Below are some of mine. Remember the first one in 2019 was onset of ME/CFS and it has since moved much closer to recovery (but not all of the way there). uBiome does provide a Diversity number, but it is a black box. I opted to count the number at each taxonomic level instead and then show as a percentile compared to other uploaded samples.
It was interesting that ME/CFS signature shows up at the species level best. A ton of new species appeared with onset.
ME/CFS caused 43% more species to appear than my healthy references
Since the original #6 report, I have entered from the uBiome site, the predicted metabolic function values for my samples (in the new entry form) and coded up a timeline view. It has been pushed to the site. NOTE: This comes from the uBiome site and is not available from other 16s test providers. There are 105 different functions reported by uBiome.
To get the charts you must TRANSCRIBE the data from ubiome. Otherwise you will see nothing. See this post.
This post looks at the most interesting charts. The 2017/2018 values are PRE-RELAPSE and show the normal values for me.
Historically, I run high on this value — it collapsed and then slowly recovered.This may be connected to ongoing fatigue. It is 4x higher than prior to relapse.A lot of major jumping around on this one
I have just revised the metabolism entry form for ubiome data to allow entering the specific value as shown below. ( http://microbiomeprescription.com/ )This makes data more meaningful and useful for citizen science analysis. By the end of day, I should have added the ability to view the Metabolism function over time (just like you can view individual taxon over time). While ubiome does have a display — it is very busy.
How to get to the data (use ALL SAMPLES always)
So get your data updated and enjoy the new charts!
I received my ubiome results today (sample done on 7/29/2019) – so 10 days from sending it off.
Back Story
At the start of this year, stress at work increased and requests to management and HR to be moved to a different group with a different manager fell on procrastinating ears. I was showing early physical signs of excessive stress. In the middle of March, there was a sudden relapse of myalgic encephalomyelitis, I could feel my body change literally within an hour. Drive home and started taking sick time.
The first thing that I knew that was essential was knowing what was happening with my microbiome and to start counteracting it via my Microbiome Prescription web site. Once I got my reports, I proceeded to implement the suggestions with retesting every month because the microbiome is a moving target.
Fast forward, all of the typical myalgic encephalomyelitis symptoms are gone except for one – very limited duration of physical activity before sudden complete exhaustion hits. Over the last month, the duration has significantly increased but still only a fraction of what I could do in January of this year.
I observed that there was immediate drop of some bacteria groups at onset, followed by additional groups dropping off in the next period. The delay drop off is expected because when the first group stop producing, the reserves of their metabolites (chemicals) are still circulating and slowly get consumed until they drop below a threshold and the other bacteria are starved out.
This post review the high lights of what has happening. The microbiome lab results agree with my observations of myself.
Ubiome Charts
The Diversity score is sitting at 87%ile (more species than 9 out of 10 people — a real cosmopolitan gut) but appears to not reflect the ME/CFS state in any way. The numbers for diversity and wellness reported by uBiome is shown below, they do not appear to correspond well with the onset and likely of limited or no value.
Anti-Inflammatory Microbiomes
Propionate continues to improve significantly, still slightly below my pre-relapse levelPolyamine continues to be in my historic pre-relapse rangeButyrate is maintaining the improvement. It was usually low pre-relapseAkkermansia and Lactobacillus has made a major improvement since the last time
And for yogurt specific strains, it is much improved
GABA production is improving, serotonin has come down a bit (but still higher than pre-lapse level)
Microbiome Site Charts
I put little value in this ratio beyond being an indicator of change happening.Bifidobacterium died with the onset, attempted to make a come back and perished again.Lactobacillus followed the same pattern, attempted a come back that failed — but eventually managed to get going — Looking at strains, they changed every sample.Similar pattern, collapse – attempt to recover that failed, then slow recovery afterwardsThis bacteria disappear with onset and has not returnedWe see this disappeared and has been making a good recovery to the typical levels from the past. Kluyvera is identical to E.Coli for 16s Reports. With onset, it disappeared — characteristic of CFS as reported back in 1998. This taxonomy may play a significant role for me. According to data punk, it is a known inhibitor of bifidobacterium BUT NOT of Lactobacillus nor Akkermansia. This is well reflected in my results.This bacteria also looks like it may be playing a significant role.
We do find this bacteria is ME/CFS associated in the literature and successful treatment.
” In conclusion, treatment with staphylococcus toxoid [ a chemically modified toxin from a pathogenic microorganism, which is no longer toxic but is still antigenic and can be used as a vaccine. ] injections over 6 months led to significant improvement in patients with FM and CFS. Maintenance treatment is required to prevent relapse. ” [2002]
Remember these are SPECIFIC to my microbiome, they probably do NOT apply to you.
Take List
Cranberries — I have been doing a glass of juice with breakfast.
Aspirin –
Most of the B vitamins, Vitamin D
NAC, Melatonin
Zinc
Monolaurin – which is new and an old favorite
Avoid List
Red Meat — I have been chickening out for the last month!
Vegetarian diet, low protein diet
Walnuts
Slippery Elm
Licorice
Lactobacillus Plantarum (i.e. Align), also Digestive Advantage, duraflora, etc
Triphala
On the probiotic list, #1 is Activia Drink, also Mutaflor. On the no known impact, I found enterogermina (which I take once a week — it is known to persist after just one dose), and miyarisan (which I use as a lozenge, sucking slowly in the mouth — it has cleared up dry-mouth and nasal issues ). Symbioflor-2 is a neutral — but since Mutaflor is on the to take list and this is also an E.Coli probiotics, it will also be done regularly (like enterogermina, it is known to persist after a single dose for several days).
Flavonoid Suggestions
Apples, Banana, Almonds as snack foods (at least one of each a day), Cinnamon, thyme,basil, nutmeg for spices. Peppermint (2-4 cups of peppermint tea a day). Oregano is high in Luteolin so I will be adding Oregano tea.
Bottom Line
I continue to move to recovery: both in terms of symptoms (decreasing) and in terms of microbiome results. This is my first recovery without the involvement of any antibiotics, which implies to me that they are not always necessary.
The pattern that I am using is simple:
Know where your microbiome is at (new uBiome test every 4-6 weeks)
Trust the AI Engine to make better than the average physician suggestions, It remembers 58,000 facts and apply them is a consistent fashion.
Be patient and consistent.
Until I got the latest results and realized from doing yard work last weekend (wife: You have been out working on the yard a long time!), I was starting to have doubts about continued improvement. This type of doubt (from slow improvement) is an ongoing challenge for recovery — people forget (especially with brain fog and memory issues) how they were a month ago and incorrectly assume no change. The joy of microbiome analysis is that you have lab results showing the changes (even when symptoms may not have changed much).
I have been active reading research and hypothesis dealing with Myalgic encephalomyelitis/chronic fatigue syndrome for 20 years. I am also well trained in mathematics, statistics and modeling with some Ph.D. courses. Every time a new hypothesis comes out I review it to see if it is objectively better than the hypothesis that I am using.
What makes a hypothesis better?
How many observations in the literature does it give a simple direct explanation for?
Can it be used to make testable predictions?
And last, for illnesses, how long before it is actionable for treatment?
Do the actions work for a significant subset or the entire population?
For the microbiome hypothesis, the values of all of these is very high, especially the last one — you can take action today.
In this post I will review some recent posts by my long time friend, Cort Johnson.
Ten years ago, Fisher’s intuition was correct. ME/CFS patients’ mitochondria are having problems producing energy. Something that’s gone wrong in one mitochondrial complex is throwing off the rest of the complex. The good news is that the problem is not subtle: Fisher appears to be seeing major problems across the mitochondrial pathways.
Microbiome dysfunction alters the metabolites that feed the body and the mitochrondria.
The bad news is how complex the mitochondria are. Fisher doesn’t think he’s going to find a single cause that responds to a single, simple fix. He also left open the possibility that the Complex V problems could be a consequence of another as yet unknown problem.
Given the reduced thyroid hormone activity in NTIS, clinicians began, as early as the 1980s, to suggest thyroid hormone supplementation in their critical NTIS patients in an attempt to increase their survival rates (Carter et al., 1977; Brent et al., 1986 and DeGroot, 1999). This approach continues to be debated today (Davis, 2008; Kaptein et al., 2010; De Groot, 2015; De Neto et al., 2016; Breitzig et al., 2018)… Given the impaired conversion of T4 to T3 in NTIS, some researchers also propose T3 supplementation (as opposed to T4 supplementation) (Biondi, 2014).
Positive results for some subsets of patients. I have the words “positive results” because that is often wordsmithing to keep funding grants coming.
Results with thyroid supplementation have been mixed (Farwell, 2008), but have most often been beneficial (see review in Fliers et al., 2015). Interestingly, positive results have reportedly been achieved by supplementing thyroid hormones in NTIS patients who had become ill after mold exposure (Somppi, 2017)….. supplementation doses have to be very high to achieve results (Debavaye, 2008). These suggestions regarding the type and quantity of thyroid hormone supplementation in NTIS echo the arguments made by some practitioners on T3 supplementation for ME/CFS (see my previous blog post).
EBV related hypothesis has been around a long time and appears to apply to a subset. For other patients it is Q-Fever, Rickettsia, Giardiasis and Lyme. For all of these we hear terms like re-activation or occult form of the infection. While antibodies are found, those infections appear to be controlled. We now hit two paths: these turn on genes (an epigenetic change) or these cause a microbiome shift (with the change of metabolites produced perhaps triggering epigenetic changes).
We have no predictions here. Nor do we have any know actions to turn off pathogenic genes (assuming we can identify them).
Bottom Line
People often ask me what I think of this or that hypothesis. I evaluate them with the rule above. 95% of the time I quickly see that it is a speculative hypothesis “perhaps this may explain…” without sitting down and looking at the historic facts reports in decades of research. Often, I hate to say, the research is a specialist in area A and trying to see if his area of research may work for CFS — and perhaps get a grant to research.
When a new theory come across your groups, try applying the above criteria.
