Sick since a child from contaminated water

My back story –

I’m now 35. As a child I contracted a bacterial gut infection from water that had cow poop in it (broken pipe through a field), and was unable to eat sugar without being sick. As a teenager I had relatively bad insomnia, acne and eczema. I was prescribed months of antibiotics as treatment and put on a contraceptive to address the acne. I also had a spinal injury that I was prescribed painkillers including ibuprofen and codeine, and a painkiller that’s no longer approved for distribution that I forget the name of. By the time I was 19 I was in a high stress job, sleeping well, but taking guarana and caffeine pills on top of coffee to stay functional due to fatigue. 

Doctors took blood tests, and everything was in the normal range so no diagnosis. 

At 22 I had sever food poisoning in the Netherlands. 

At 25, in 2016, I took a trip to California – I’m from New Zealand – and contracted giardia, during a heatwave, and ended up in hospital in hypovolemic shock. I was prescribed fluids which where intravenous and an anti-psychotic, which as a New Zealander I didn’t take. My sister flew over to help me get home. Once back in NZ, I was found to have irregular heartbeat, giardia, and neck injury from severe vomiting. I had an allergic reaction to the first antibiotic to treat giardia, was given a course of prednisone then a different antibiotic which killed off the giardia. 

During this time, I had extreme fatigue, brain fog, heart palpitations, insomnia, panic attacks, tension headache and the worst, internal vibrations or tremors that could not be seen. I developed a dependency on sleeping pills, which quickly stopped working all together. Doctors couldn’t find anything physically wrong with me, and eventually one decided to try b12 injections. This, along with osteopathy and rest, resolved most symptoms, leaving only tinnitus. I have had b12 injections 1-3 monthly ever since, and this mostly controls the vibrations. I resolved my dependence on sleeping pills by using natural sleep aids and pushing through several sleepless nights. I was left with an inability to eat gluten and dairy.

By 2021 I was in good health – able to regularly exercise and hold down a high pressure job. I had my first Covid vaccine no issues, the second vaccine I became violently ill for 48 hours with fevers, fatigue, and body aches. I took the recommendation to get the third shot, still Pfizer, and was bedbound for 2 days with fevers, rigours, vomiting, headache, weakness and fatigue. In December 2022 I contracted Covid. My symptoms included sore throat, swollen lymph nodes, vomiting, fevers, rigours, fatigue, elevated heart rate. By day 7 I was weak but recovering. On day 8, internal vibrations started with severity, followed by blurred and double vision (I required a new prescription following this), breathlessness walking across a room, heart palpitations, tension headache, brain fog, PEMS and extreme fatigue. I was diagnosed after 3 months with long Covid. 

I tried every treatment suggested by the internet and then some, from HBOT to magnesium floats to ozone sauna, thousands of dollars of supplements, osteopathy, massage, and more. After almost 2 years I’m working full time again, and most symptoms are managed enough to wake up, work, clean up a bit, and sleep again. However they are not fully resolved – I can’t exercise without an extreme energy crash, and I have to continually practise meditation and other calm down methods to regulate. It’s certainly not a life lived well, and one in constant fear of catching so much as a cold.

I am hesitant to accept a ‘long Covid’ diagnosis, despite it being the only thing on offer. This is because I experienced the same set of symptoms I after having giardia and dehydration, neither of which are viral so not a “post viral syndrome”. My lifelong battle with fatigue indicates to me that serious illness triggers a specific set of symptoms, and my Biomesight results strongly indicates a gut issue. I have tried various diets, each resulting in my becoming more fatigued – keto, Mediterranean, low carb, vegetarian, carnivore, low formal, and high protein. 

I find the microbiome prescription results a little overwhelming and difficult to sort through, so your advice would be so appreciate

Analysis

First, about “overwhelming”. I agree! Just like “No man can serve two masters”, “No site can server all users”. My primary focus has been correctness, depth of coverage and other technical (nerd) aspects. This came out of seeing failure after failure of simplified and naïve approaches. The “new UI” has been an attempt to simplify the process while maintaining a reasonable level of accuracy.

You have had a long history of microbiome insults causing dysbiosis. Some are known to cause ME/CFS, see IBS/CFS/Long Covid Insight from Bergen’s Giardia Infection [2018]. Rather than retracing past events, let us focus on your current state and go forward.

Looking at predicted symptoms versus reported symptoms, we see a high number of matches.

This usually indicate that “Beginner-Symptoms: Select bacteria connected with symptoms” is likely the best start, This will focus on the probable bacteria that are causing most of the symptoms (and ideally ignore bacteria shifts that are likely just noise).

Usually the number of bacteria identified is a fraction of the symptoms. In this case we have 63 bacteria identified for 55 symptoms. The suggestions are shown below. I usually suggest keeping to those above 50% of the highest weight (1706 x 50% =853) and avoiding to those below 50% of lowest value (-1375 x 50% = -865). The reason is that the higher (or lower) the weight, the more probable it will have an impact).

I retried checking all types of microbiome modifiers (usually overwhelming). Mainly to see if antibiotics often used for ME/CFS rank high. Going to the Consensus Report and filtering to antibiotics we see that none made it over the threshold – which means that they are likely to be really helpful.

At this point, I typically decompose suggestions into types, first with probiotics. VSL#3 is rarely a clean choice because there were changes in the formula and other issues.

I would go for the following probiotics (two weeks of one at a high dosage – 50-150 BCFU) and then rotate to the next. Given that you are “down under” , I would suggest getting them from my favorite Indian Manufacturer (usually manufactured just weeks before shipping and best prices) – I linked to the sight below. Note that doubling the capsules in a bottle often costs just 20% more and a lot cheaper than ordering two bottles!!

P.S. spirulina was a coding error – just fixed it.

Your inability to handle gluten or diary means that some suggestions must be excluded. I would be tempted to try an experiment with oats flakes, then barley flakes, then 100% rye bread — mainly to see if it is wheat gluten that is the issue (there are many types of gluten).

A handful of almonds and walnuts everyday is an obvious item. Do not do a B-Complex — some B vitamins will help and other hurt. Keep to Vitamin B7, B2. Hopefully you can tolerate dark chocolate (Cacao). Lime is suggested (as is Vitamin C).

The avoids should be pretty clear.

Alternative Paths

At this point, we branch into two additional paths — one by using Kyoto Encyclopedia of Genes and Genomes (KEGG) data on compound being produce and consumed by your microbiome. With KEGG we look for probiotics that can provide enzymes etc that you are deficient in. Why these alternative paths? Simple, there is not enough data available so we use inference.

The second path is going to the food site to identify foods rich in suggested nutrients. The foods may not have been used in studies, but the dominant nutrients in the foods may have been studied.

KEGG

The top suggestions are below. #1 item is common for ME/CFS, Mutaflor is available in Australia, I warn people that it may cause a major die-off / herx reaction. Symbioflor 2 is the same probiotic species but at ~ 1/100 of the BCFU and unlikely to cause die off. To the above list I would add these two

Foods

We see that you may be eating a lot of beans – they appear to be providing some of the nutrients that caused wheat to be suggested above.

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes. outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.