If you look at my 2018 post “What is the best diet in your opinion?” [repost in 2022], you will find a logic that is simple: your microbiome adapts over generations to the food available. When food choices quickly, issues arise in the microbiome. One known issues:
The other day I spotted a non-alcoholic Imperial Pale Ale at Costco and picked up a dozen. During the summer when I am working outside, I like having a cold one when I come inside. Health Canada in 2023 updated their guidance to restrict alcohol use to 2 standard drinks or less per week with discussion about putting health labels (like tobacco labels) on all drinks. This product tastes like a good IPA, but has no significant alcohol — likely close to the common beer that my ancestors had for breakfast, lunch and dinner.
The light went on! Up until around 1900, beer and ales were common daily drinks –including for children. The reason was simple, water was often deadly due to bacteria in it. Clean drinking water was scarce or unreliable. Milk was fine. Coffee and Tea was fine. Water was not. The beer was not the typical 8% alcohol often seen in American Beers, but 2% or less.
This leads to the speculation that removing regular gluten exposure during childhood — via weak beers and plain-old-school porridge (oats, barley etc.) is the cause of the exploding gluten sensitivity!
It is very likely that gluten sensitivity is connected to diet changes – most of our wheat was breed for specific things, like yield per acre — those changes may contribute too. It is impossible to find clear evidence — but blaming drinking water is an amusing suggestion!
SIBO or Small Intestinal Bacterial Overgrowth was first proposed as a medical condition in 1970. The first use of breath tests for it was around 1974. The key things to remember is that this condition was the naming of a collection of symptoms. The name reflected the speculation on the general cause without any specifics. Over the years, this condition has been broken down in 6 general subsets depending on the results of breath test (and a potential 7th, if the symptoms are there but no positive breath test results).
Assuming that it is a bacteria overgrowth — which bacteria is overgrown? The breath test does not provide evidence on which specific bacteria a person has.
The clinical practice is often applying a simple logic “If it is an overgrowth, we just toss the appropriate antibiotic at it and it is solved!”. Experience has shown that some are generally effective, i.e.
Amoxicillin (500 mg 3 times a day per, during the first month), followed by ciprofloxacin (500 mg twice a day per, during the second month) and metronidazole (500 mg 3 times a day per, during the third month) about 56% effective [2023]
With effective usually being defined as symptom improvement not remission. Reporting adverse reaction is poorly done.
The reality that using herbs, oil of.. , tinctures, etc. have the same problem as antibiotics. With the evidence above there is not way to determine which ones will be effective for the individual.
There is a recognized and accepted way to better determine the bacteria involved: Small Intestine Aspirate. This is a quasi-surgical procedure to take a sample from the Small Intestine.
The gotcha is the handling of the sample, the treating physician or the lab may do one of several possible things:
Just report the quantity (confirming an overgrowth) — most common
Classic culturing of the sample — which will report on the culturable bacteria (most are NOT culturable)
16s testing of the sample – better resolution
Shotgun testing of the sample — best resolution
Cost issues can be complicated by insurance companies not covering the costs in most situations.
The Downstream Proposal
Whatever is in the small bowel or intestine eventually makes it way thru the entire system and ends up in a stool. The amount will likely differ because of passages through multiple environments.
The motivation for this post was a reader telling me that his hydrogen sulfide levels have become a problem. His latest sample had a significant amount of them. This suggests that 16s sampling can be helpful for detecting the species involved and thus treatment suggestions based on the bacteria that appear to be in overgrowth (by virtue of the breath test elements).
The video below takes you through the process.
A Walkthru
Note that the top antibiotics suggested from Microbiome Prescription are those used for treating SIBO.
Suggested Readings
Many older articles have stale information, the following are very recent publications.
Evaluation of small intestinal bacterial overgrowth [2023] “SIBO was conventionally defined as a total bacterial count >100,000 colony forming units (CFU) per mL on quantitative culture of upper gut aspirate. The threshold for the diagnosis of SIBO has been reduced to >1000 CFU per mL of aspirate recently.” That is 100x decrease of the amount need to get the diagnosis!
I’ve been reading the cfsremission.com site for a few years now and respect and appreciate your work very much! Today I received results from my first test with Biomesight and have uploaded to microbiomeprescription.com, however I’m struggling to know where to go from here.
It looks like I have high F. prausnitzii which goes against some of the CFS research. I can also see zero E. coli (I think) and low bifidobacteria/lactobacillus, but not sure there are strep/staph/klebsiella/other pathogens which I was expecting to see, owing to my issues with histamine/bloating, am I correct?
I’m reluctant to go ahead with taking herbal antimicrobials as I’m not sure exactly what I should be trying to kill off. The suggestions that come up mostly seem to be fibres/prebiotics which I haven’t typically responded well to in the past (worsened bloating and oily skin).
My backstory:
My issues started with the persistent abdominal bloating and sneezing/nasal congestion about 5 years ago. The bloating never goes away, and now I’ve progressed into a state of moderate but unrelenting fatigue, muscle pain and inflammatory issues (dry eyes, etc.), made worse by COVID and then the Pfizer jab last year which pushed my ’steady state’ in terms of energy to a lower level than it ever has been. I know that the root cause of this all is my gut. For example, I can eat regular yoghurt and the next day I will wake up with a back ache, 50% more tiredness and very sneezy. I did test positive for SIBO around 3 years ago but multiple rounds of rifaximin did nothing to help, neither did herbal antimicrobials. The bloating seems to be inflammatory/mast cell related rather than actual gas.
Symptoms:
– Crushing fatigue/muscle weakness/PEM (do not have a CFS diagnosis but the symptoms fit)
– General inflammation/muscle pain
– Freezing cold hands/feet all the time
– Sneezing/nasal congestion/itchy throat especially after histamine containing foods
– Persistant abdominal bloating which never goes away
– Brain fog
– Acne/very oily skin
– Dry eyes
For other analysis of the microbiome of people with ME/CFS, see this index.
First Questions Researched
Low Faecalibacterium prausnitzii is seen in several studies for ME/CFS. This person’s level is at a huge 23.7% of the microbiome — the 93%ile. However, for ME/CFS sibling (Long COVID) we have two studies reporting high levels for Long COVID (with 4 reporting Low) and three for COVID being high and one being low. In other words — atypical levels are to be expected. Note that he had COVID and then the Pfizer jab – so Long COVID is likely a better diagnosis than ME/CFS (at this point). The two tend to merge over time.
Usual Analysis Approach
The percentile x percentage breakdown shows the typical pattern for ME/CFS and Long COVID: Over representation on the low percentiles and under representation of the high percentiles.
He wrote “For example, I can eat regular yoghurt and the next day I will wake up with a back ache, 50% more tiredness and very sneezy. ” Most yogurt contains large amount lactobacillus acidophilus (probiotics) which is high on his to avoid list. In general lactobacillus should be avoided with brain fog because many species produces d-lactic acid (See my 2019 post Reminder of D-Lactic acidosis and ME/CFS – which contains the name of bacteria that may contribute to the issue). If you cannot find a yogurt free of these bacteria, you may wish to give yogurt up. I would suggest the following probiotics as likely being good choices:
He wrote ” multiple rounds of rifaximin did nothing to help, neither did herbal antimicrobials.” Well, that antibiotic is a negative, and like the lactobacillus yogurt above is likely to contribute to the microbiome issues. He did not specify the herbs that he tried.
He wrote “The suggestions that come up mostly seem to be fibres/prebiotics which I haven’t typically responded well to in the past (worsened bloating and oily skin).’ We see that almost all of the prebiotics are below 100 priority (item #170), so they would not make it into my preferred list (I prefer to keep to the to 100 or less). 25% of these are actually below a -200 priority. We also see low fiber diet is high priority. So his experience and the computations are in agreement
In my years of reviewing literature on ME/CFS, the typical results are similar to the Azithromycin study above: it works for X% of the people and has no or negative effect for the rest. It is my hypothesis/belief that the microbiome determines if a substance works or not.
Above, you see my preferred approach — look at the top 5-10% of suggestions and then cross reference the literature to see which are known to help some. The alternative of working from studies (without reviewing the microbiome) has failed to produce consistent positive results over the decades that it has been tried. The other key item is to look at the bottom 20% of suggestions and eliminate as many of them that you can.
For “Just give me suggestions”, I prefer the priority to be over 150 if possible for takes, and below 0 for avoids.
Remember this is a multiple path journey. Keep on the suggestions for 6-12 weeks and then retest. The suggestions may shift a bit with each course correction.
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.
Covid infection last year. Little to no symptoms. Some stomach issues but nothing big. Then got vaccinated. Then got Covid again, January of this year and has been off since. Burping. Pressure. IBS. Gerd. Pain.
I am sure I have SIBO due to lots of PPI’s and ibuprofen during Covid. Also did a round of antibiotics a few months ago also. Looking for guidance to correct.
Greatest Concern: Is it Long Covid?
Comment on Concern
A May 2023 article states “1 in 10 People Get Long COVID After Omicron“. Since Long COVID often results in an inability to work or do fun things — most well read people that I know (including myself) continues to wear masks (in my case, a 3M P100, 99% better than a N95). This is much better than earlier versions: “Earlier this month, he reported in the British Journal of Haematology that his patients’ risk of Long Covid symptoms 3 months after infection had dropped from 46% with the original coronavirus strain and another called Alpha, to 35% with the Delta variant, to 14% with Omicron.” The strains are getting milder — but still a 10% risk with its severe financial (and fun) impact should be respected.
Analysis
The initial good news is that we do not have the typical pattern for Long COVID and/or ME/CFS. Those conditions typically have over representation of 0-9%ile count. We have under representation. There is always the chance that it could cascade in that direction, but taking action now will likely decrease those odds.
Percentile
Genus
Species
0 – 9
4
6
10 – 19
17
26
20 – 29
20
26
30 – 39
20
24
40 – 49
24
46
50 – 59
29
48
60 – 69
31
27
70 – 79
21
35
80 – 89
25
36
90 – 99
21
40
There was no matches to patterns from the US National Library of Medicine nor to our own citizen science patterns.
Going over to Dr. Jason Hawrelak recommended levels, we have the following of greatest concern. FYI: Lactobacillus was at desired ranges.
There is a faint echo of suggestions seen with Long COVID and ME/CFS.
Going over to technical details, we find that berberine (from looking at one bacteria only) is not a recommended from the consensus. The top priorities are (skipping prescription items) are (in decreasing priority):
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.
Addendum
You can see below how much he failed to match studies from the US National Library of Medicine.
The three episodes of ME/CFS that I have had were all caused by stress:
In University days — Doing triple honors and a life threatening condition hit my father
At Microsoft — Assigned to a bad boss that created endless non-productive stress (he was “asked” to leave shortly after I went off sick — co-workers also has issues)
At Amazon — similar to the above, except no co-operation from fellow employees — everyone was trying to have other team members be who was cut on the next review cycle.
Society and family often expects you to put up with stress. In some cases, it may be needing a job and stress is “just a normal aspect of that“. In other cases, there may be “drama queens”, “gas lighters” and other personality types that uses stress to manipulate people.
There have been many studies finding that ME/CFS is associated with prior stress. Some literature:
One study is particularly interesting:Distinctive personality profiles of fibromyalgia and chronic fatigue syndrome patients. [2016] and likely applies to many people with microbiome dysfunctions. For many years, “Personality Type A are more prone to get ME/CFS” that is people with a pattern of behavior and personality associated with high achievement, competitiveness, and impatience. This study refines that paint brush more. Please read this study.
“Well, I can’t do anything about it”
Most people can do many things. For myself, I have (finally) accepted this simple rule: “If the stress cannot be resolved in X weeks, promptly exit stage left/abandon ship”. In terms of work, if I quit a job, take a financial hit for a while, and get a less stressful job — that is a better alternative than risking a ME/CFS relapse and being unable to work at all. In terms of family, decline contact with stressful members of the family. The latter often require a smoke screen so you agree to come to family gathering and then car troubles, work emergency, prevents you attending.
In other cases, it may take help from others to identify and unlearn habits/conditionings from childhood or prior relationships.
Society and friends can be a major source of stress. This can come from many sources “high expectations of you” to “keeping up with the Jones” to “you are not doing your duty”.
IMHO, your first duty is for your own health. How can you support and care for others when your health is blocking things.
Stress is a co-factor
Other factors are involved, diet, past virus, DNA. Stress is a significant factor and for many people it is the hardest to change because people often resign to their current stress level. For myself, I often surprise my wife by being hyper-reactive to issues. I avoid procrastination and attempt to deal with issues promptly — it is an effective way of reducing stress. Procrastination on the grounds of having to think thing over (or hoping things will resolve themselves) adds to your stress queue in small amounts. If you can’t do anything about it, then accept that reality and don’t worry about it.
Bottom Line
Take a hard look at stress in your life and then resolve them. Your health is the cost of not resolving them.
This is a series of samples from a long time suffer from Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). In looking at the samples, we must keep in mind two factors:
Lab Read Quality. A low read quality reports much fewer bacteria than a high read quality.
1.8 reports 300, a high read quality can triple the bacteria counts selected.in a category
This usually does not impact the broad stroke criteria such as Dr. Jason Hawrelak (JasonH)
A sickness (COVID, Flu) or even vaccination will alter the microbiome and create the appearance of lost ground. This was seen and covered in the post below
My usual practice is compare the latest with the prior only. Trying to weave a dialog covering all prior tests is contra productive with going forward. What is past, is water under the bridge.
This reader had one major question — the suggestions seem to have changed a lot. That is the focus of this post. Have there been a dramatic change, or are the changes likely connected to a few bacteria dropping off the list and a few new ones being added.
Person’s Subjective Report: “Symptom-wise and treatment-wise, I don’t have much to report that is new or an outlier to previous years of samples and treatments.”
Review over Multiple Samples
Data from the same lab (using Ombre data, Biomesight version is also available).
Compared to the prior sample, we see:
Less extreme percentiles than prior sample
Less rarely seen bacteria
Less pathogens
Less outside of:
Outside Lab Range (+/- 1.96SD)
Outside Box-Plot-Whiskers
Outside Kaltoft-Moldrup
No change using a multitude of 3rd party criteria.
Less compounds at high levels, more compounds at low levels
General impression, there has been objective improvement
Criteria
4/18/2023
2/2/2023
11/1/2022
4/11/2022
1/11/2022
03/09/2021
5/27/2020
Lab Read Quality
4.8
5.3
8.6
15.3
1.8
2.9
4.3
Bacteria Reported By Lab
638
734
800
750
312
394
544
Bacteria Over 99%ile
4
14
12
3
9
3
4
Bacteria Over 95%ile
36
42
24
21
30
10
12
Bacteria Over 90%ile
56
79
46
49
46
25
36
Bacteria Under 10%ile
25
46
154
329
16
26
32
Bacteria Under 5%ile
10
21
54
287
10
15
11
Bacteria Under 1%ile
2
1
7
84
1
5
0
Lab: Thryve
Rarely Seen 1%
10
15
7
8
0
2
9
Rarely Seen 5%
36
61
58
70
2
4
18
Pathogens
27
34
32
30
21
26
30
Outside Range from JasonH
4
4
4
4
7
7
7
Outside Range from Medivere
13
13
19
19
14
14
14
Outside Range from Metagenomics
10
10
7
7
9
9
9
Outside Range from MyBioma
13
13
10
10
8
8
8
Outside Range from Nirvana/CosmosId
22
22
22
22
17
17
17
Outside Range from XenoGene
51
51
48
48
42
42
42
Outside Lab Range (+/- 1.96SD)
18
24
14
17
8
5
5
Outside Box-Plot-Whiskers
67
97
63
63
58
28
45
Outside Kaltoft-Moldrup
143
218
290
400
89
102
141
Condition Est. Over 99%ile
0
0
0
5
2
1
0
Condition Est. Over 95%ile
0
0
2
24
6
5
1
Condition Est. Over 90%ile
0
7
3
38
11
9
2
Enzymes Over 99%ile
13
47
44
4
1
41
56
Enzymes Over 95%ile
114
179
99
72
7
311
465
Enzymes Over 90%ile
469
266
242
152
54
683
512
Enzymes Under 10%ile
133
123
219
430
70
141
106
Enzymes Under 5%ile
58
47
108
310
47
88
53
Enzymes Under 1%ile
7
1
1
64
6
14
5
Compounds Over 99%ile
11
31
22
3
1
27
53
Compounds Over 95%ile
37
122
67
46
9
305
276
Compounds Over 90%ile
146
190
231
93
38
488
365
Compounds Under 10%ile
954
809
823
998
530
617
800
Compounds Under 5%ile
906
789
788
961
521
599
787
Compounds Under 1%ile
872
783
757
892
515
582
776
Comparing Suggestions
The reader noticed a significant change of suggestions between the samples. So I am going to document out how to verify or see the results. Also, remember that you can merge consensus from two different samples. Minor items like taking samples at different time of days, unusual food, significant dosages of herbs, probiotics or supplements within 48 hours of taking a sample can cause temporal shifts.
Step by step:
Do “Just Give Me Suggestions” for 1st sample
Click “For more technical details”
Click Download, save the file
Repeat for 2nd sample
Open Excel or equivalent on the .csv file downloads
Each sample will be in a difference instance of Excel
Add a new work sheet to one
Copy one set of data to the other
Rename worksheets as “Current Consensus” and “Prior Consensus”
Copy the Mid2 column to the first column in the Prior Consensus”
Insert a blank column after the Mid2 column,
Insert into this new blank column: =VLOOKUP(I2,’Prior Consensus’!A:J,2,FALSE)
This brings the net value over.
You can brink other values over by changing “2”
I have done a video below of the process.
Wait! This is more for your mobile phone users
Go to Multiple samples, then pick your samples as shown below
You will now see a summary at the top
In this case we have 80% agreement on suggestions between samples
Bottom Line
I have not done further analysis etc. The reader has acquired those skills already. I have address only the issue of shifting suggestions. My best advice is simple: Do an uber consensus between the present and the last sample. The logic is simple — samples has some volatility based on time of day that the sample was taken as well as substances consumed in the prior 48 hours. Remember we are dealing with a lot of fuzzy data — both in what is reported from your sample, and what changes what from the literature.
The result of an uber consensus is a continuation of the prior suggestions (with a little pruning) and incorporation of the current suggestions.
This is a continuation of a nerdy technical series with Predicting Conditions from PubMed Studies earlier. I continue using depression as my canary. We use two data sets from two different retail providers: Ombre Labs (USA) and Biomesight (UK).
Means, T-Scores – Walking Two Paths
There are two paths available, with no clear best choice:
Compare averages from samples that reported some amount (thus excluding zero values)
Lower degree of freedom and thus T-Scores
Compare averages from samples with a zero being used when an item is not reported.
Higher degrees of freedom and higher T-Scores
Picking one or the other of these paths seems to be done a priori by most researchers. To get a feel for the differences, I processed data from Ombre Labs and Biome Sight by both methods. Ombre Labs is almost solely from American Samples. BiomeSight is from around the world. The data suggests that Americans are more prone to depression.
Measure
Biomesight
Ombre Labs
Bacteria Taxon Seen
1,878
2,586
With Depression
87
101
Without Depression
639
343
Percentage with Depression Reported
12%
23%
Highest T-Score with reported only (No Zero values)
95
60
ABs(T-Score) over 3.2 (No Zero values)
1135
1185
Highest T-Score with Zero if missing
282
176
Abs(T-Score) over 3.2 (with Zero if missing)
1391
1492
Highest Composite T-Score (Sqrt of the above t-score multiple by each other)
158
92
Composite T-Score over 3.2 ( < 0.001)
1193
1306
Percentage of Bacteria with T-Score over 3.2
63%
50%
Larger total sample size results in higher t-scores
We then did a composite T-Score between the two labs by bacteria to see the best indicators (in decreasing order of significance). We then compared to results from studies on the US National Library of Medicine
Bacteria
Depression
PubMed
Blautia wexlerae
Increased
Genus has 50% high and 50% low
Catonella
Increased
Catonella morbi
Increased
Pseudobutyrivibrio
Increased
Clostridiaceae
Decreased
Sutterella wadsworthensis
Decreased
Match (genus)
Slackia
Increased
Match
Anaerobranca
Decreased
Actinobacillus
Decreased
Haemophilus parainfluenzae
Decreased
Match (genus)
Proteinivoraceae
Decreased
Bacteroides ovatus
Decreased
Thermoclostridium
Decreased
Eggerthellales
Increased
Match
Eggerthellaceae
Increased
Thermoanaerobacterales
Increased
Prevotella
Decreased
General Match at genus
Veillonella dispar
Decreased
Match (genus)
Blautia glucerasea
Increased
Genus has 50% high and 50% low
Blautia hansenii
Increased
Genus has 50% high and 50% low
Lachnospira
Decreased
General Match at genus
Alphaproteobacteria
Increased
[Ruminococcus] torques
Increased
Disagree
Desulfallaceae Watanabe et al. 2020
Increased
Bifidobacterium bifidum
Decreased
Disagrees, but the genus was a match
Where there was a study available, we had our results in good agreement. Note that our sample sizes far exceed those of any of the studies we found.
We had about 20% less significant bacteria by eliminating those samples with no/zero counts. By requiring both methods to be significant reduces the risk of false positives. In this case, we have an abundance of significant bacteria and such a criteria is viable.
Many of the items deemed very significant were of low frequency of being seen in samples
Erwinia tasmaniensis: seen in 7.2% of Biomesight samples, not reported in Ombre.
With Condition: Seen in 3% of samples with count of 353 /million
Without Condition: Seen in 7.7% of samples with count of 128 / million
Significant with excluding (11.2), significant with deeming zero (23)
This takes us to the phrase of the analysis: Given a random sample, what is the probability of correctly predicting depression. The end goal is to determine the most influential bacteria responsible for depression. One approach is using random forest on the data trimmed to those bacteria deemed significant or very significant. Another approach is use splines mixed with logistic regression. We must be careful not to shove this problem into an existing square or round hole, instead we need to allow the data to speak to us.
Remember, bacteria do not operate independent of each other. They are highly dependent on the metabolites of each other. Some of my earlier explorations found the KEGG Enzymes estimators were better predictors than bacteria. To be continued.
It all started in February 2018, I am a nurse by profession and after having worked in various cities in my country. I finally got a stable job in my birthplace , my work always caused me stress, and I always thought that sooner or later stress would affect me. I would go to work and notice how the anxiety was going to my digestive system but when my working day ended it was as if a deep sensation of peace would come to me as if a valve opened and let out the gas from a pot..
I have seen that stress is one of the factors that can cause a change in the intestinal microbiota. I was finally diagnosed with a Generalized Anxiety Disorder and Major Depression in September 2018. In September of that year I was also diagnosed with ME/CFS since my fatigue was palpable (non-refreshing sleep). My wisdom teeth were extracted since I was diagnosed with temporomandibular joint dysfunction and I have to say that my instability problems dissipated over the months but everything else remained. Throughout these years I have been struggling with this, without knowing what I really had: CFS/ME, depression, generalized anxiety disorder, irritable bowel syndrome…
But what I do know for sure is that I was a happy person, with a partner, with economic stability, without any debt problem, nor work problems and from one day to the next my life changes to such an extent that I end up with depression and suicidal ideas.
Analysis
This person did the results with Xenogene which gives more information than 16s tests. Unfortunately, they do not provide percentile rankings so we have to borrow those estimates from elsewhere.
The pattern matches that of most people with ME/CFS: over representation of the 0-9%ile. An ideal microbiome should have the number in each 10%ile range being the same.
Percentile
Genus
Species
0 – 9
23
70
10 – 19
4
13
20 – 29
8
16
30 – 39
10
17
40 – 49
7
9
50 – 59
4
13
60 – 69
6
16
70 – 79
6
12
80 – 89
2
17
90 – 99
8
5
Looking at other health issues:
Dr. Jason Hawrelak Recommendations is at 89%ile, with the following of most concern:
Faecalibacterium prausnitzii – too low (lab agrees)
E.Coli — is too high, (lab agrees)
Roseburia – too low (Lab identifies one species too low, but two normal)
These levels of Salmonella and Shigella are of conventional medical concern. Potentially, you could negotiate with the MD for antibiotics that are effective for them and which will also help your microbiome.
Going Forward
As is becoming my norm, “Just give me Suggestions” button runs 4 sets of suggestion that will usually produce good suggestions.
And add this to make 4 sets of suggestion. While these may already be selected in the other suggestions, this additional run will emphasis those suggestions more.
Consensus – antibiotics
The topic antibiotics suggested (considering everything) are:
Cross checking with Special Reports (which computes a different way), we find that both lists have many in agreement. This list is full of the antibiotics often prescribed by ME/CFS specialists.
There are many antibiotics that are listed in the avoid list. If the MD is willing, I would suggest following the Cecile Jadin’s approach for antibiotics, single course of one antibiotic, a break, then a different antibiotic (preferable a different family).
Consensus – Other
The top ones of the non-antibiotics list are also familiar supplements to many ME/CFS patients. In decreasing priority:
I would suggest (after discussing with your medical profession) to keep to the above for 2-3 months and then do a retest. You are sailing your microbiome to safer waters though an archipelago. The winds and the charts will often require many course corrections.
Reader Feedback
From what I have seen of your recommendations, the conventional antibiotic treatment would be shorter than that of products such as oregano, thyme…
There is no doubt that I will talk to my doctor, precisely in a few days I have an appointment with my internal medicine doctor (infections) and I will take my test result so that if he wishes he can prescribe antibiotics, although I am afraid that taking them will further imbalance my microbiota but there is no doubt that possibly my digestive problems (abdominal pain) do not have their origin in irritable bowel syndrome or irritable colon and are produced by these bacteria that I may infect myself having worked in an infectious unit before falling ill .
I know of several MDs that specialized in treating ME/CFS patients who after a few years also came down with ME/CFS. Bacteria is easily transferred by skin contact, inhalation – in most cases, each exposure compound the very low odds of contagion from a single contact. Over time, the risk increases.
“Is CFS contagious? Because the cause of CFS remains unknown, it is impossible to answer this question with certainty. However, there is no convincing evidence” Wisconsin Department of Health
” The chronic phase of ME/CFS does not appear to be particularly infective. Some healthy patient-contacts show immune responses similar to patients’ immune responses, suggesting exposure to the same antigen (a pathogen).” [2015]
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.
We’ve had COVID over half a dozen times since early 2020. My primary symptoms are fatigue, brain fog, and breathlessness/lack of endurance. But the full list of symptoms is long… It’s gotten so bad that I’m out of work.
I felt brief but significant improvement with low-dose naltrexone, and with low-dose nicotine patches (wasn’t a fan of using that, but it was a successful experiment).
We’re on a ton of supplements with the guidance of our doctors, but our symptoms are worse than ever, and getting worse with time. We think our microbiomes have been damaged, which the Biomesight results seem to agree with.
Looking at what is reported for Long COVID, we have few matches: (5 %ile) 24 of 212, but wtih Coronary artery disease (93 %ile) 6 of 18. This hints at a different direction which the literature indicating that it is possible.
Patients with COVID-19 were at increased risk of a broad range of cardiovascular disorders including cerebrovascular disorders, dysrhythmias, ischemic and non–ischemic heart disease, pericarditis, myocarditis, heart failure, and thromboembolic disease.
”As with ongoing symptomatic COVID-19, multiple Prevotella species (38) are associated with long COVID. Prevotella species are overrepresented in patients with COVID-19 and are thought to produce proteins that can promote SARS-CoV-2 infection and increase clinical severity of COVID-19 (42).” which may account for the multiple COVID.
Dr. Jason Hawrelak Recommendations is at 99.9%ile with low Akkermansia and Bifidobacterium being main item of concern.
We have the typical over representation of bacteria in the 0-9%ile.
I am inclined to suggest diet changes with rotating probiotics every 2 weeks (making sure that you have therapeutic dosages). Retest after 8 weeks and see where we moved to.
Bottom Line
The assumption of typical long COVID or ME/CFS were reasonable assumptions with no microbiome data. You may wish to review other reviews of Long COVID patients. see Analysis Posts on Long COVID and ME/CFS. However, when we add in microbiome data we do not find a match — instead we have indicators of possible cardiac issues arising out of COVID. I would suggest asking for an in depth analysis by your medical professional in this direction.
For the last decade I have been citing literature for the appropriate dosage levels of Vitamin D. The RDA level is not sufficient for a healthy microbiome — it is sufficient only to stop rickets from occurring.
“Several diseases have been linked to vitamin D deficiency, such as hypertension, diabetes, depression, Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, and chronic pain syndromes such as fibromyalgia. ” [2013]
“Vitamin D deficiency was defined as a serum 25-hydroxyvitamin D concentrations ≤20 ng/mL (50 nmol/L). The overall prevalence rate of vitamin D deficiency was 41.6%,” [2011]
“Older adults are advised to maintain serum 25(OH)D concentrations >75 nmol/L.” [2006]
Dr. Mercola recommends 45-50 ng/ml or 115-128 nmol/l [source]
“Vitamin D intakes required to maintain serum 25(OH)D concentrations of >80 nmol/L in 97.5% of the sample[of men and women aged 20-40 y] were … 41.1μg/d (1640 IU), respectively.” [2008]
“The clinical trial evidence shows that a prolonged intake of 250 mug (10,000 IU)/d of vitamin D(3) is likely to pose no risk of adverse effects in almost all individuals in the general population; this meets the criteria for a tolerable upper intake level.” [2007]
“Evidence from clinical trials shows, with a wide margin of confidence, that a prolonged intake of 10,000 IU/d of vitamin D(3) poses no risk of adverse effects for adults,” [2009]
NOTE: there was no evidence going 50% higher has any risks. The studies just tested the 10,000IU level.
“Vitamin D, important for maintaining bone health in Crohn Disease[CD], may have potential as a treatment for the core inflammatory disease process. There is plausible evidence in favour of vitamin D as an anti-inflammatory from animal models, epidemiological and cross sectional studies of CD.”[2015]
“Active Crohn’s disease was associated with low serum 25-OH vitamin D.”[2013]
“In addition, low vitamin D has been associated with disease activity in CD patients, and supplementation appears to be beneficial in improving clinical scores and reducing inflammation.” [2014]
“Vitamin D is an inexpensive supplement which has been shown to improve IBD outcomes.”[2014]
“people with IBD may remain in remission longer when treated with oral vitamin D…suggest that vitamin D may modify the immune response in IBD.” [2015]
“Our findings showed that the high-dose supplementation of vitamin D[9 of 50000 IU cholecalciferol capsules for 3 months taken at weekly intervals] affects measures of systemic inflammation: reductions in High-Sensitivity C-Reactive Protein level and Neutrophil-to-lymphocyte ratio (NLR) distribution.” [2017]
“The results of the meta-analysis of 10 trials involving a total of 924 participants showed that vitamin D supplementation significantly decreased the circulating hs-CRP level by 1.08 mg/L” [2014]
I mentioned a formula from 2010 in the first post. Fortunately, there are several Vitamin D calculator available. I put in the numbers from the above post below
Males 15% drop in the ability to absorb once you get over 50.
Females 45% drop in the ability to absorb once you get over 50.
This suggests that the dosage computed by the calculator needs to be doubled for a female over 50.
In addition to classic role of vitamin D in musculoskeletal health over the last decade it was shown that low blood serum concentrations of 25(OH)D are associated with a number of non-skeletal disorders including cancer, high blood pressure, age-related cognitive decline, disorders of the immune and reproductive systems, etc. The prevention of the development of these diseases is reached under considerably higher concentrations of the vitamin in the blood serum, than is necessary to maintain the normal state of the bone tissue, to regulate calcium absorption and homeostasis
“Vitamin D was first discovered as the curative agent for nutritional c, and its classical actions are associated with calcium absorption and bone health. However, vitamin D exhibits a number of extra-skeletal effects, particularly in innate immunity. Notably, it stimulates production of pattern recognition receptors, anti-microbial peptides, and cytokines, which are at the forefront of innate immune responses. They play a role in sensing the microbiota, in preventing excessive bacterial overgrowth, and complement the actions of vitamin D signaling in enhancing intestinal barrier function. Vitamin D also favours tolerogenic rather than inflammogenic T cell differentiation and function. Compromised innate immune function and overactive adaptive immunity, as well as defective intestinal barrier function, have been associated with IBD. Importantly, observational and intervention studies support a beneficial role of vitamin D supplementation in patients with Crohn’s disease, a form of IBD. This review summarizes the effects of vitamin D signaling on barrier integrity and innate and adaptive immunity in the gut, as well as on microbial load and composition. Collectively, studies to date reveal that vitamin D signaling has widespread effects on gut homeostasis, and provide a mechanistic basis for potential therapeutic benefit of vitamin D supplementation in IBD.”
Vitamin D signaling in intestinal innate immunity and homeostasis [2017]
There is no appropriate dosage to take without lab results. I know females over 50 that freaked out their physician when they stated that they were taking 20,000 IU of vitamin D3 daily for the last 2 years. Lab tests were quickly ordered!! The lab tests showed her just above the middle of the normal range. The ability to absorb is significantly reduced with IBS, IBD, UC, Crohn’s disease, etc. It’s a matter of getting the labs, take an aggressive dosage for 6 months, retest and then adjust the dosage according to the new results.
“The biggest problem is that MDs are often behind the times and do not work from the latest literature. For example a single dosage of 600,000 IU of vitamin D is deemed safe on medscape, or 10,000 IU/day for months [source]. One of the studies above cited an average of 60,000 IU/day for 3 months! [2017]”
From my 2017 post
Target Dosages?
At least 128 nmol/l or 50 ng/mL. You want to be at the TOP of the normal range. You will get push back from MD with higher level because of medical myth that above this is toxic. I say myth because there is no evidence in the literature. There were issues with Vitamin D2 supplements which was sold for a while because it was cheap to produce and is chemically different.
Of 20,308 measurements, 8 percent of the people who had their vitamin D measured had levels greater than 50 ng/mL, and less than 1 percent had levels over 100 ng/mL.
“We found that even in those with high levels of vitamin D over 50 ng/mL, there was not an increased risk of hypercalcemia, or elevated serum calcium, with increasing levels of vitamin D,” says study co-author Thomas D. Thacher, M.D., a family medicine expert at Mayo Clinic. [2015]
Of course, there are some rare DNA mutations that could cause problems with that level. One person’s experience with the details. If you have adverse reaction — get the additional tests described below.
“The evidence is clear that vitamin D toxicity is one of the rarest medical conditions and is typically due to intentional or inadvertent intake of extremely high doses of vitamin D (usually in the range of >50,000-100,000 IU/d for months to years).”
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