As a result of doing an analysis for a 19 month old toddler, I added a new option that can also be used with Transcribed tests. This post applied to the following tests:
When you logged in, you will see your saved tests, CLICK ON Review.
And then we have the details you entered below with an important column, taxon number.
Below this are conditions where your pattern matches at least 5 shifts reported in Published Studies.
There may be many items listed. This is by pattern matching and is not predictive.
If you have any of these conditions, or suspect you may have. Just click the appropriate button.
An example is below. These are tuned safest-suggestions for the matches. What do I mean by safest? It means the items are not reported in any study in the database to adversely impact any of bacteria listed. Many substances have contradictory reports on shifts — this substances are excluded.
Not Listed Condition?
This person believes they may have Autoimmune, so going to https://microbiomeprescription.com/Library/PubMed we find that it is listed.
If it is not listed, search for bacteria shifts reported and use those (please send me the studies so I may add them).
The bacteria are shown in a tree. You have to manually match between the two.
In this we have:
Escherichia ⬇️ but our sample is high,
Roseburia intestinalis ⬆️ - we are high on Roseburia, we will include it
We have only one match — this tests with limited reporting is not a good fit for this condition. Doing a test like Biomesight, Xenogene, Thorne or Ombre is likely the best choice.
We just copy the taxon number into the form at the bottom of the page, and then click suggestions.
In this case, we get a short list. Remember, doing a single bacteria means you are ignoring a lot of interactions and factors. The suggestions could feed other bacteria that are too high.
A sample result dated 29/10/2023 it’s for 19month old son born via C section and having lots of ongoing tummy pain since birth.
Fully breastfed for well over 12 months but the microbiome doesn’t appear that way.
Analysis
This is a very much “flying by the seats of my pants” analysis. Why? From birth for the next 10-20 years the microbiome has dramatic natural changes. The Fuzzy Logic Expert System on Microbiome Prescription is tuned for adults and not these age ranges. If you are dealing with a child, the approach below is suggested.
I am going to use ChatGPT selectively to make analysis easier, checking that it’s answers agree with my memories from reading studies..
“There is certainly a transient difference in the gut microbiota of infants born by Cesarean delivery compared to their VD counterparts. While this difference appears to be corrected after weaning, it may have lifelong impacts on the development of the immune system. ” [2018]
“When comparing the gut microbiota composition of CSD babies with vaginally delivered (VD) babies, the former show a microbiome that closely resembles that found in the environment and the mother’s skin, while VD babies show a microbiome more similar to the vaginal microbiome. Although these alterations of normal gut microbiota establishment tend to disappear during the first months of life, they still affect host health in the mid–long term since CSD has been correlated with a higher risk of early life infections and non-transmissible diseases, such as inflammatory diseases, allergies, and metabolic diseases.” [2021]
Too late, but important for any future babies “Lab analysis showed that the microbiota of the C-section babies swabbed with their mother’s vaginal fluids was close to that of vaginally born babies” [2021]
Bifidobacteria and Firmicutes Dominance: In healthy infants and toddlers, the gut microbiome often shows dominance of beneficial bacteria like Bifidobacteria and Firmicutes. These bacteria play crucial roles in digestion, immune system development, and protection against pathogens.
Generally, Bifidobacterium can comprise anywhere from 10% to 40% or more of the total gut microbial population in toddlers.
In healthy toddlers, Firmicutes can typically constitute a substantial portion of the gut microbiota, often ranging from around 30% to 60% or more of the total bacterial population
From ChatGpt
Looking at Bifidobacterium, the numbers are lower (57%ile) than expected for a child of this age but with a rich diversity of species. Bifidobacterium is 2.4%, well below the expected 10-40%. Bacillota (formerly known as Firmicutes at 83%ile) is 79.4%, well above expected 30-60%.
Switch to consequence, ChatGpt reports: “Some of the health implications of low Bifidobacterium levels in toddlers may include:
Digestive Issues: Bifidobacterium species contribute to the breakdown of complex carbohydrates, aiding in the digestion of certain fibers and sugars. Low levels of these bacteria may result in digestive problems such as constipation, diarrhea, or irregular bowel movements.
Weakened Immune Function: Bifidobacterium species are involved in regulating and supporting the immune system. Insufficient levels of these beneficial bacteria may compromise the immune response, making toddlers more susceptible to infections and illnesses.
Increased Risk of Allergies and Asthma: Some research suggests that alterations in the gut microbiota, including low levels of Bifidobacterium, might be associated with a higher risk of developing allergies and asthma in children.
Potential Weight and Metabolic Effects: The gut microbiome, including Bifidobacterium, can influence metabolism and energy regulation. Low levels of these beneficial bacteria in toddlers’ gut microbiota might potentially be linked to metabolic issues or an increased risk of obesity later in life, although this connection is still an area of ongoing research.
Impact on Neurodevelopment: Emerging studies suggest a possible link between the gut microbiota and brain development. Some evidence indicates that alterations in gut bacteria, including Bifidobacterium, might influence cognitive development and behavior in children.
Susceptibility to Infections and Antibiotics: A decrease in beneficial bacteria like Bifidobacterium can leave the gut more vulnerable to colonization by harmful bacteria. Moreover, toddlers with low levels of these beneficial bacteria may face a higher risk of complications after antibiotic treatments, as antibiotics can further disrupt the delicate balance of the gut microbiota.
Digestive Imbalances: In some cases, an overabundance of certain Firmicutes strains might affect the balance of gut microbiota and contribute to digestive problems, including irregular bowel movements, bloating, or discomfort.”
At this point, using the Fuzzy-Logic Expert System on Microbiome Prescription is not a good choice to get suggestions. It is tuned for adults and not toddlers. All of the values are in the normal range for an adult, but definitely out of range for a toddler.
What we want is to increase one bacteria and decrease another bacteria without looking at the percentile. I just added a subsection on the Research Features tab to make that available. It requires the the taxon numbers be entered. In this case: Decrease: 1239, Increase 1678 (Bifidobacterium).
See this video for a walk thru of the process.
This results in this page
You can click on each modifier to verify that it only impacts the bacteria named by taxon in the desired way.
In toddlers, several Bifidobacterium species are commonly found in their gastrointestinal tract. Among these species, Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium infantis are frequently observed in the gut microbiota of toddlers. These species play essential roles in maintaining gut health, aiding in digestion, and supporting the immune system during early childhood.
ChatGPT
We can take this one step further, picking specific children :
Increase: 1678,1680,1682,1685 (the usual toddler species)
I usually send drafts to the person for comments, concerns etc. This was the response:
I wondered whether prevotella/segatella buccae was a concern as it was the highest species in the sample and bacteroides was extremely low. The practitioner we saw prescribed HMO and lactulose after reviewing Biomesight raw data.
Mother of child
The HMO suggestion is reasonable if you do not check all of the literature. We have contradictory results from studies for HMO. Remember Bacillota is the modern name for Firmicutes.
Similarly, we have some contradiction in results with Bifidobacterium — so it was not deemed ultra safe.
This suggests adding segatella buccae (NCBI 28126) be added.
The results are similar, with less items on the to avoid.
Trying a different combinations, for example
We get different ordering and a few changes.
Bottom Line
We have various sets of suggestions, doing a consensus is likely the best path forward.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I can compute items to take, those computations do not provide information on rotations etc.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.Posted on b
April 2022 strong antibiotic treatment against another pathogen flared my chronic borrelia/babesia/bartonella. [I had Ceftriaxone iv and 1500mg of azithromycin as a single dose].
Shortly after this stinging started in the belly and burning when passing a stool and urinating. Its yeast symptoms. I have mthfr mutation and low bifido bacteria.
“chronic borrelia/babesia/bartonella” is also known as Chronic Lyme disease. See Lyme Disease Co-Infections | LymeDisease.org. It is a close sibling to ME/CFS, Long COVID and Occult Rickettsia. There are 77 samples uploaded marked with Lyme, 45 of these also indicate ME/CFS (58% overlap). There was no statistically significance difference in the microbiome between these two groups.
This person requested a video walkthrough due to cognitive issues with reading.
Analysis
Looking at the Percentile-Percentage distribution, we see the common pattern with ME/CFS and Long COVID: over representation of the 0-9%ile range. The numbers in each percentile range should be about the same. They are not.
Looking at the new Anti inflammatory Bacteria Score [Score: 12.56 or 16.9 %ile], we see that bacteria controlling inflammation appears to be very deficient. Dr. Jason Hawrelak Recommendations is at 89%ile with the following anti-inflammation bacteria being flagged as low: Roseburia, Bifidobacterium, Lactobacillus and Akkermansia.
Looking at the Potential Condition lists, we see many that we would expect to see
I checked the KEGG suggested probiotics none of the suggestions were strong. On the other hand we have a good number of supplement suggestions from KEGG (shown below). The higher the Z-Score, the more important they are.
Looking at probiotics we see the best ones being bifidobacterium (which is good because many lactobacillus produce d-lactic acid that causes brain fog).
bifidobacterium pseudocatenulatum,
bifidobacterium infantis,
bifidobacterium breve
There are some lactobacillus also suggested:
lactobacillus casei — documented to be good for allergies and hay fever. Usually I suggest Yakult, one vial around each meal.
lactobacillus reuteri — biogaia (reported not to produce d-lactic acid)
For supplements, checking the items from the KEGG list above, we found that all items suggested which we have data on, agreement that they should help:
N-Acetyl Cysteine (NAC), +185
l-proline + 161
l-glutamine + 76
l-arginine +45
l-phenylalanine +40
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I can compute items to take, those computations do not provide information on rotations etc.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
38yr Old now, Issues started around the age of 24-27 i think [gradual onset]
From the age of 17-35 my diet has been really bad ( Coca cola, pizza, burger, fries, candy and sweets etc)
From 23-25 I started getting really tired everyday followed by pains in various locations
Later, started loosing weight in the face, eyes started to sink deeper and deeper, my face become really gaunt. All my life i have been thin and could never gain weight nomatter how much i ate.
I also startet getting extremly fatigue after eating.
definitive stomach issues started around the age of 30-33, may have been before.
Since I turned 34, i have been trying to figure out what is wrong with me.
Allof the standard checks at the docs Office(ultrasound of organs and stomach area, CT/MRI of stomach area, Colonscophy and gastroscophy)
Nothing found
So everything points towards gut dysbiosis or something like that
I started to change around with my diet July 2022. Details of various attempted changes (Gluten free, no dairy, no sugar, carnivore diet) — currently on Keto with resistant carbs.
But many symptoms are still there.
I have been taken multiple rounds of antibiotics from november 2022 until Jan. 2023 (80 days) because i had a sinus and deviated septum surgery. I have also taken 7 days of metrodinazole and amoxicilin 12 weeks ago because of the H Pylori infection i had. Retest was negative for H. Pylori Got diagnosed with methane SIBO via breath test in september 2023
I have been diagnosed by a GI Map test in May 2023 with:
candida
E coli overgrowth
Streptococcus overgrowth by a gimap test in May 2023
I feel like my body is destroying itself. A long list of symptoms was given
Analysis
Potential Medical Conditions Detected
Nothing stood out. By this I mean that the Percentile ranking is well into the Prevalence. The closest was SIBO where the borderline would be 100-52= 58%ile. He was reasonably over that. He wrote “Got diagnosed with methane SIBO via breath test in September 2023”, so this was a definite matching forecast from PubMed literature.
Bacteria deemed Unhealthy
The one item of interest was Faecalibacterium prausnitzii, which was 19% of his microbiome and associated with increased Candida risk (which he has had).
This is my quick way to statistically determine if there is statistically significant dysfunction. The significance is 0.99999.. etc, so yes.
Forecast Symptoms
In the top ones we had the following agreements with reality:
cold extremities
Rapid muscular fatigability
Joint pain
Sinus issues with headaches
Onset: Gradual
Sinus issue
Onset: 2010-2020
Gender: Male
General: Headaches
Post-exertional malaise
The ones that did not match were connected to cognitive issues.
Pattern appear to match a subset of myalgic encephalomyelitis/chronic fatigue syndrome. Many MDs will suspect it, but will not give a diagnosis if the person is not totally disabled. The reason is simple, no treatment plan and likely a negative psychological impact.
Going Forward
This looks likes a good candidate for a two stage building a consensis:
“Just Give Me Suggestions”
THEN using special studies (everything at once – skipping Gender) to add a fifth set of suggestions
The suggestions are short and tight. Barley porridge with Walnuts for breakfast for most days.
I would suggest taking Danish product Biogaia Lactobacillus Reuteri just before bed each night for two weeks, then switch to clostridium butyricum for two weeks. The other probiotics – do 1 at a time for 1-2 weeks, take them 1-2 hours after breakfast.
Akkermansia Muciniphila probiotics and Swedish Filmjölk (on your porridge?) are two probiotics with no known negative impact and some positive impact. The list above are the highest predicted impact.
What to avoid
Keep up the no alcohol but reduce/drop beef in your carnivore diet. Go for herring, eels and other fish product. It is interesting that the two E.Coli probiotics are listed as avoid (the logic does not look at E.Coli levels, but other bacteria levels to make that suggestion)
Prescription Items (if you have a willing MD)
Doing antibiotics is usually consider if the above do not cause sufficiently improvement over time. I mentioned that the history looks quasi-ME/CFS. I was not surprise to see many ME/CFS antibiotics on the list, including:
AMOXICILLIN (ANTIBIOTIC)S[CFS]
AMPICILLIN (ANTIBIOTIC)S[CFS]
CIPROFLOXACIN (ANTIBIOTIC)S[CFS]
If you and your MD decide to try antibiotics, I would suggest on of those (using Dr. Jadin approach of pulsing).
Browsing the Details
High value was 701, low as -391. Usually these two numbers are about the same magnituded. Items spotted of note:
Q: Regarding your sugestion of all the probiotics. Usually the probiotic comes in bottles where there is like 4-10 different strains. Should i avoid that and only buy single strains in each bottle of all the ones you mentioned?
A: Each strain impacts things in different ways. My preference is always single strains, ideally ones that have been researched with the ideal being ones researched for your condition or symptoms and found effective. See https://microbiomeprescription.com/library/ProbioticSearch , There are reports of some probiotics making people worse. A major issue is that probiotics are not well regulated Many “retail mixtures” have over 60% of their contents misidentified. See Deceptive Probiotic Labels or Assessment of commercial probiotic bacterial contents and label accuracy, When the bottle gives an explicit strain (not species), then the owner of that strain has motivation to insure quality control.
Looking at the challenges of getting probiotics in Denmark. What may be an acceptable compromise is to find a probiotic mixture that does not contain any probiotics with an estimated adverse risk. In your case these are:
symbioflor 2 e.coli probiotics
colinfant e.coli probiotics
bacillus subtilis natto (probiotics)
bifidobacterium longum,lactobacillus helveticus (probiotics)
Example: lactobacillus rhamnosus gg (probiotics) is an explicit strain (“GG”) is the second highest positive, while generic lactobacillus rhamnosus is # 54 and negative.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I can compute items to take, those computations do not provide information on rotations etc.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
Over the last two weeks, there has been a couple of email pointing out possible errors in some citations. I am not surprised. I expect 90-95% correctness (i.e. 1 in 10 or 1 in 20) may be incorrectly entered. To improve the quality, we need independent review of the data. In one amusing case, I quoted my source correctly but that review study incorrectly cited it’s source. The data entry was right, the source document was wrong.
The articles are technical studies which often require advance reading skills and knowledge of this topic. Some of the sources are available in full on the web for free, others are behind a paywall. If you are connected with a university or college, you may have access thru your institution.
If you cannot access the full text of the source, then skip it. Extracts and summaries can contain errors.
Process
Just email me from the email account that you logged in with and I will add auditor or QA permissions to your account.
Doing it
When you logged in, you should see:
When you look at citations, you will see the ⚖️ icon (or a ✅ if someone has already checked) beside the citation.
Example for a list of citations
Note that there may be more in the study then what the titles implies. Often data is from Appendix and tables.
Clicking ⚖️ will take you to a page showing what was extracted and gives you an opportunity to correct it,
Click [Report above Issue] will send emails to me and to your self. If all of the information is correct, then click [I have verified..] and the next time you see the citation, there will be a ✅ beside it. Your email is stored beside the citation as the reviewer.
You will get an email confirming stuff
If there is information that was missed (more likely) please include the TAXON numbers of the bacteria. This speeds up the process. Often information was missed because of alternative spelling.
That’s the process. Short, simple and with the ability for me to quickly make corrections.
Bacteroides/Bifidobacterium (Ba/Bi) ratios “with Low Ratio showing a significant increase in propionic acid and being enriched in glycolysis functions, whereas High was enriched in amino acids and aminoglycolysis functions”
Of course, the question becomes what are low and high ratio? To answer that question, I pulled some data by lab
Ubiome Ratios
Ombre Ratios
BiomeSight Ratios
Bottom Line
I would suggest a ratio > 500 to 1000 is High, Below 200 is low
The following is based on Biomesight data uploaded with some annotated by uploaders. Technically, interpretation of microbiome results should factor these issues in. At least 10 samples had to have Symptom Name to be included. The numbers shown are averages (on count per million) on samples that reported the bacteria.
As a spot check, we see multiple Bifidobacterium in the 0-10 range which agrees with the literature.
In general, the symptom has more than the population because we filtered by using a high T Score to keep the list shorter for illustration purposes. A variety of other factors are not shown, for example: FUT2 non-secretor or FUT2 secretor.
Dropping the T-Score filtering to 1.96 resulted in 3600 rows.
I wanted to share some good news with you. In the last 3 weeks I’ve noticed my time going to the bathroom has decreased in half and my gut has been less irritable. Over the last 2 weeks, my mood has steadily improved and I’ve enjoyed more energy than usual. It appears that your guidance has pointed me in the right direction!
Note: I didn’t end up performing the FMT.
I thought about why my Firmicutes would get to 97%+. It’s most likely because the majority of the foods I eat are continually pushing my gut towards Firmicutes. And it could also explain why after adding 5+ daily supplements to push my gut the other direction, it hasn’t worked. You noted that my being a vegetarian may be acting as a significant counter balance to the direction we’re trying to go.
Besides adding a small amount of meat in the morning, I cut out the foods I eat most frequently. Bananas, raspberries, blueberries, nut bars. And then I added in the Seaweed you recommended. I think the seaweed has made a massive difference and with all these changes implemented collectively, the boat has begun to turn around! I’m hoping this continues
Backstory
I’m 39 and have suffered from moderate CFS since i was an early teenager. My major 3 symptoms are low energy, brain fog, and IBS. My CFS didn’t affect me as much when I was 18, but combined with the effects of aging, I’ve been feeling the fatigue more impactfully the last two years.
Journey over last 10 months
When I first began working on this in January, my samples showed my Firmicutes at 98%. That seemed to be the smoking gun as you described it, and I was eager to begin shifting my microbiome. Over the next 6 weeks I felt markedly better but unfortunately I now believe that was merely a placebo effect. Once I started to believe the benefits I had received were from a placebo, I rapidly returned to baseline. Over this time period, I cut out many of the foods that pushed my gut in the wrong direction, and I was taking 4 supplements 2-3x a day. By my second test 2 mos later, my firmicutes adjusted downwards from 98% to 93%. In terms of how I felt, it was difficult to assess whether it was better than my baseline. I was hopeful that it was, but I couldn’t say for sure.
Over the last 6 mos my Firmicutes has reduced from 93% to 89%. During this time period I continued to cut out foods that were counter-recommended. I ordered 4 more vitamins & supplements that were in my consensus list, and I was taking 4 supplements 1X/ day, while also rotating the supplements every 4 weeks to prevent resistance.
Once again, it’s difficult to assess now how i feel versus my baseline. I don’t feel significantly better, that I know. And while I’m disappointed my sample isn’t improving drastically, the upshot from my perspective is that at least my sample results match how i’ve been feeling.
Reader Addendum After reading
“I’m mostly vegetarian… which may help to explain why after 9 months of supplements I’m partially moving in the wrong direction. I’ll incorporate the seaweed and increase my red meat.”
Analysis
We have three samples to compare.
Percentage of Percentiles
We see significant shifts between samples with chi2 values increasing (meaning more abnormal) instead of decreasing. What is interesting is that the two earlier samples does not the typical ME/CFS or Long COVID pattern, but the third sample shifted to the pattern of spikes in the 0-9%ile range. This is open to many interpretations; some good and some concerning.
Evaluation Criteria
The numbers below are mixed, some showing improvement, others showing loss.
Criteria
1/6/2023
3/29/2023
9/12/2023
Lab Read Quality
4.3
5.9
8.7
Outside Range from JasonH
3
3
6
Outside Range from Medivere
18
18
20
Outside Range from Metagenomics
8
8
7
Outside Range from MyBioma
9
9
15
Outside Range from Nirvana/CosmosId
23
23
24
Outside Range from XenoGene
38
38
43
Outside Lab Range (+/- 1.96SD)
18
15
10
Outside Box-Plot-Whiskers
54
53
56
Outside Kaltoft-Møldrup
85
125
181
Bacteria Reported By Lab
431
553
591
Bacteria Over 90%ile
49
32
34
Bacteria Under 10%ile
43
72
174
Shannon Diversity Index
2.852
2.937
2.49
Simpson Diversity Index
0.083
0.098
0.101
Chao1 Index
8592
11807
15969
Pathogens
26
35
40
Condition Est. Over 90%ile
11
7
2
Kegg Compounds Low
821
731
1190
Kegg Compounds High
134
251
99
Kegg Enzymes Low
359
204
259
Kegg Enzymes High
208
311
243
Kegg Products Low
201
124
170
Kegg Products High
130
199
158
Kegg Substrates Low
195
114
156
Kegg Substrates High
149
216
162
Forecast symptoms
The top 3 forecasted items are below. See this post: Post Exertional Malaise (PEM) with diminished ME/CFS for more information on forecast symptoms in use. The earliest sample had no forecasts being reliable (i.e. > 60% match). What we also see in that the symptom patterns are becoming stronger. Again, this is usually not desired.
2023-01-06
54.3 % match for Neurological-Vision: Blurred Vision on 35 taxa
52.4 % match for General: Headaches on 42 taxa
50 % match for Immune Manifestations: new food sensitivities on 56 taxa
2023-03-29
65.9 % match for Pain: Pain or aching in muscles on 44 taxa
56.2 % match for Immune Manifestations: Diarrhea on 89 taxa
56 % match for Neurocognitive: Brain Fog on 50 taxa
2023-09-12
65.7 % match for Neurocognitive: Difficulty paying attention for a long period of time on 70 taxa
62.3 % match for Neurocognitive: Can only focus on one thing at a time on 53 taxa
61 % match for Neurological-Vision: Blurred Vision on 41 taxa
Impression and Possible Model
This is the first follow up sample where there was neither clear objective or subject improvement. What we see clearly above was that the microbiome has changed. Subjectively, there was no deterioration reported.
Objectively it seems that the microbiome has been de-noised. This person has had ME/CFS for 20+ years and thus the microbiome dysfunction will evolve. His latest sample changed to the typical pattern for ME/CFS for percentage/percentile chart above. The forecasted symptoms values are increasing for what are likely correct forecasts. The bacteria associated with ME/CFS and IBS are showing themselves better and other bacteria causing noise are diminished.
Going Forward
I first looked at the US National Library of Medicine studies for bacteria reported for the conditions he reported.
Symptom matching on these is a clear miss. I did note some high matches that are typical symtpoms so I add in the results from these selections:
The result was just 84 unique taxa and we have 5 sets of suggestions in our consensus.
So we fall back to the “Just give me suggestions”. The high priority value was 300 and the low priority value was -405. Adding in special studies suggestions moderated the ranges but most items stayed the same.
Antibiotics: There was only 1 over the 150 (300/2) threshold. None are associated/studied with his conditions so I would pass one them. This antibiotic is usually used for tuberculosis.
It looks the a modified Surf And Turf diet, i.e. Steak and Seaweed (our local Costco does sell a nice seaweed salad that is a regular for me)
The AVOIDS
The avoid values are so high compared to the takes that we need to review them to try reducing or excluding them. The threshold value is -300 (-600/2).
This has been a challenging set of samples to do an analysis on. I have often used the analogy of going from the port of sickness to the port of health in a sailing ship along a rugged coast. There may be a long series of course corrections needed.
The suggests above are very atypical. Given that there appear to be a lot of noise in his microbiome, we may have some more denoising to do (bring out more the ME/CFS and IBS bacteria into the light). I would advocate attempting to get a course of rifaximin. It has been well used for his IBS diagnosis so there should be little push back from his MD.
Questions and Answers
Q: I’ve read through my new Simplified Suggestions List, and The suggestions of what I need to take and avoid are the same as before…. but the impact score of each was adjusted. Although you’ve noted in the past that a higher impact doesn’t indicate it works more effectively, it looks from your suggestions that you stick to the highest impact items as there are the most studies to support them, right?
Correct. One study may report honey increases a bacteria, and another study report that it decreases the same bacteria. To determine the confidence of a suggestion we look at all reports. If you have 10 honey studies (8 increases and 2 decreases) and one study alone for roasted whale increasing the bacteria; most people will have greater confidence that honey is a better choice to try.
Q: One initial inquiry comes to mind- for complex cases, have you given any additional consideration to (probiotic) enemas as a way to make a big impact, and then to adjust with oral supplements from there?
I work from published clinical studies and not from influencers opinion. There is a good summary on WebMD, What to know about probiotic enemas that gives pros and cons.
Using commercial/retail probiotics have two significant risks:
Very often the declared species is not what is in the bottle, the exception is for those strains that are owned by someone.
Often they contain fillers that will be well consumed before they reaches the nether regions. These fillers being inserted here may give a feast to some bacteria that usually do not get much, sparking an unexpected overgrowth.
Q: Below are the supplements I’ve been taking each day. My plan is to cut out everything that doesn’t have an impact score north of a 150. Does that sound like a reasonable approach?
ground flaxseed. I took this every day for 4 months and had to stop because it began to make me nauseous. — Try it again at low dosages after one month
Luteolin – low positive
carboxymethyl cellulose — definite take
Dietary Fiber Cellulose – definite take
partially Hydrolyzed Guar Gum (SunFiber) — remove
licorice root —remove
Vit B1, B6, B7 — low positive
Gaba — definite take
Vit C — remove
Melatonin — low positive, suggest you try removing for a week then trying for a week to see if it still help sleep
Diosmin – low positive
Astragalus – low positive
Answer: The logic is good but I would restrict to only items that are negative. You may wish to revisit the reason that you started each; if it was symptom related and improved — then monitor that symptom and return it if the symptom returns. I have annotated the list above
Reflection
Suggestions could also be described as influencers. There is no need to get religious about taking everything. Take what you are comfortable with is my usual advice. In this case, the person being a vegetarian may have significantly counter-indicated the other influencers. Once the microbiome is normalize, a return to be a vegetarian is viable.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
This is from a person that have been using Microbiome Prescription for a while with significant success. He messaged me about a new sample and asked me to take a look. It was good timing because I have over the last week refactor forecast symptoms as well as allowing them to be used to generate suggestions. This gave me an opportunity to test the analysis and suggestions.
My impression is that they are both working well with better sensitivity than the older method. Prior posts include:
-PEM -Fatigue on and off specially in the morning. Lowest energy point -Some brain fog. If I take a binder my brain fog is much better. Guessing that could be related to mold/fungus issues? -unrefreshing sleep -hair shedding unless I take Lactoferrin -difficulty losing weight
– Reader
Review of Test Results
I am skipping the sample comparison table because the forecast symptoms seem more useful for between samples comparisons.
Percentages of Percentiles
These are helpful overview to see if there are problems. At the top is a chi2 value which a healthy person should have a value below 0.90 . All of his values were .99999…. indicating abnormal shifts.
Prior to 2023
2023, the impact of COVID in the latest sample is quite apparent.
Forecast Symptoms
What shocked (and delighted) me was how accurate the forecasts were, especially with the main issue, PEM being near the top on every sample. The percentage match ebbed and flowed with improvements and set backs (typically from COVID).
2023-11-02 – After recent COVID
74.2 % match for Neurological: Cognitive/Sensory Overload on 31 taxa
63.5 % match for Immune Manifestations: new food sensitivities on 52 taxa
61.5 % match for Neuroendocrine Manifestations: cold extremities on 65 taxa
60.9 % match for Neurological-Vision: Blurred Vision on 87 taxa
59.6 % match for Condition: ME/CFS with IBS on 52 taxa
58.3 % match for Post-exertional malaise: Worsening of symptoms after mild physical activity on 36 taxa
2023-07-07
57.1 % match for Post-exertional malaise: Worsening of symptoms after mild physical activity on 42 taxa
54.2 % match for Condition: ME/CFS with IBS on 59 taxa
48.1 % match for Post-exertional malaise: Post-exertional malaise on 54 taxa
2023-05-10
63.2 % match for Post-exertional malaise: Post-exertional malaise on 38 taxa
59.3 % match for Post-exertional malaise: Muscle fatigue after mild physical activity on 59 taxa
59.1 % match for Pain: Pain or aching in muscles on 44 taxa
57.1 % match for Condition: ME/CFS with IBS on 42 taxa
2022-12-05
82.4 % match for Official Diagnosis: Autoimmune Disease on 51 taxa
81.9 % match for Comorbid: Histamine or Mast Cell issues on 83 taxa
79.5 % match for Post-exertional malaise: Next-day soreness after everyday activities on 39 taxa
71.8 % match for Post-exertional malaise: Physically tired after minimum exercise on 39 taxa
2022-10-29
64.4 % match for Neurological-Sleep: Inability for deep (delta) sleep on 45 taxa
62.7 % match for Official Diagnosis: Mast Cell Dysfunction on 75 taxa
60.9 % match for Post-exertional malaise: Next-day soreness after everyday activities on 46 taxa
60 % match for Condition: ME/CFS with IBS on 40 taxa
55 % match for Post-exertional malaise: Muscle fatigue after mild physical activity on 60 taxa
54.5 % match for Post-exertional malaise: Post-exertional malaise on 44 taxa
2022-03-23
85.4 % match for Neurological-Sleep: Inability for deep (delta) sleep on 41 taxa
82.1 % match for Immune Manifestations: Inflammation (General) on 67 taxa
77.5 % match for Immune Manifestations: Inflammation of skin, eyes or joints on 111 taxa
75 % match for Post-exertional malaise: Worsening of symptoms after mild physical activity on 32 taxa
71.4 % match for Post-exertional malaise: Next-day soreness after everyday activities on 42 taxa
Drilling down on PEM
With the revised symptom-taxa association tool, I went to the 2022-12-05 sample because it had very high values for PEM in forecasting. I then went to [Special Studies] and selected all of the PEM items
Some 78 bacteria were selected with the following being the top suggestions:
While this is not his current sample, it is reasonable guidance for dealing with the bacteria associated with PEM.
Going Forward
I am going to do [Just give me suggestions] and then special studies selecting only PEM items that are shown. We thus ended up with 5 packages. Looking at the details we have high at 555 -> 277 for high threshold and -542 –> -271 for low threshold
In general, it looks very pro-forma ME/CFS. He may wish to check the PEM suggestions against the details and include anything that is positive.
Bottom Line
I have often used the analogy of going from the port of sickness to the port of health in a sailing ship along a rugged coast. There may be a long series of course corrections needed. While there are still ME/CFS taxa shifts seen in his samples, subjectively the only symptom left of concern is a PEM after playing basketball for a while.
This is a good illustration that taxa/bacteria does not rule — DNA and other factors are involved with symptoms and the ability to tolerate microbiome dysfunctions.
Questions and Answers
Q: I may do another Thorne test if they’re back in stock. Wondering how much aspergillus is holding back healing/gut shifts
Aspergillus usually impacts lungs and breathing [CDC] (thus ability to get oxygen in). An alternative mechanism for oxygen issues than with hypercoagulation.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
The following are bacteria that have very unusual statistical behaviors in uploaded samples. This hints that they may be connected to some disease or symptom state.
The common pattern seen with most bacteria is shown below. You can view each bacteria pattern by clicking on the chart icon after searching for a bacteria on https://microbiomeprescription.com/Library/Lookup
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