History of Gut Pain and Epigenetic Malnutrition
I am 32 years old and have suffered from ill health all of my life. From as long as I can remember, I’ve experienced gut pain, fatigue, and hyper-sensitivity. If there was something to catch, I would catch it. I react to everything and suffer chronic gut and nerve pain.
As a young child, I had chronic abdominal pain in the lower right quadrant and would often be buckled over in pain. Doctors thought it was appendicitis so removed my appendix but the pain continued. I was chronically tired and sensitive to the cold. I would struggle to get up in the morning to go to school and would stand in the shower dousing myself in hot water for as long as I could to warm up my body. Cold hands and feet has continued into adulthood.
I was born into a family that struggled with spine, neck, head, and gut issues. I was raised on cow’s milk and barley formula as my mother was unable to breastfeed. My mother and aunt had Ehlers Danlos Syndrome. I was diagnosed with it 8 years ago. My mother has Arnold Chiari malformation, my aunt scoliosis. They were post-war children. My grandmother had spinal issues and likely was very deficient in the B Vitamins. My grandfather, aunt and mother all suffered from gut issues, my grandfather eventually dying from bowel cancer. He was sensitive to many foods, particularly FODMAP rich ones.
I had many allergies – dust mite, grass, cow’s milk etc. I suffered an adverse reaction to the MMR vaccine when I was eight – with an intense full body rash. I was bedridden with intense fatigue for two weeks. Around the same time, tests found huge numbers of the parasite dientamoeba fragilis (D fragilis) in my stool. Dientamoeba fragilis together with Blasto hominis, another intestinal parasite, have been found in large numbers in my stool ever since. Despite trying many things, I’ve never been able to get rid of them.
Increasing Food Sensitivities, Weight Loss, Amenorrhea, and Osteoporosis
By the age of ten, I was struggling with depression and increasing sensitivities to many foods – particularly gluten and dairy. The only thing that seemed to help was exercise. I played competitive soccer, did cross-country and athletics and rode my bicycle everywhere. At this time, I started becoming vegetarian, in response to my growing concern about the state of the world, animal cruelty and the environment. This meant consuming a lot of gluten and dairy based foods. As I entered puberty, my body couldn’t keep up with the energy demands of this stage of development and I began losing weight rapidly, despite eating a ton of carbs.
I was working hard at school, and have always pushed myself to succeed, but as my body became more and more unwell, I struggled with focus and concentration. My depression became worse and the world felt very bleak. Everything I ate caused pain, bloating, and fatigue. I was eating lots of pasta and cheese to try to fuel my sports but I continued to lose more and more weight. Throughout my parents had been doing everything to investigate and treat the cause of the illness, but I just kept getting more and more unwell. My weight dropped dangerously low, I developed bradycardia and I struggled to think clearly.
The years passed through adolescence and into early adulthood. Through sheer willpower and making myself eat, despite the intense pain it caused, including severe abdominal cramping, sulfur gas, burning, over-heating, swelling, headaches and more, I could get some extra weight on for a while, but it would quickly fall off again. My growth and development suffered. My bones froze in time – a bone age at 19 showed the bones thought they were 13. I had amenorrhea. I developed osteoporosis. An endoscopy showed an inflamed caecum and inflammatory spots in my sigmoid colon.
Through my teenage years and twenties, I had to follow extremely restrictive diets. I had to quit being vegetarian, as it didn’t leave anything to eat and my body clearly needed nutrients from animal foods to survive. I reacted to FODMAPs, histamines, too much fat, too many carbs – there was so little I could eat without feeling extremely unwell.
I would often experience intense nausea attacks, severe bouts of sudden pelvic pain, stomach bugs, and caught giardia several times. I got shingles at the age of 21, a strange fever induced by tick bites at 22, and viral meningitis at the age of 26.
Gut Dysmotility, Progressive Neuropathy, and Migraine
My gut was becoming lazier and lazier. At the age of 23, I wound up in emergency in extreme abdominal pain after it stopped moving altogether and my intestines became fully impacted. The pain was excruciating. Eight sachets of heavy duty laxatives did nothing to the situation. I was started on prucalopride (an enterokinetic drug) to help get it moving again. I cannot function without this drug now. When I stop taking it, my gut ceases to move altogether.
Through my twenties, I also started suffering from tingling in my arms and legs and increasing peripheral neuropathy. By the age of 27, I would experience episodes where an entire arm or leg was completely numb. Blood work showed my B12 had dropped very low. I went on B12 injections and increased food sources of B12. Things improved for a while but then the neuropathy returned. I subsequently developed Reynaud’s syndrome.
Around the same time, I started developing worsening headaches and a few years later migraines. The migraines were so bad I couldn’t move without intense vertigo and extreme nausea. I had to lie in a pitch dark room and wait it out. Some migraines were preceded by a confusional aura where I couldn’t tell what anyone was saying to me. I could understand the individual words but not when they were strung together in sentences. The vertigo continued for about 6 months.
Exercise became more painful too. Despite being fit, I would suffer from intense DOMS, headaches and nausea after running. Muscles started becoming more and more sore and painful despite taking electrolytes, being careful about my nutrition and warming up and down.
I woke up every morning feeling exhausted and sleep studies revealed I had developed sleep apnea – something I had thought wasn’t so common in women of my age and build.
Stress Fractures, Worsening Neuropathy, and Hypoxia
Earlier this year, I wound up with a bad stress injury in my hip – several stress fractures in my femoral neck despite no blow to the area and no fall – which doctors thought quite unusual for someone of my age who was running low mileage recreationally. The injury brought with it chronic nerve pain along my right side on top of worsening neuropathy.
I would wake up in the middle of the night with numb limbs. Nerves would fire spontaneously in my legs and arms. Nerves in my jaw felt constantly stimulated and my tongue would swirl uncontrollably around in my mouth. My gut stopped moving more and more frequently and I would have to take laxatives regularly to clear it out.
I had severe GI burning and was unable to eat anything other than clear broth and coconut water without pain. An endoscopy found bleeding in my sigmoid colon. My hemoglobin dropped 17 points and I struggled with breathlessness, unable to get up a flight of stairs or even walk a few hundred meters without feeling deeply exhausted.
To date, I have been diagnosed with POTS, Ehlers Danlos Syndrome, dysautonomia, gastroparesis, severe osteoporosis of the lumbar spine, and peripheral neuropathy. This comes against the backdrop of the gut problems experienced since childhood. These other health issues were, to no small degree if not caused, then significantly worsened by my gut issues. I have had long periods of time where I couldn’t absorb food or eat very much due to my gut problems, so I have been underweight for most of my life. As a result, I am likely deficient in many nutrients.
Current Diet, Activity, and Recent Testing
- Breakfast: steamed greens (e.g. some combo of broccoli, beans, spinach, asparagus, etc.), 1-1.5 scrambled organic egg, 1 cup bone broth with 1 desert spoon collagen peptides + 1 desert spoon seaweed.
- Lunch: 1 cup bone broth with 1 desert spoon collagen peptides + 1 desert spoon seaweed with 1 egg yolk stirred through OR some homemade chicken liver pate on carrot sticks instead of the egg yolk; 1 raw carrot and/or raw cucumber sticks; sometimes 1 packet of roasted nori.
- Snacks: 1 glass homemade carrot, celery and ginger juice; some blueberries and/or a kiwi fruit.
- Dinner: some protein (e.g. half a single piece of salmon, 8 prawns, small amount of red meat), green veggies (e.g. steamed beans, asparagus, spinach, broccoli), a starchy veggie (e.g. pumpkin, sweet potato, beetroot), sometimes some green salad.
- After dinner: a few blueberries and/or pieces of mandarin, 30-40g vegan carob (cocoa butter, carob powder, no sugar), a cup of herbal tea.
Activity and Exercise
- Daily: walking – approx. 12-13km over the course of a day including daily activities, as measured on Fitbit.
- Running: 3x per week – currently at 9km total over the week; very slow 6’20” pace.
- Yoga: 2x per week 1hr classes – beginner.
- Physio: 3x 20-25min per week – core exercises for lower back, hips, shoulders etc as set by exercise physiologist.
These tests were conducted by RN Labs and Great Plains Laboratory before I began thiamine.
Stool – GI-360
- Klebsiella pneumoniae – very high
- Proteobacteria – very high
- Akkermansia muciniphila – very high
- Escherichia spp. – very high
- Bacteroides spp. – very high
- Endolimax nana – very high
- Eubacterium siraeum – very high
- Enterobacter cloacae – high
- Elastase – low
- Butyrate – low
- Clostridia – very low
- Faecalibacterium prausnitzii – very low
- Veillonella spp. – very low
- Secretory IgA – very low
Urine – Organic Acid Test
Yeast and fungal markers:
- 3-Oxoglutaric – 0.69 (<0.33) – Elevated levels of 2-Oxoglutaric suggest dietary vitamin deficiencies or supplementation with 2-ketoglutaric acid. Coenzyme A (derived from pantothenic acid), flavin adenine dinucleotide (FAD) (derived from riboflavin), and thiamine are required for conversion of 2-oxoglutaric acid to succinyl-CoA.
- Arabinose – 70 (<29) – Urinary levels higher than the reference range may simply reflect a high dietary intake of these fruits. However, arabinitol (which converts to arabinose) is also documented to be produced by the Candida genus of yeast. When elevated in body tissues, it can link with lysine and arginine. In theory, this may block some binding sites for coenzyme pyridoxal phosphate, biotin or lipoic acid at the lysyl residue in apoenzyme proteins. This would impair enzymatic processes, such as transamination of amino acids (in spite of “normal” intake of vitamin B6). A finding of high arabinose, without dietary intake of the above-mentioned fruits, suggests a stool analysis or other tests/examinations for Candida overgrowth.
- Tricarballylic – 2.3 (<0.44) – Tricarballylic acid is a chemical by-product released from fumonisins during passage through the GI tract. Fumonisins are fungal toxins produced primarily by F. verticillioides. Tricarballylic acid is an inhibitor of the enzyme aconitase and therefore interferes with the Krebs cycle.
- 4-Hydroxybenzoic – 1.9 (<1.3) – A marker for intestinal dysbiosis.
- Glyceric – 16 (0.77-7) – High glyceric levels on an organic acids test usually relates to primary hyperoxaluria type 2.
- Oxalic – 389 (range = 6.8-101) – High oxalic with or without elevated glyceric or glycolic acids may be associated with the genetic hyperoxalurias, autism, women with vulvar pain, fibromyalgia, and may also be due to high vitamin C intake.
Glycolytic Cycle Metabolites:
- Lactic – 51 (<48) – Elevated by a number of nonspecific influences, such as vigorous exercise, bacterial overgrowth of the GI tract, shock, poor perfusion, B-vitamin defciency, mitochondrial dysfunction or damage, and anemia, among others.
Mitochondrial Markers – Krebs Cycle Metabolites:
- Succinic – 24 (<9.3) – The most common cause of elevated succinic acid is exposure to toxic chemicals which impairs mitochondria function.
- Malic – 2.7 (0.06-1.8) – Higher levels of malic acid in urine indicates inefficiencies in energy production. Elevated malic acid values suggest increased need for niacin and CoQ10. When malic acid is simultaneously elevated with citric, fumaric, and alpha-ketoglutaric acids, it strongly suggests cytochrome C oxidase deficiency, indicating dysfunction in the mitochondrial energy pathways.
- Aconitic – 6.6 (6.8-28) – Elevated in mitochondrial disorders. Aconitase metabolizes citric and aconitic acids, and is dependent on glutathione. Increased levels may indicate additional requirement for reduced glutathione.
- HVA / VMA Ratio – 2.3 (0.16-1.8) – An elevated ratio is often the result of decreased conversion of dopamine to norepinephrine by the enzyme, dopamine beta-hydroxylase. This inhibition is commonly caused by Clostridia by-products, including HPHPA, 4-cresol, and 4-hydroxyphenylacetic acid, which are also measured in the OAT.
- Dihydroxyphenylacetic (DOPAC) – 3.9 (0.08-3.5) – DOPAC levels may be elevated due to inhibition of dopamine beta hydroxylase (DBH) from Clostridia metabolites, the mold metabolite fusaric acid, pharmaceuticals such as disulfiram, food additives like aspartame, or to deficiencies of the DBH enzyme due to copper deficiency, vitamin C deficiency, or malic acid deficiency.
- Quinolinic – 0.58 (0.85-3.9)
Ketone and Fatty Acid Oxidation:
- 3-Hydroxybutyric – 5.7 (<3.1) – A moderate urinary increase in 4-hydroxybutyric acid may be due to intake of dietary supplements containing 4-hydroxybutyric acid, also known as gamma-hydroxybutyric acid. Very high levels may indicate the genetic disorder 3-methylglutaconic aciduria involving succinic semialdehyde dehydrogenase deficiency.
- Acetoacetic – 32 (<10) – High levels of acetoacetate in blood may result from decreased availability of carbohydrates (eg, starvation, alcoholism) and/or abnormal use of carbohydrates storage (eg, uncontrolled diabetes, glycogen storage diseases).
- Methylsuccinic – 5.7 (0.1-2.2) – Very elevated values may indicate a genetic disorder. Fatty acid oxidation defects are associated with hypoglycemia, and lethargy. Regardless of cause, intake of dietary supplements containing L- carnitine, or acetyl-L-carnitine may improve clinical symptoms.
- Sebacic – 0.39 (<0.24) – Sebacic acid is a breakdown product of fatty acids. Higher levels can be seen when the breakdown of fats is impaired or blocked. May be associated with Vitamin B2 (aka Riboflavin) deficiency. Riboflavin is needed for fatty acid breakdown.
- Vitamin B2 – 0.38 (0.04-0.36)
- Vitamin C – 598 (10-200)
During this time, I was fortunate enough to learn about the work of Dr. Lonsdale and Dr. Marrs and have started talking high dose Lipothiamine. After several months, the chronic nerve pain is reducing and my gut has improved somewhat however I still struggle with pain and am very sensitive to a lot of foods.
I also have been learning more about the role of genetics and epigenetics in my condition. I am compound heterozygous for the MTHFR mutations and also have SNPs of the PEMT, NOS3, COMT, MOAB, GST genes alongside a number of other SNPs (including CYP, PONI, GAD, GGH, HTR2A, MMAB, NAT2, SLC, SULT, ALD, CBS, DHFR, MTR, TCN1, CBS, DDC, DRD and more).
I am currently taking 1000mg of Lipothiamine orally per day. If IV was possible, I would do that given my gut problems, but we have not been able to find anyone able to administer that here in Australia. In addition to the Lipothiamine, I take magnesium (800mg), liposomal Vitamin C (6000mg), glutathione (450mg), probiotics, a multivitamin, cod liver oil, B-complex, Alpha Lipoic Acid, zeolite, zinc and methylated b12 (shots occasionally and drops in between).
I follow the Auto-immune Protocol diet (including all fresh, unprocessed food, no sugar, lots of veggies and fruits, organic fish, meat, eggs, etc.), walk daily, practice yoga, meditation, daily stretching and gentle jogging a few times a week.
Improvement with Thiamine and Outstanding Questions
In recent weeks, I’ve been finding the nerve pain has significantly improved on this high dose (1000mg) of Lipothiamine however my gut symptoms are quite bad – with a lot of GI burning. I experienced this when I first started taking the Lipothiamine but it subsequently subsided so I am unsure if this is something I need to just push through or if I am on too high a dose.
I would love to hear others experience and hope that sharing mine is of use to others. I am deeply grateful to Dr. Lonsdale and Dr. Marrs for their groundbreaking work in this area and hope to do whatever I can to spread the word about this vital information so that more people can experience full health and happiness in their lives.
We Need Your Help
More people than ever are reading Hormones Matter, a testament to the need for independent voices in health and medicine. We are not funded and accept limited advertising. Unlike many health sites, we don’t force you to purchase a subscription. We believe health information should be open to all. If you read Hormones Matter, like it, please help support it. Contribute now.