly related to the degree of abnormal behavior. The concentrations of HVA in the urine of some children with autism are markedly abnormal.


In addition to alteration of brain neurotransmitters, the inhibition of the production of norepinephrine and epinephrine by Clostridia metabolites may have a prominent effect on the production of neurotransmitters by the sympathetic nervous system and the adrenal gland. The major neurotransmitter of the sympathetic nervous system that regulates the eyes, sweat glands, blood vessels, heart, lungs, stomach, and intestine is norepinephrine. An inadequate supply of norepinephrine or a substitution of dopamine for norepinephrine might result in profound systemic effects on physiology. The adrenal gland which produces both norepinephrine and epinephrine might also begin to release dopamine instead, causing profound alteration in all physiological functions. In addition, to abnormal physiology caused by dopamine substitution for norepinephrine and dopamine, dopamine excess causes free radical damage to the tissues producing it, perhaps leading to permanent damage of the brain, adrenal glands, and sympathetic nervous system if the Clostridia metabolites persist for prolonged periods of time, if glutathione is severely depleted, and if there is apoptotic damage caused by the dopamine metabolite N-acetylcysteinyl dopamine thioether.

Depletion of glutathione can be monitored in The Great Plains Laboratory organic acid test by tracking the metabolite pyroglutamic acid which is increased in both blood and urine when glutathione is depleted. In addition, The Great Plains Laboratory also tests the other molecules involved in this toxic pathway, the dopamine metabolite homovanillic acid (HVA), the epinephrine and norepinephrine metabolite vanillylmandelic acid (VMA) and the Clostridia metabolites 3-(3-hydroxyphenl)-3-hydroxypropionic acid (HPHPA) and 4-cresol.

In summary, gastrointestinal Clostridia bacteria have the ability to markedly alter behavior in autism and other neuropsychiatric diseases by production of phenolic compounds that dramatically alter the balance of both dopamine and norepinephrine. Excess dopamine not only causes abnormal behavior but also depletes the brain of glutathione and NADPH and causes a vicious cycle producing large quantities of oxygen superoxide that causes severe brain damage. Such alterations appear to be a (the) major factor in the causation of autism and schizophrenia. The organic acid test (see sample organic acid test report below) now has the ability to unravel a major mystery in the causation of autism, schizophrenia, and other neuropsychiatric diseases, namely the reason for dopamine excess in these disorders. In the past, some physicians would order the organic acid test once a year or less. With the new knowledge of the mechanism of Clostridia toxicity via inhibition of dopamine beta-hydroxylase, it seems that the control of such toxic organisms needs to monitored much more frequently to prevent serious brain, adrenal gland, and sympathetic nervous system damage caused by excess dopamine and oxygen superoxide. Below is a test report of a child with autism tested with The Great Plains Laboratory Organic acid test.

In the graph above, the vertical bar is the upper limit of normal and the patient’s value is plotted inside a diamond (red for abnormal, black for normal). The above results were from a boy with severe autism. The HPHPA Clostridia marker was very high (979 mmol/mol creatinine), about 4.5 times the upper limit of normal. However, the metabolite due to Clostridium difficile was in the normal range indicating that Clostridium difficile was unlikely to be the Clostridium bacteria producing the high HPHPA. In other words a different Clostridia species was implicated. The major dopamine metabolite homovanillic acid (HVA) was extremely high (87 mmol/mol creatinine), almost 7 times the upper limit of normal. The major metabolite of epinephrine and norepinephrine, vanillylmandelic acid (VMA) was in the normal range. The HVA/VMA ratio was 15, more than five times higher than the upper limit of normal, indicating a severe imbalance in the production of epinephrine/norepinephrine and that of dopamine. The very high dopamine metabolite, HVA, indicates that the brain, adrenal glands, and sympathetic nervous system may be subject to severe oxidative stress due to superoxide free radicals and that brain damage due to severe oxidative stress might result if the Clostridia bacteria are left untreated. Below the same patient’s results are displayed in a form that is related to the metabolic pathways. This graphical result now appears on all organic acid results from The Great Plains Laboratory, Inc.

 

[Keyhole]

Re: The importance of functional testing!

I think Dr. Cate Shanahan's thesis on this subject is also very important to take into account. She basically blames metabolites of oxidized PUFAs as the main culprit that ruins the host, which then is more susceptible to environmental pollutants, microbes and poor digestive health.

Rancid fats not only mutate DNA directly, they also make DNA more susceptible to mutations induced by other environmental pollutants (glyphosate, mercury, aluminum, etc). Vegetable-oil derived toxic products cause a breakdown in the systems for accurately duplicating genes, a process that if gone wrong, leads to instability in our genetic material and also to de novo (new) gene mutations. In this sense, Dr. Shanahan describes how vegetable oils may possibly be the primary culprits behind the increase in Autism Spectrum Disorders and many other common diseases, describing at least three PUFA-derived compounds which bind to DNA and create new, de novo mutations. As she explains in Deep Nutrition (2017), "Nearly every day a new study comes out that further consolidates the consensus among scientists that autism is commonly a genetic disorder. The latest research is focusing on de novo mutations, meaning mutations neither parent had themselves but that arose spontaneously in their egg, sperm, or during fertilization. These mutations may affect single genes, or they may manifest as copy number variations, in which entire stretches of DNA containing multiple genes are deleted or duplicated..." This highlights the importance of discussing the toxicity of vegetable oils in our diet and their role in inducing mutations in our DNA which leaves us vulnerable to environmental pollutants.

In this sense, transfats and vegetable oils have an explosive (TNT-like) effect in our DNA and cells, affecting the health and resilience of the terrain (host).

This is a pertinent point, and in line with Dr Peat and Chris Masterjohns work.

Young children no doubt come into contact with large amounts of PUFA. This reminds me of the chicken and egg scenario... what comes first? Perhaps nothing comes first, and it is a conglomeration of all factors which overwhelms the system. It also seems these kids commonly have genetic SNPs aswell, so they are probably pre-disposed before birth.

On this line of thought, we know that PUFA intake dramatically increases the need for vitamin E. Low vitamin E = higher susceptibility to PUFA damage. So excess PUFA means that there is a probable deficit in vitamin E.

We know that vitamin C regenerates vitamin E, and glutathione regenerates vitamin C. In the above article, Dr Shaw shows how excess dopamine requires glutathione to become neutralised.

So if glutathione and NADPH is being depleted by dopamine-o-quinone, then there is gonna be less available to regenerate vit C and vit E, and therefore less protection against PUFA radicals. I imagine this is his line of thought anyway. It seems like anyone can approach this from any angle, and all point to the same problem - a complete inundation by toxic substances - whether it be PUFA or whatever else.

The PUFA connection highlights the importance of getting these kids (and probably everyone else) onto low dose vitamin E for a couple of years at least, just to support the system. Thanks for sharing that information Gaby.

Keyhole, wow, so much info!

I have occasional digestion issues and was curious to do the test through great plains. Is the organic acid test the one that you found to help the most?

Unfortunately it seems for the USA, it's complicated though and not in NY state!

https://healthlinkpartners.com/testingkits/
"For all domestic orders, the test requisition form (included in test kit) must be signed by a medical practitioner and accompany all specimens sent to the Great Plains Laboratory. Alternatively, practitioners can submit signed kit requests to our lab via fax or through our online test requisition form. The Great Plains Laboratory does not offer testing in the state of New York."

I wonder if there is an alternative source for those of us in the USA, and New York State?

Unfortunately, NY state is like the only place these tests are unavailable. Can you go out of state to a friend or relatives for a day or two, take the test, then go home?

The organic acids is the one I am biased towards, but I think for fair reason. It is such a comprehensive panel and when compared with other organic acids, it really shines. Stool testing is another option, but as you have seen above, stool testing simply does not cover everything and missed out on my clostridia infection! I would opt for both in clinic, but it can get pricey.

 

[Divide by Zero]

Re: The importance of functional testing!

Unfortunately, NY state is like the only place these tests are unavailable. Can you go out of state to a friend or relatives for a day or two, take the test, then go home?

I can ship it to a friend's house in another state and send it in with his address as the return one.
... but I'm not sure if the doctor has to be from that state too or can that be signed by any doctor (and I wonder who checks anyway, perhaps it's just a legalese way to make people depend on doctors but Great Plains may not even verify?)

 

[Keyhole]

Re: The importance of functional testing!

Unfortunately, NY state is like the only place these tests are unavailable. Can you go out of state to a friend or relatives for a day or two, take the test, then go home?

I can ship it to a friend's house in another state and send it in with his address as the return one.
... but I'm not sure if the doctor has to be from that state too or can that be signed by any doctor (and I wonder who checks anyway, perhaps it's just a legalese way to make people depend on doctors but Great Plains may not even verify?)

You could go with that option. One way you can get a doctors signature is to go through this website called "Mymedlab". It may cost a little extra, but they will sign the test for you. This is the official way that people acquire test results without seeing a health practitioner. You will still need to get it sent to a location outside of NY state though.

If you get the results, it might be a good idea to post them up here so we can network about them as well. Also, Great Plains Lab offer a free 30 minute consultation for all patients/practitioners to help you interpret the results - which is really helpful :)

 

[nature]

Re: The importance of functional testing!

Very impressive work you've done, Keyhole. Congrats and thanks!

 

[Chu]

Re: The importance of functional testing!

You two seem quite healthy and energetic in general, so if your results are such, then the rest of us have no hope!

More seriously though (and this is without having watched the videos you shared, so apologies if it's too simplistic), what bothers me a bit about this is that it seems to be focused on solving one issue only. Depending on your diet, your environment, etc., your gut flora can change a lot, as far as I understand. So, as much as taking specific supplements might benefit you for a while, what makes the "good critters" stay and win on a more constant basis? How can you make it sure that you will "win the war", so to say, if the real root of the problem is not treated (and very often, that root is basically unknown and/or multi-factorial).

It seems to me that the explanation is a bit too simple: It's not the first time we hear that one thing (in this case the Clostridia bacteria) is possibly the major cause for autism and schizophrenia, for example. Not that it may not be involved, but basically it seems that science knows hardly anything about it. And then, what if it is a frequent issue with those two, but also with many other problems that never get tested for the same bacteria, and basically it's a more generalized issue, not a causative factor? And what about people whose concentration of Clostridia is high as well, but who don't present any of the typical traits of autistic or schizophrenic people?

I don't know. But every time they start talking about this or that substance inhibiting this or another substance, I get a bit suspicious, FWIW. Because we know how chemicals work all together, and the little that is known about them in terms of information theory and even genetics, for example. IMO, it needs to be taken case by case, and with careful observation when one tries a new thing, whether there is a test like this or not (and there could also be a monetary interest in these labs),

Anyway, I don't mean to discourage you if you want to try it. It does sound interesting. Let us know how your experiment goes, and take care!