A reader wrote:

“Hi Ken,

The only symptom that showed significant improvement was ADHD, a proxy for the ability to focus (which agrees with feeling good enough cognitively to seek writing work).

A followup email potentially explained what is happening.

“I stopped taking almost anything that wasn’t on my take list, especially vitamin d because I remember seeing it promoted bifidobacteria. I took melatonin and valerian throughout purely to help me sleep, a lot of monolaurin as it was a recommendation and for possible antiviral benefits, and curcumin (if I stop taking it I get really bad lower back pain). I took Lactobacillus gasseri for two weeks (made me feel great while taking it) and symbioflor 2 for 1 week which also made me feel better but less so.

Going forward Recommendations

#1 Get back on a core set of recommendations for CFS/FM/IBS — click here to review

#2 For dealing with HIGH counts — there was nothing on the default recommendations. When I changed to LOW counts,  a lot of things appeared.  (Remember — the original recommendations ONLY dealt with High counts, the site has evolved from there).

REMINDER: the numbers are NOT the degree of effectiveness, they are the confidence that this would change bacteria based on the number of studies reporting it.  Olive Oil may be 100x better than inulin — but inulin has 4 times the number of studies!!! In general, relative effectiveness is not available in studies. Studies are usually, “Olive oil decreases…..”

As a result of this, I modified my profile summary page to report high and low separately, as shown below:

Clearly, most of the change was due to more bacteria dropping below normal, almost a 35% increase in low counts.

Hand Curated List

I am trying not to do this (time consuming and only benefits one person), but in this case it may be of general benefit.  The settings I used was LOW COUNTS, not aggregated, some evidence; then it’s common sense or remember this or that odd fact from reading.

• Given some extract (often sold as a supplement) and the real whole food that contains it, I always favor the real whole food!

Take

• Apples — especially Pink Lady
• Pomegranate
• Blueberries
• Black raspberry
• Jerusalem artichokes / Inulin
• Sea Weed — snacks or supplement
• Walnuts
• choline supplements
• fish oil
• barley and oats porridge for breakfast
• Probiotics:
  • bacillus coagulans
  • clostridium butyricum miyairi probiotics
  • General Biotics’ Equilibrium
  • lactobacillus acidophilus
  • lactobacillus reuteri
  • Prescript Assist
  • saccharomyces cerevisiae

Avoid:

• No Vitamin D (which is usually part of the standard recommendation 😦 )
• Neem
• Rosemary
• Thyme
• Triphala
• L-Taurine supplements
• Stevia, sulfites
• Monolaurin
• Probiotics:
  • bifidobacterium longum bb536
  • lactobacillus rhamnosus

Bottom Line

The earlier recommendation targeted at high counts only, appear to have worked based on two pieces of evidence:

• Subjective report from reader (Improving from a 10 down to a 5 for severity)
• No recommendations for high counts!

We are now moving over to repopulating the low counts. Once that is done, we may find that another adjustment is needed. It is not a one-step linear path to rebalance the microbiome.

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

From medical literature I have added several hundred drugs and their likely impact on the microbiome. A common problem with CFS patients is that they are only aware of some trademark name and not the standard scientific name.

I have started (it’s a long process) adding the common or trademark names to various drugs — for example Antivirals:

Now becomes

This process will likely take a few weeks to complete.

Antivirals and CFS

I have posted about this in the past ,”Valganciclovir antiviral and CFS[2016]” and  “Valacyclovir, EBV and CFS [2016]”.

I decided to look at the microbiome shifts seen with the valacyclovir hydrochloride  antiviral,  And was quite surprise to see a high number of bacteria taxonomy are reduced — which may account for the success reported in the above post “All patients were treated subsequently with valacyclovir, with 93% having a positive response” [2014]. The other antiviral, Valcyte or Valganciclovir, is not in my sources.

So, the question must be asked — was it’s antiviral nature OR microbiome modification nature that causes the reported improvement?

I am just finishing a course of high dosage antibiotics for cellulitis that sent me to the hospital last week. With the http://microbiomeprescription.azurewebsites.net website data, I realized that I do not need to do random things to recover from the antibiotics.

First, the antibiotic that I was using was a cephalosporin i antibiotics that antibiotics and many many antibiotics and prescription drugs are listed at http://microbiomeprescription.com/Library/GutModifiers.

Clicking on it showed what changed:

cephalosporin i antibiotics

• beta-lactam antibiotics

The following are impacted

I just added a link below the table:

Recommendations to contradict the shifts

When I click this, it takes me to the recommendations page.

Recommendations from cephalosporin i antibiotics Lab Results

etc,

Bottom Line

I have recommendations of what to take and to avoid that are specific to the antibiotic / prescription drug that I took! No random picking of stuff from the air.

In the near future, I will extend this to allow microbiome information from ubiome to be incorporated (i.e.  if you are low, and the prescription item increases it — then we attempt no correction).

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.

On my commute today I had a conversation with an old colleague whose teenage daughter had a physical brain trauma(included cerebral ischemia) in January. As she described her symptoms, I recognized a lot of symptoms that are often seen with CFS. I also recall reading some articles about gut shifts seen with physical trauma.

Cognitive impairment is common with CFS and other autoimmune conditions.

• The bidirectional gut-brain–microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease.[2017]
• The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders.[2018]
• “Specifically, Bacteroidales and Clostridiales, the two most prevalent bacterial taxa in mouse gut (Eckburg et al., 2005; Krych et al., 2013), were inversely regulated by traumatic spinal cord injury (SCI): Bacteroidales decreased while Clostridiales increased (Fig. 2, B and C). Significant changes in these taxa were accompanied by lesser but consistent changes in minor taxa, including Anaeroplasmatales, Turicibacterales, and Lactobacillales (Fig. 2 A). Open-field locomotor (Basso mouse scale [BMS]) scores were negatively correlated with the relative abundance of Clostridiales and Anaeroplasmatales, suggesting that the proportion of these bacteria can predict the magnitude of functional recovery and might be useful as a biomarker of injury severity” [2016]
• In conclusion, our results are the first to show specific changes in the microbiota due to a change in brain function, and also to surgical stress following tissue injury, with the likely involvement of the autonomic nervous system and goblet cells under certain conditions.  [2016]
• “Higher percentages of Clostridiales and lower expression of Bacteroidales in high-energy diets were related to the poorer cognitive flexibility in the reversal trials. ” [2015]
• Clostridium butyricum attenuates cerebral ischemia/reperfusion injury in diabetic mice via modulation of gut microbiota.[2016]
• Dysbiotic microbiome in patients with stroke and TIA: ↑ genera Enterobacter, Megasphaera, Oscillibacter, and Desulfovibrio; ↓ genera Bacteroides, Prevotella, and Faecalibacterium correlating with disease severity. ↓ TMAO in stroke/TIA group compared with patients with asymptomatic atherosclerosis [14]

Bottom Line

The number of bacteria taxonomy identified is lower than with other conditions but it is definitely work creating a profile on. An example with the demo ubiome result is shown below.

Analysis Web Site:  http://microbiomeprescription.azurewebsites.net

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.

Today I got a comment from someone with Hashimoto’s thyroiditis, often co-morbid with CFS, IBS etc.  I thought that I would check to see if there had been any microbiome work done on this condition. I was delighted to see a February, 2018 article, “Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients.”  and converted it results into a profile that can be applied to uBiome results.

This is added to the existing series shown below

• ADHD – Attention-deficit syndrome
• Alzheimer’s Disease
• Autism
• Autoimmune Disease
• Chronic Fatigue Syndrome
• Diabetes Type 2
• Crohn’s Disease
• Depression
• Fibromyalgia
• Gout (Arthritis)
• Hashimoto’s thyroiditis
• High Blood Pressure
• Histamine Issues
• Inflammatory Bowel Disease
• Irritable Bowel Syndrome
• Metabolic Syndrome
• Mood Disorders
• Rheumatoid arthritis
• Schizophrenia
• Systemic Lupus Erythematosus
• Ulcerative colitis

Analysis Web Site:  http://microbiomeprescription.azurewebsites.net