A reader email me informing me that Microba no longer supplies 4 files, just one — Species. So no Phylum, Family or Genus information. I have modified the upload to handle just having one file available for whatever usefulness is possible.
A Long Time Pain
Microba does not provide data with the official NCBI Taxon numbers (which is what drives Microbiome Prescription AI). This means having to do name match over 3,635,527 different names on the NCBI database. Unfortunately, we still do not find matches, a few examples:
Pauljensenia MIC9711
QAMI01 MIC9451
Ruminiclostridium_C sp000435295
UBA1191 MIC6579
UBA1191 MIC9444
Getting more information usually result in this from Google:
I have written them in the past hoping they would be more willing to cooperate. No luck.
What is Available
When you look at the microbiome tree, you will see values only for species. Everything else is 0. It is impossible to accurately estimate genus etc from species alone.
Prior, we would see something like this:
And you will get nothing from Dr. Jason Hawrelak Recommendations. Only one species is in it.
On the positive side, you will still get reasonably accurate KEGG based data (since that is based on species).
“Just Give Me Suggestions” will still work to some extent. Other suggestions can be tricky. The AI will work to the extent of the data available (which is greatly reduced compared to Thorne, Ombre or Biomesight).
Bottom Line
For those people in Australia, I would suggest moving over to BiomeSight, you will likely get six times more data at a lower cost.
How does having Ehrlichia and Rickettsia in high values in the sample correspond to having these Lyme coinfections systemically? These are fairly common to see in the sample but my values are very high 96 and 99%.
From a reader
What is he talking about?
Ehrlichia is a genus of Rickettsiales bacteria that are transmitted to vertebrates by ticks. These bacteria cause the disease ehrlichiosis, which is considered zoonotic, because the main reservoirs for the disease are animals… Originally called Rickettsia ruminantium, and is currently named Ehrlichia ruminantium. [Wikipeadia]
Rickettsia is the name of a single genus, …Many new strains or species of Rickettsia are described each year… Some Rickettsia species are pathogens of medical and veterinary interest, but many Rickettsia are non-pathogenic to vertebrates, including humans[Wikipedia]
He mentions they are common to see, let us look at the upload stats. From Ehrlichia: NCBI 943
For both of the above, the species or strains you have may be non-pathogenic (or even you are not susceptible to them). There are two steps that should be considered:
If you have symptoms — then take the microbiome results to your MD quickly and ask for further testing (the above pages enumerates the appropriate tests)
If you do not have any symptoms, then for your next regular appointment, mention this — your MD may or may not do tests. Typically some symptoms is needed to justify the testing cost to insurance.
Is the Microbiome a Leading or Trailing Indicator?
A leading indicator is one that has the microbiome shifting before the diagnosis is usually done. This could be viewed as the microbiome shift feeding the condition. A trailing indicator means that the condition develop and then the microbiome changes.
We so not know the answer. I tend to favor it being a leading indicator, thus, when the shifts are towards a known condition then you can take action and either slow the progression or prevent it. Since the main mechanism (diet change) is extremely safe and usually very affordable — it appears to be rational.
I’ve had bloating and burping since hospitalized as a child for a lump on my throat. I received antibiotics at this time
I went into 80% remission for about 6 years from age 50-56. I don’t know what did it but I was on a low FODMAPS diet and started using hydrogen peroxide as a mouth rinse
Symptoms
in addition to the bloating and burping I have the following symptoms
fatigue
sometimes a numb feeling in parts of my hands and feet
orthostatic intolerance (although I did the tilt table test and tested negative)
halitosis
tinnitus
a strange feeling in my head
shortness of breath
I took inulin before my remission and my symptoms intensified immensely (especially burping and fatigue and shortness of breath)
I had a culture of my upper duodenum done in 2013 and it showed 10000CFU/ml of rothia, prevotella melaninogenica and streptococci viridins. A recent Bristle Health oral biome test showed the prevotella melaninogenica in the 90th percentile
Analysis
I was not surprised about getting ME/CFS after a cold. Cold virus include COVID which can cause Long COVID — a sibling of ME/CFS. The wrong cold virus combined with other catalysts can send someone down that path.
First, I look at the distribution of percentiles. A normal/typical microbiome should have the same count (percentage) in each of the 10%ile. As is often seen with ME/CFS and Long COVID, we have a major overrepresentation of the 0-9%ile — 4x the count of most other groups.
Percentile
Genus
Species
0 – 9
62
89
10 – 19
14
22
20 – 29
15
22
30 – 39
16
16
40 – 49
15
19
50 – 59
20
25
60 – 69
10
14
70 – 79
18
22
80 – 89
20
17
90 – 99
21
35
I interpret this as a host, “a mafia”, of odd bacteria that cross support each other and pumps disrupting metabolites (chemicals) into the body. Thus it is not a bacteria(person) that causes the problems but a big gang of bacteria.
There was not a strong bacteria that predominate this shift, Phocaeicola massiliensis was the only candidate. Looking at Potential Medical Conditions Detected, there were no significant matches (not surprising with an abundance of low percentile bacteria).
Looking at some of the conditions we see a marginally better match for Long COVID than for ME/CFS! Not sufficient to ascribe to a cold virus as the onset cause, but interesting.
It provides information on selected strains by role:
As an exercise to understand the “end-to-end” process (literally), I have created the table below. Since the data is by species we have an issue of different tests reporting different species. For more details see The taxonomy nightmare before Christmas… The * indicate that there was no match at the strain level, so we use the genus as a proxy.
First thing to remember is that bacteria is pH sensitive so the quantity in each location is expected to be very different.
Bacteria
Bristle
Percentile
Actinomyces dentalis
1.8
90
*
Actinomyces graevenitzii
1.9
90
*
Actinomyces odontolyticus
0.4
90
*
Atopobium parvulum
6.8
69
*
Atopobium sp
8
69
*
Campylobacter concisus
5.2
98
*
Campylobacter gracilis
5.1
98
*
Candida albicans
1.8
Candida dubliniensis
1.5
Candida glabrata
2.2
Candida sp
1.1
Capnocytophaga granulosa
7.3
Capnocytophaga sputigena
0.19
*
Capnocytophaga sp
0.18
*
Corynebacterium matruchotii
8.3
86
*
Dialister micraerophilus
0.4
94
*
Eikenella corrodens
2.6
Enterobacter cloacae
2.5
Fusobacterium nucleatum
1.9
19
Fusobacterium sp
0.3
92
Gemella haemolysans
1.8
48
*
Gemella morbillorum
0.12
48
*
Granulicatella adiacens (30%)
4.8
15
Haemophilus haemolyticus
4.8
Haemophilus parainfluenzae
7.2
Haemophilus pittmaniae
0.79
Helicobacter pylori
2.3
61
*
Lactobacillus fermentum
3.5
5
*
Leptotrichia trevisanii
0.99
Megasphera micronuciformis
8.5
24
*
Neisseria elongata
0.15
*
Neisseria flavescens
2.1
Neisseria mucosa
3
Neisseria subflava
1
Oribacterium sp
0.098
26
Porphyromonas sp
2
100
Porphyromonas catoniae
0.27
100
*
Prevotella sp
10
73
Prevotella fusca
2.2
73
*
Prevotella histolica
9.5
73
*
Prevotella loescheii
1.6
1
Prevotella melaninogenica
9
73
*
Prevotella pallens
0.1
73
*
Prevotella salivae
8.8
73
*
Prevotella tannerae
0.56
73
*
Prevotella veroalis
7.5
73
*
Propionibacterium acidifaciens
2.1
Rothia aeria
0.8
Rothia mucilaginosa
5.2
Selenomonas noxia
4.4
72
*
Solobacterium moorei
0.3
89
Stomatobaculum longum
0.18
Streptococcus constellatus
2.7
48
*
Streptococcus infantis
7.9
48
*
Streptococcus intermedius
1.9
0
Streptococcus mitis
7.8
48
*
Streptococcus oralis
7.2
1
Streptococcus parasanguinis
1.3
49
Streptococcus peroris
1.6
48
*
Streptococcus salivarius
5
48
*
Streptococcus sanguinis
2
48
*
Streptococcus tigurinus
8.7
48
*
Tannerella sp
0.88
Treponema sp
0.73
Veillonella atypica
8.5
18
Veillonella dispar
7.5
18
*
Veillonella sp
2.7
18
*
I noticed something interesting with strains that were in both samples.
My subjective conclusion is that this strongly supports the hypothesis that the mouth microbiome feeds the microbiome of the rest of the digestive track. We have 4 rare strains in the above list of 7 where only 1 would be expected to be below 14% (1 in 7).
We can get suggestions for the mouth approximately by using this feature and entering by the genus items above 7 for high, 9 for very high or below 3 for low, below 1 for very low.
Suggestions include (for mouth) are below. This is an experiment to see how suggestions for the “other end” compares! Values below 0.4 are usually low significance.
There are some subjective issues in entering the contents and getting suggestions. For suggestions, doing parent and/or children can be debated many ways. Some species are low of a genus and others are high… do you mark the genus high, low or normal? It is unclear if the bacteria listed are pure bad or just bad in excess. That is, should anything not zero be deemed too high or only those over 7. Things are not sufficiently cleared from this report. If I get more requests to do analysis of Bristol Health reports, I will invest more time and add a custom manual entry page. I will need to research every single species to know the appropriate handling.
The adage “No man can server two master” is good to keep in mind in this scenario.
I did the usual “Just Give Me Suggestions” path since there was nothing that stood out that could require special handling. “Just Give Me Suggestions” obtains 4 sets of suggestions using different logic to try to derive the best suggestions. I will start by taking the above list and see how they rank in terms of the microbiome.
As expected, with my two masters preamble, we have disagreements. All of the mouth items came in as weak suggestions against BiomeSight suggestions (range: -460 to 465), so doing them will likely not have significant impact on the other end’s microbiome.
Back to Microbiome Suggestions, we have in decreasing priority (excluding antibiotics):
For the top one, a nutrient unfamiliar to most people, we see this list to choose from. We See Barley on it. It Barley is a problem, then almond, peanut or pistachio are good alternatives. For Peanuts, I actually did some posts in the ME/CFS context.
Hesperetin is in Lime, Blond Orange, Lemon and Grapefruit (AGAIN Grapefruit!)
Questions
Q: What testing method is BristleHealth using?
A: “Shotgun microbiome test examples: Bristle (oral microbiome).” [src] Biomesight is using 16s which provides less data. Thorne uses shotgun testing and thus would be a better match.
Q: On cfsremission and/or cort johnsons blog you discussed the importance of breaking down biofilms with things like nac as well as rotating herbs, probiotics and antibiotics. Is that a layer that should be added onto the items selected by microbiomeprescription (I plan to reread those posts before starting).
A: Yes, I have posted about biofilm in the past: Combating an Infection Defense Mechanism: Biofilms [2014] and Probiotic Biofilm Breakers[2016]. It is not a simple matter “Biofilms provide survival sites for both beneficial and opportunistic pathogenic bacteria, by providing protection as above and increasing the potential of the bacteria to survive and evolve” [2013]. It impacts antibiotic resistance [2020]. In other words, we have yin-yang. If you are intending to aggressively reduce bacteria known to use biofilms, especially with antibiotics, then it is a wise choice. In most cases, I would not do it by default. For example, Akkermansia muciniphila and Lactobacillus rhamnosus GG both form biofilms [2020].
Q: What can you suggest to deal with Halitosis (Bad Breath)
A: The bacteria involved are nicely listed in your report.
The same approach may be done for other mouth bacteria that you wish to eliminate, you should cross check that none of the substance are strong avoid for the “other end”.
“The detrimental effects of oral microorganisms are not confined to the oral cavity, they can also contribute to systemic disorders, such as type 2 diabetes mellitus, cardiovascular disease, and inflammatory bowel disease (IBD) (Hajishengallis and Chavakis, 2021). “
“In the article by Chen et al. the influence of periodontal pathogen infection on gut mycobiome was explored. The authors demonstrated the first evidence of gut fungal dysbiosis with periodontal pathogen administration. “
The oral microbiome impacting the entire flow (including SIBO) seems to be well illustrated with this data. The bacteria strains from the Bristle Health report appear to be those known to cause issues in the mouth (and most are not reported on by other tests). This implies that the ideal pair of tests to deal with systemic health issue is likely Bristle Health and Thorne.
Allergies are often tossed into a big box of “all allergies are the same”. I have learnt from studies that often different items are clustered together to avoid needing to learn and detail with the details. I know people that have very specific allergies — i.e. to birch but not grass or other tree pollens. Most MDs will toss such people in the seasonal allergic rhinitis bucket; treating them proforma.
This appears borne out by some studies:
” A delayed correlation between the birch pollen concentration and the symptom scores was seen up to two days after the pollen measurement. For grass pollen this effect lasted up to three days after the pollen measurement.”[2023]
“the most effective treatments for allergic rhinitis were in order as follows: sublingual immunotherapy_dust mite, subcutaneous immunotherapy_dust mite, sublingual immunotherapy_ grass mix plus pollen extract, placebo, and pharmacotherapy. ” [2023] – note that placebo was more effective that traditional medicine!
The goal of this exercise is see if there are any new options or approaches for addressing this issue.
Environment May Be a Factor
Some of my university professors refused to believe that allergic rhinitis existed. They were born and raised in a part of the middle east and never encountered people with it before moving to North America. This saying from the prophet recorded by Salamah b. al-Akwa, implies that allergies may have been unknown in that part of the world:
“When a man sneezed beside the prophet (May peace be upon him), he said to him : Allah have mercy on you, but when he sneezed again, he said : The man has a cold in the head.“
This seen in the following charts: (A) Unspecified rhinitis; (B) allergic rhinitis; (C) non‐allergic rhinitis.
Worldwide prevalence of rhinitis in adults: A review of definitions and temporal evolution [2022]
“A family history of allergic rhinitis, asthma, or atopic dermatitis increases a patient’s risk of being diagnosed with allergic rhinitis. People in the United States are commonly sensitized to grass, dust mites, and ragweed allergens.” [2023]
“Subjects with persistent rhinitis and asthma had higher levels of total IgE at baseline and after 10 years, and exhaled nitric oxide and eosinophil cationic protein at baseline compared with those that remained healthy. ” [2023]
Exhaled nitric oxide implies a breath test and thus we have 1135 bacteria the produces this chemical, hence a potential overgrowth as a contributing factor.
B cells are key players in the mechanisms underlying allergic sensitization, allergic reactions, and tolerance to allergens. Allergen-specific immune responses are initiated when peptide:MHCII complexes on dendritic cells are recognized by antigen-specific receptors on T cells followed by interactions between costimulatory molecules on the surfaces of B and T cells. In the presence of IL-4, such T-B cell interactions result in clonal expansion and isotype class-switching to IgE in B cells, which will further differentiate into either memory B cells or PCs. Allergic reactions are then triggered upon cross-linking of IgE-FcɛRI complexes on basophils and mast cells, leading to cell degranulation and the release of pro-inflammatory mediators.Mechanisms underlying effective allergen-specific immunotherapy (AIT) involve the induction of Tregs and the secretion of blocking IgG4 antibodies, which together mediate the onset and maintenance of immune tolerance towards non-hazardous environmental antigens.
Oralair, a biologic, has grown in use in Europe (approved in 2008 from 8% to 29% by 2012 [2015]) and is approved in the USA (2013) Link to FDA documents. It is prescription with a base cost of $5 or more per tablet — hence, antihistamines are more likely to be recommended in the US due to cost, not effectivity.
Similar items are also available, (2800 BAU grass SLIT-T) [Relative to placebo, grass AIT treatment improved total combined scores by 20% 2011], Grazax [The active group demonstrated a 31% reduction in median rhinoconjunctivitis symptom [2011]], MK-7243. There are not cures, rather reduces severity for a percentage of people.
“The only treatment available to treat grass allergy is immunotherapy treatment. This is when you are exposed to small but increasing doses of allergens over a long period of time to help stop your allergic reaction. It takes a long time to work and needs to be prescribed by an allergy specialist.” Australian Department of Health
Treatment via Microbiome
For grass allergy we have the following available retail with studies which boils down to 2 probiotic species worth considering.
And this delightful title “Role of Probiotics in Patients with Allergic Rhinitis: A Systematic Review of Systematic Reviews” [2022] found no hard evidence for any specific probiotics.
Bottom Line for Probiotics: It seems that they need to be taken well in advance of allergy season with sufficiently large dosages.
Next, I went to samples that are annotated with Official Diagnosis: Allergic Rhinitis (Hay Fever) – about 200 samples, and then cross apply them to the above 1135 bacteria. There are no strong statistical significance found.
This exploration failed to produce any significant finding or insights. 🙁
Exploring Immunoglobulin (IgE etc)
As a starting point, Immediate Hypersensitivity Reactions [2023] is of special interest for those who have reactions within 24 hours. “Antibodies including IgE, IgM, and IgG mediate them… Allergic rhinitis is another atopic disease where histamine and leukotrienes are responsible for rhinorrhea, sneezing, and nasal obstruction. ” Typically only IgE is involved. IgE increase in response to grass pollen exposure and are responsible for the allergic symptoms.
“Patients with pollen allergy but not control donors have a population of circulating allergen-specific B cells with the phenotype and functional properties of adaptive memory B-cell responses. These cells could provide precursors for allergen-specific IgE production upon allergen re-exposure.” [2015] – which implies repeat exposure may increase severity.
Omalizumab: reduced significant clinical exacerbation within 24 weeks [2023]
Symptom relief via antihistamines or DAO for a subset for immediate response, or months of preparation for allergy season by probiotics and biologics.
DAO levels were lower in AR patients compared with the controls. The DAO level did not significantly correlate with the severity of AR according to the Allergic Rhinitis and its Impact on Asthma (ARIA) score, though it was lower in patients with persistent or moderate to severe symptoms. The total IgE, eosinophil percentage, and SNOT-22 score all had an inverse relationship with DAO.
Above memory B-cell responses were cited in research which I translate that repeated exposure will make it worse, hence one approach is aggressive avoidance.
Wearing a N95 or better mask when outside from the start of pollen season onwards. In some cases a full face mask may be better. When you arrive home, do a complete change of clothes as soon as possible (ideally outside) and take a shower.
Aggressively reduce pollen in your living place (i.e. pollen leaking into the house via windows and open doors)
Our Approach
This household’s solution for grass allergy has been HEPA air filters oversized for the room size. For example, this $90 unit is rated for 183 sq ft. We would use it for 90 sq ft only — the size of a small bathroom (8′ x 10′). A 10x more expensive unit (Austin HEALTHMATE PLUS ) is rated for 1500 sq ft, so we will use it to cover only 750 sq feet. This means that a 2,000 sq ft house would need at least three operating. Note that this intentional oversizing is to reduce the time to remove grass pollen that comes in.
Time to Reduce Pollen from opening a door
The Austin does 400 cubic feet per minute and we can assume that for one complete room exchange that the pollen level will drop by 50%. It will not remove all in one room exchange. You remove 400 cf in a minute and shoves the clean air back into the room — diluting the air that is there. A little calculus finds that after one cycle, we are down 50% only.
Sample Calculation: 750 sq ft x 8 ft ceiling = 6000 cu feet … thus 15 minutes for one exchange with a 400 cfm unit (i.e. the Austin). If we go with manufacture specifications of 1500 sq feet, than 30 minutes to remove half of the pollen.
PPM, or pollen per cubic meter.
Consider a High Grass level at 340. After one room exchange, it would be 170 (still high), after two room exchanges it would be at 85 (still high), after three exchanges down to 43 – moderate, and at 4 exchanges we are at 20 — into the low range at last. In short, after opening a door for a short while, it may take 2 hours for the pollen level to get reduced to acceptable levels.
Conclusion: Keep the doors open for the least amount of time possible. Consider adding automatic door closers to all doors. Windows should not be open and they should be tight seals. A furnace that brings air in from the outside as part of normal operation should have HEPA filters installed on the intake.
We went one step further, we added to our house an air pump that takes air thru a HEPA filter and creates a positive air pressure in the house. This is one way to address leaky doors and windows — instead of pollen leaking in, the positive pressure pushes it away. We originally installed it to address wild fire smoke (works nicely), but this pollen season it has made a noticeable difference.
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.
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