Back Story

I have been suffering from fatigue for about 8 months now and would like your advice. I have seen multiple doctors now and they have not been able to figure anything out despite running multiple labs. My fatigue started around August of 2022 when I was put on antibiotics. I had an infected wound from a martial art that got infected. After that, I got c diff from a friend I had been taking care of, so in late August I was put on another course of antibiotics. Then in September I got c diff again and was put on another course of antibiotics. My fatigue became very severe at this point. I could barely make it out of bed, etc. I still have fatigue now. I can walk around but I get tired pretty easily. I still cannot go to the gym or exercise. Just the thought alone of pushing my body seems tiring. Please assist.

Antibiotics can be good or bad. Each type alters the microbiome in different manners. Recently I added a new tool to help people negotiate with their MD to find the best candidate antibiotics that will address the MDs concern while looking at their microbiome impact (which is not an area they are knowledgeable). See this video for more information. What has happened, happened — let us move forward.

The antibiotic given were:

• Cephalexin (Keflex, Daxbia) for the wound – which I lack any significant information on
• Dificid (A Macrolide, fidaxomicin)  for c diff

Analysis

First, we see the type of distribution often seen with Chronic Fatigue Syndrome and Long COVID — two conditions with fatigue being a signature symptom. Many many token genus and species.

Percentile	Genus	Species
0 – 9	77	99
10 – 19	22	27
20 – 29	8	8
30 – 39	13	12
40 – 49	5	10
50 – 59	9	15
60 – 69	6	13
70 – 79	5	15
80 – 89	7	7
90 – 99	3	5

This tool also flags the bacteria that may be causing it. What was flagged is shown below — through the roof on these one bacteria (parent-child), This is known to be a very pro-inflammatory bacteria. It is 61% of the microbiome!! It is strongly associated with rheumatoid arthritis [2013] [2023] [2019]. High levels also may indicate mycotoxin (fungi) is present in the environment (house, places he goes) or person [Citation]. For more information see this excellent summary.

Rank	Name	Your value	Percentile
genus	Prevotella	618680	99
species	Prevotella copri	617760	100

The chart below shows how extreme it is.

Looking at Potential Medical Conditions Detected, we had 12 items – which is to be expected with this type of shifts, and we will ignore. It is interesting to note that Dr. Jason Hawrelak Recommendations are at the 99.7%ile — with all of the ones with issues being too low which is expected from one bacteria over-whelming the microbiome.

Antibiotics

There is a lovely study from [2013] that reports on antibiotic resistance of  Prevotella copri [Table 1]. It states “suggesting that resistance to these antibiotics amongst Prevotella … microbiota is not intrinsic, but selected by previous antibiotic treatment”. Which suggests that the multiple courses in a short period of time contributed. I have no data on the two antibiotics that he took.

This hints that taking additional antibiotics may be ineffectual.

If blood tests for fungi has not been done, it should be suggested to the treating physicians.

We have an elephant in the Igloo! Let us address this item first. Then retest after a few weeks. I asked for suggestions including antibiotics, shown below.

A good start would be Vitamin B3 (niacin). Which can cause flushing (i.e. white skin going lobster red), so a low dosage of 100 mg/day and increasing slowly. The other non-prescription items of note are:

• mastic gum (prebiotic)
• clostridium butyricum (probiotics),Miya,Miyarisan
• Possible: saccharomyces cerevisiae (probiotics) BUT saccharomyces boulardii (probiotics) is an avoid.
  • Often this is mislabeled by retail product — so I would suggest skipping it.
• glycyrrhizic acid (licorice) – I prefer Spezzatina by Amarelli  – available on Amazon and other stores
• Slippery Elm
• Triphala – an Indian herb mixture that we usually make into capsules. You could also make tea of it (if you can stomach it’s taste. It’s on Amazon.
• lactobacillus reuteri (probiotics) — not mixed with other species. Most lactobacillus and bifidobacterium are to be avoided.

Second Pass

.Should I do anything other than add b3, mastic gum, licorice, etc to my diet? Do I need to alter my diet in any way to lower the prevotella copri count? My diet right now is pretty bad. Burgers, pizza, etc. I went keto for a couple weeks a few months back to see if it made a difference and it didn’t so I figured if I was going to be miserable, I might as well enjoy what I eat.

From reader after reviewing above.

First the BAD NEWS, Keto is known to increase Prevotella copri, so the no positive impact is not unexpected. More BAD NEWS – what you are eating (high fat foods) will likely have adverse effects.

Above I focused on the Elephant, let us look at the ants and mice in the igloo. This is very easy to do and I made a video of it below.

Bottom line, cut out beef that are high fat content — lean beef only. Burgers and Pizza both use cheap high fat beef. Shift to rice for your source for starch (There are rice based pizza available). No soft drinks or sweets (cut sugar way down – sugar withdrawal can be rough).

Follow up: I would suggest doing a retest after 6 weeks of trying to alter your microbiome with the above suggestions. This will give us data to do your next “diet correction”. It is usually a multi-leg journey back to health.

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.

I get a few emails asking about apparent contradictions from Microbiome Prescription AI Engine. With the new “Just give me suggestions!” option, they have been reduced — this post explains the root issue of these conflicts. It does not solve the issue — only time and a lot more published studies will resolve it.

Data From Studies

The data entry attempts to keep true to what is actually reported in the studies on the US National Library of Medicine. A simple example, the following are subjects of different studies:

• Grape seed extract
• Grape polyphenols
• Grape Fiber
• Resveratrol
• Grapes
• Red Wine
• Red wine polyphenols

It is human nature to try to consolidate information. There are numerous historic examples where such consolidation failed. A simple one is that all antibiotics are the same. In some nations, antibiotics are over the counter — so if you have an infection like tuberculosis, some people would walk in and buy the cheapest antibiotics expecting it to work. It is no surprise that it would have no effect. “They are almost the same” is not an approach that I subscribe to.

The second aspect of studies is that they report on different levels of the bacteria hierarchy, and rarely report on multiple levels. In some cases, the report is only on the highest levels.

When looking at your sample. You may be high at the genus level but normal in the family and order levels. So data from studies about what is impacted at the species, family, order or class level may be ignored. Some people, including medical practitioners, may consolidate this information and after reading one study that mentions a genus apply that to all related species, family, order or class — occasionally to the phylum level. The human tendency to consolidate information strikes again.

Last, the study may have been done on people with a specific condition or type of diet. Diet is often based on location in the world: India (many eat no meat), America (lots of junk food), China (high rice content). The shifts seen with some modifiers with different conditions or diets are different and sometimes in opposite directions. We may not get consistent studies. The human tendency to consolidate information by deeming everyone to be the same strikes again.

Below we have seven similar items — but very different information on what the studies report on.

Sum of Count	Column Labels
Row Labels	class	family	genus	norank	phylum	species	subspecies
grape fiber			3			1
grape polyphenols			13			3
grape seed extract	1		8			1
grapes	1	3	9			6
red wine		12	28	1		169	3
red wine polyphenols			5	1		3
resveratrol		40	72	1	6	114	6
Grand Total	2	55	138	3	6	297	9

While they are similar, there are difference between them that may be significant. One contains sugars, another contains fiber, another contains alcohol — these minor differences can alter different bacteria significantly.

This is why you may see apparent contradictions in suggestions. We a have a mixture of information about your microbiome and each of the above is a sieve of different mesh and fabric.

I choose not to consolidate information. I keep the information as reported. A medical practitioners is not able to keep all of this information in their head. They will proceed to consolidate, and consolidate and simplify – the art of medicine. The Artificial Intelligence Engine is the result of processing over 41 Gigabytes of information — that is likely far more than any medical practitioners had actually read in their career. Is the detail needed? That’s a personal judgement. I prefer to have it. Using AI, I can work with all of the information available without needing to consolidate or simplify.

When there is a contradiction – which should I choose? My standing answer, is avoid the substance. We do not know with confidence what the outcome may be. On the other hand, I often seen suggestions reinforcing each other — for example Positive: Gluten Free, Negative: Wheats.

We do not want to take gambles with our health — keep to where there is consensus.

“Just give me suggestions”

This picks common items often seen on the internet for a variety of conditions. When there are “similar” items, the one with the most data will usually be selected. It gives higher confidence. These choices are evolving as I review the data.

The intent is avoid showing contradictions, and work where we have the most data. It’s a simple best path forward.

It has been a year since I had Covid-19 I started to deteriorate after it and fell into a limbo of not having the energy to do anything and move on with treatment, I have gave up supplements, antibiotics, probiotics not taking anything, even if I had them in stock, pretty dire, even had very dark thoughts from nowhere that life is not worth living. I got cervical instability diagnosis in 2020 and the Covid-19 infection that made me abandon the microbiome manipulation road, a very bad decision when I look back now. I got diagnosed with a possible mast cell disorder, MCAS is much more worse then CFS, I got a reaction in airport in September 2022 wanted to travel to Italy for a consultation, reacted to fumes in airport was unable to board the plane, almost called the ambulance, the MCAS appeared after Covid-19. I am taking a H1 and H2 for it, and used to take sodium cromoglicate but I got insomnia from it, doctor here told me I am the first patient that has gotten insomnia from sodium cromoglicate. The interesting thing my cognition improved but my physical state deteriorated, I got POTS.

I have also started a YouTube channel to share my story and to keep me motivated to continue:

To recap what Covid-19 in 2022 infection gave me and I still have:

• -Insomnia
• -Lack of motivation
• -POTS
• -New food intolerances
• -Reaction to the environment(possible MCAS)
• -Easy bruising(now afraid to take “thick blood” supplements)
• -High cholesterol and triglycerides

From Reader

Questions from Reader

First, the site does not diagnosis — it is based on association. What is association? It just means that two things tend to happen at the same time. Sometimes there is a real connection — other times the connection is due to other factors. For example, the number of children in a family has declined over the last 50 years. The usage of the internet has increased. There is a statistical association between the two but it does not mean that internet use causes less kids, nor does it mean that having less kids mean more internet use (which may actually be true!).

• Does it show I have POTS, I attached my CellTrend result which is positive for POTS
  • You only have a 10% match to bacteria seen in other people who have reported POTS. So, if it is POTS, it is likely atypical POTS.
  • I do NOT see on the CellTrend results any thing about POTS. Was it a MD’s opinion based on ???
• Does it give avoid food all casein and lactose foods and nuts, I have attached my IgG intolerances testing
  • No, it does not deal will allergies. It suggests food that are likely to positively or negatively impacts the complete microbiome.

Analysis

Going over to Special Studies, COVID Long Hauler leaps out!! It is the best description of the current state. This appears to be common pattern of ME/CFS people Post COVID: The signature of Long COVID dominates over ME/CFS. This may be due to the variation of bacteria over time with ME/CFS. With a recent case of COVID, there is much less variation and thus a stronger signature is found.

Looking at the distribution of bacteria by percentile, we do not see the count for each range being close to each other (expected result for a “normal’ microbiome). The 0-9% is only 32% instead of expected 10%, which is less than other samples that I have seen at 60%.

Percentile	Genus	Species
0 – 9	72	79
10 – 19	17	28
20 – 29	14	15
30 – 39	20	32
40 – 49	24	24
50 – 59	20	22
60 – 69	13	20
70 – 79	14	19
80 – 89	9	7
90 – 99	8	12

Below this on the page (added on April 1, 2023) are “Likely Key Bacteria Causing Above”

Rank	Bacteria	Importance
species	Faecalibacterium prausnitzii (in prior)	3.4
genus	Faecalibacterium (in prior)	3.3
genus	Roseburia (in 2021)	2.3
species	Phocaeicola massiliensis	1.9
species	Bacteroides stercoris	1.9
species	Roseburia faecis (in 2021)	1.8

Looking at trend over 4 samples, we see the dramatic jump in the %age of bacteria that are under 10%ile.

Criteria	9/26/2022	1/9/2022	3/8/2021	7/26/2020
Lab Read Quality	11	3.3	3.6	3
Bacteria Reported By Lab	808	476	632	463
Bacteria Over 99%ile	1	5	1	20
Bacteria Over 95%ile	15	31	17	55
Bacteria Over 90%ile	28	54	48	88
Bacteria Under 10%ile	280	18	6	50
Bacteria Under 5%ile	246	5	0	35
Bacteria Under 1%ile	226	1	0	16
Percent Under 10%ile	35%	4%	1%	11%
Lab: BiomeSight
Rarely Seen 1%	6	2	3	1
Rarely Seen 5%	37	10	20	18
Pathogens	40	35	33	34
Outside Range from JasonH	5	5	6	6
Outside Range from Medivere	17	17	13	13
Outside Range from Metagenomics	6	6	7	7
Outside Range from MyBioma	3	3	9	9
Outside Range from Nirvana/CosmosId	18	18	20	20
Outside Range from XenoGene	34	34	37	37
Outside Lab Range (+/- 1.96SD)	2	10	7	23
Outside Box-Plot-Whiskers	45	72	88	99
Outside Kaltoft-Moldrup	192	89	86	133
Condition Est. Over 99%ile	1	4	2	14
Condition Est. Over 95%ile	1	8	5	26
Condition Est. Over 90%ile	4	8	7	36
Enzymes Over 99%ile	0	55	0	51
Enzymes Over 95%ile	14	144	13	133
Enzymes Over 90%ile	91	186	60	231
Enzymes Under 10%ile	218	62	92	552
Enzymes Under 5%ile	161	17	37	408
Enzymes Under 1%ile	86	0	2	163
Compounds Over 99%ile	0	43	0	28
Compounds Over 95%ile	17	95	13	79
Compounds Over 90%ile	65	145	43	128
Compounds Under 10%ile	1104	983	960	958
Compounds Under 5%ile	1088	977	950	934
Compounds Under 1%ile	1067	975	948	913

Going Forward

To build a consensus, I will do.

•  Standard Lab Ranges (+/- 2 Std Dev)
•  Box Plot Whisker
•  Kaltoft-Moltrup Normal Ranges
• “Likely Key Bacteria Causing Above”

This now rolled into a single click! “Just give me suggestions” – It results in the short dumb down list with links to the full details. See the video below.

The suggestions are attached:

• Melatonin, NAC, Quercetin
• Gluten Free Diet,  low carbohydrate diet
• Antibiotics ( metronidazole, azithromycin) with 2nd choices being (doxycycline,  Rifaximin (Xifaxan))
• Echinacea, Flaxseed, Piperine, Turmeric, Whey (non denatured), Black Cumin,  Garlic,  Glycyrrhizin/Pure Licorice, Wormwood,  chitosan
• Gum Arabic,  Racetams, Vinpocetine, lactobacillus brevis, lactobacillus gasseri, Mutaflor e.coli probiotics (Germany),  symbioflor 2 e.coli probiotics (Germany)
  • E.Coli probiotics was on the top of the KEGG computed probiotics. All of the other suggested were also on the KEGG recommendations.
• Selenium,  Magnesium Most of the B-vitamins but not Vitamin B2 Riboflavin

The detail lists are below

That’s enough for Now

I could start digging into the symptoms and other issues cited above, but with the Long COVID signature being so strong let us not over-engineer. We have a course for the first leg of recovery.

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 a change from the usual microbiome. The microbiome has impact on getting cancers and on the effectiveness of various treatments. A little bit of recent literature is below.

• Colorectal cancer (CRC) is associated with gut microbiota dysbiosis. [2022]
• The role of the bacterial microbiome in the treatment of cancer [2021]
• Role of the Microbiome in Immunotherapy of Melanoma. [2023]
• Defining the Role of the Gut Microbiome in the Pathogenesis and Treatment of Lymphoid Malignancies.[2023]
• Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria. [2023]
• Examining the Role of Microbiota-Centered Interventions in Cancer Therapeutics: Applications for Urothelial Carcinoma. [2023]
• Prospect of bacteria for tumor diagnosis and treatment. [2023]

Analysis

This person is atypical — they find the markers for cancer, but cannot locate where it is.
We see a large number of bacteria with only token representation (0-9 Percentile). Statistically, you would expect each of the ranges below to have similar numbers.

Percentile	Genus	Species
0 – 9	73	91
10 – 19	16	14
20 – 29	14	21
30 – 39	19	20
40 – 49	12	21
50 – 59	16	18
60 – 69	8	23
70 – 79	11	27
80 – 89	33	20
90 – 99	22	32

The new feature “Likely Key Bacteria Causing Above’ show items of concern:

Rank	Bacteria	Importance
genus	Megasphaera	2.6
species	Megasphaera elsdenii	2.5
genus	Klebsiella	2.2
species	Klebsiella oxytoca	2.1
genus	Bifidobacterium	1.9

From the Potential Medical Conditions Detected, we see gut disturbances (Gastroesophageal reflux disease (Gerd) including Barrett’s esophagus, Histamine Issues,Mast Cell Issue, DAO Insufficiency) as well as neurological impacts (Brain Trauma, Epilepsy).

Looking at Bacteria deemed Unhealthy, we have the following with significant counts and percentiles.

Name	Rank	Percentile	Count	Comment	More Info
Collinsella	genus	98	15880	proinflammatory	Citation
Enterobacter	genus	98	12700	Urinary and respiratory infections	Citation
Klebsiella	genus	100	74750	Pathogen	Citation
Parabacteroides merdae	species	94	24150	Infectious bacteria	Citation
Prevotella copri	species	76	1990	Over 70%ile Indicator of mycotoxin present	Citation
Salmonella enterica	species	98	600	Salmonellosis	Citation

The Prevotella copri may indicate a mold/fungi issue in the house, or it could be a side effect of the immune system being impacted by treatment.

Dr. Jason Hawrelak Recommendations is at 89%ile with the main items well out of range being:

• Akkermansia – too low
• Blautia – too high
• Proteobacteria – too high (specifically  Gammaproteobacteria)
• Faecalibacterium prausnitzii – too low

Going Forward

Doing consensus building with following criteria:

•  Standard Lab Ranges (+/- 2 Std Dev) – 21 bacteria
•  Box Plot Whisker – 53 bacteria
•  Kaltoft-Moltrup Normal Ranges – 107 bacteria
• Hand picking all of the bacteria cited above -11 bacteria

The new “just give me suggestions” had the following being clear thumbs up:

• Melatonin
• metronidazole
• NAC
• Gluten Free Diet
• high-protein diet
• low carbohydrate diet
• Aspirin
• Arbutin (polyphenol)
• Fisetin
• Guaiacol (polyphenol)
• Hesperidin
• Luteolin
• Turmeric
•  Ajwain (Indian Herb)
• etc

Remember they are suggestions — just pick items that you can afford, can get, and that you are happy taking.

The list of items to take was actually surprising. It was a large list with all 4 sets of suggestions saying take (over 110!) . The top items are below

• foeniculum vulgare (Fennel)
• Curcumin
• Vitamin B-12
• syzygium aromaticum (clove)
• Hesperidin (polyphenol)
• garlic (allium sativum)
• nigella sativa seed (black cumin)
• Caffeine
• thiamine hydrochloride (vitamin B1)
• oregano (origanum vulgare, oil)
• Arbutin (polyphenol)
• diosmin,(polyphenol)
• pyridoxine hydrochloride (vitamin B6)
• retinoic acid,(Vitamin A derivative)
• thyme (thymol, thyme oil)
• luteolin (flavonoid)
• kefe cumin (laser trilobum l.)
• neem

On the avoid list we have many items which for other people tend to be on their take list

• Many prebiotics ( galacto-oligosaccharides, arabinoxylan oligosaccharides, inulin )
• high fiber diet (oats, resistant starch)

Going over to the Food site, we see the following items near the top: Kidney, marmite, Cream of Wheat. The main reason is that they are high in B vitamins.

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 key item is to realize every antibiotic make different changes, often very different changes. Studies on the U.S. National Library of Medicine document many antibiotics and their changes. We use that information and the Artificial Intelligence Engine (which is not Machine Learning or Chat_GPT like) to compute the substances that will best compensate, as well as substances that may amplify the changes caused by the antibiotic.

Process Is Simple

Go to https://microbiomeprescription.com/Library/ModLookup and enter the name of the antibiotic. The database contains most of the brand names used around the world. Enter the name, for example: amoxicillin. Surround it with % % on each end. Click [Search]

This will take you to a page similar to below

The resulting page is shown below

Clicking on Bacteria Detail will list the bacteria that decreases and those that will increase! Yes, antibiotics will encourage the growth of some bacteria.

Below this are the items that impacts these bacteria, Most items impacts multiple bacteria. Balancing the impact is done by the Artificial Intelligence.

In this taking Vitamin B1 supplements (or foods rich in B1) should be avoid for sometime after finishing the course of antibiotics. Similarly with Hesperidin (polyphenol). You may not know what has it — so just click the food icon 🍱 to see the foods:

Similarly with any To Add items that you are not familiar with, for example: resistant starch,

That is it — Lookup, click suggestions, for anything unfamiliar look for the food icon and just click. Often there is no need to buy supplements when you can get sufficient from food. For example, you get 4.3 grams of resistant starch by eating a 100 grams (3 oz).

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.

I have written about this in the past:

• A mouth full – for better or worst [2014]
• Oral Probiotics [2015]
• Your mouth can trigger flares [2017]
• Science based mouth wash for ME/CFS [2019]
• Probiotics for mouth, sinus and eyes [2019]

When I first started Microbiome Prescription the main and most popular provider was uBiome (dearly departed) which explicitly offered oral microbiome analysis. I had about a dozen uploads. Eventually I stopped support because there was not going to be sufficient uploads, even if I was waited for a decade.

Stomach Acid does not nuke probiotics!

This is a common internet legend which disagrees with both studies and common sense!!!

Common Sense Anyone?

This is the key question: “If you have a bacteria in your gut, how did it get there?”

Assuming that you do not believe that bacteria has perfected teleportation, then there is just one route: Through the mouth, the stomach, etc. It is the great trek!

Studies Supporting No or Little Impact

There are two German probiotic that are suspended in water, added to water and drunk. These studies indicate that they do survive! In fact, they persist!

• Persists: Symbioflor-2 E.Coli
• Symbioflor-1 [2012] Enterococcus faecalis

Looking at Vet Practices, adding probiotic to food or water is well establish. Some sites actually advocates opening capsules. Custom Probiotics advocates all of their probiotics be taken in a glass of water.

Where does this myth come from?

I strongly suspect marketing — if you compare the cost per BCFU from Custom Probiotics to your usual health food store probiotic capsules you will see the costs can be 10x higher in the capsules That is NOT the cost of putting them into capsules. In marketing, claims about the importance of capsules is differentiate product to get you to buy brand X and not Y.

People are also willing to pay for convenience. Buying flour to bake a load of bread is much cheaper than buying a ready made load of bread. At our local coop, a custom loaf of bread was selling for $11.95 — people are lazy.

Vendor Distractor?

I also suspect that stomach acid eliminating probiotic has been used as an excuse by many vendors. The likely cause of probiotics not staying around is where they were sourced: Human or Animal. “In general, their optimal growth temperature ranges between 36–38°C and 41–43°C for human and animal origin strains,” [2011] A probiotic bacteria is unlikely to thrive at a temperature 7°C (or 12°F) from it’s preferred temperature. It will likely reproduce less and be less robust (allowing other bacteria to beat it up).

This comes back to my old soapbox: Buy Only Probiotics where the STRAIN (and not just the species!) is listed – and that specific strain has been researched (Ideally for the condition that concerns you. Use this link to look up most, for example periodontal disease), and that the origin is human. I would suggest constantly emailing the manufacturers!!! It is likely the only way that the situation will improve.

Oral Microbiome Is associated with many conditions

• ” In conclusion, this study suggests significant associations of the Oral Microbiome diversity with certain mental health dimensions such as depressive symptoms and anxiety.” [2023] [2022][2020]
• Oral Microbiota, Its Equilibrium and Implications in the Pathophysiology of Human Diseases: A Systematic Review. [2022]
• Share 
• Profiling the oral microbiomes in patients with Alzheimer‘s disease.[2023]
• Unlocking Modifiable Risk Factors for Alzheimer‘s Disease: Does the Oral Microbiome Hold Some of the Keys? [2023]
• Oral and intestinal dysbiosis in Parkinson‘s disease. [2023]
• Oral and gut dysbiosis leads to functional alterations in Parkinson‘s disease. [2022]
• Changes in Oral Microbial Diversity in a Piglet Model of Traumatic Brain Injury. [2022]
• Fungal Infections Of The Oral Mucosa. [2023]
• Implications of oral streptococcal bacteriophages in autism spectrum disorder.[2022]
• Oral Microbiota Changes Contribute to Autism Spectrum Disorder in Mice.[2022]

My impression is that any condition with a neurological component (i.e. brain fog, impulse control, etc) is likely to have ORAL microbiome dysfunction.

Going Forward

There are many products available, for example, see this list. They will likely contain one or more of the following. For a bigger list, see researched probiotics here: mouth, sinus and oral.

• Bacillus Coagulans
• BLIS K12,
• BLIS M18,
• lactobacillus acidophilus,
• lactobacillus reuteri,
• lactobacillus paracasei,
• lactobacillus salivarius,
• salivarius thermophilus
• Symbioflor-1 [2012] Enterococcus faecalis

The “salivarius” indicate where it was first identified (mouth saliva). So it is normally in the mouth.

The key is for the probiotic to stay in the mouth for sufficient time to dislodge some other residents. To me, this appears to suggest:

• Brush and rinse after every meal
• You could do things like break apart an Oregano Oil capsule or drop Monolaurin flakes into the mouth and hold them there for as long as you can tolerate them…
• Take one or more lozenge afterwards… I would suggest taking one at a time, then perhaps change to a different one when dissolved. There are a few probiotics that are available as pressed pills. If the taste is not too bad, I personally use Miyarisan(jp) [clostridium butyricum] and shin biofermin (jp) [Bifidobacterium bifidum, Enterococcus faecalis, Lactobacillus acidophilus] in this manner. Some others to consider:
  • BioGaia Prodentis Mint Lozenges [Lactobacillus Reuteri]
  • Flora, Super 5 Probiotic Lozenges [Lactobacillus Acidophilus: 60% Bifidobacterium Bifidum: 15% Lactobacillus Bulgaricus: 15% Streptococcus Thermophilus: 5% Lactobacillus Salivarius: 5%]
  • NOW Supplements, OralBiotic™, [Streptococcus salivarius BLIS K12]

The ideal would be to take an oral microbiome test that reports percentile ranking of each bacteria (against other oral samples). I do not know of any one providing that. uBiome likely had that data, but they are no more.

For more Analysis Posts on Long COVID and ME/CFS click here.

Back Story

I’m male, 5’ 10”, currently 145 lbs, 60 years old. I first became ill suddenly in 1987, with what at the time seemed to be food poisoning or a stomach bug. The nausea, stomach upset and loss of appetite lasted months after, I became bedridden. Dozens of tests, doctors, revealed nothing.

Gradually over time, the symptoms subsided and I began to eat and gain weight again. After about a year and a half, I became functional, but never recovered to my previous state. This has been the course of life since. The symptoms would reoccur, last several months, then subside. With no definitive cause for beginning, nor treatment for ending.

The ongoing fatigue over the years was relentless. I somehow managed to complete a 30 year carrier, and took retirement at first opportunity. Doctors speculated that my work was a stress factor responsible for my condition, and retirement would solve it. It didn’t.

For the past several years, I’m mostly housebound, able to go outside and do minor tasks on occasion. Currently, my worst of symptoms are LPR/ reflux related. Not in the traditional sense, mine is a gas/ aero, that I believe is being caused by severe dysbiosis/ imbalance.

I cite this study as an example,

Accompanied with voice loss, throat and chest pain, severe at times.

A recent endoscopy showed “mild gastritis”. Doctors offer me benzodiazepines and antidepressants, stating my symptoms do not correlate with their findings.

Previous endoscopes/ colonoscopies were unremarkable. Gastric empty test normal.

I have tested negative for SIBO several times. IBS Smart test, h pylori, celiac, mast cell (MCAS), all negative.

Numerous diets, eliminations, supplements, herbs, prescribed medications have brought no help or relief. Most have made symptoms worse.

I did manage to have a biopsy taken and sent to Dr John Chia, to test for entero virus. It came back highly positive, however, I am somewhat skeptical that it could be a red herring. My vague attempts with pre/ probiotics resulted with increased gas and/ or diarrhea.

One clue, on two occasions (1995, 2014) after having colonoscopy, I mysteriously had remissions afterwards, that lasted several months. The speculation, is that the prep somehow created a reset of bacteria/ flora. I recently tried to replicate, by doing a prep cleanse. However, despite drinking a full gallon plus, I ran out of solution before being completely cleared out. I felt a brief improvement, but have suffered with horrid lower gas/ flatulence since.

Not the result I was after.

Initial Comments on Back Story

For myself, stress was the trigger of each of my ME/CFS episode so the speculation by his MDs was reasonable. The 1987 event, and the resulting cascade of the microbiome is the root concern. The microbiome evolves, just like society evolves. In 1987, most homes had a VCR and a few lucky people had digital pagers. Today, very few have VCRs (in use) and almost every one has a smart cellular phone. In 2023, arguing whether the right choice should be BetaMax or VHS has become irrelevant. Similarly, focusing on the cause in 1987 is really irrelevant. It may have been a virus, Lyme disease or a dozen other culprits – it is very unlikely to be relevant to addressing today’s microbiome.

Analysis

Looking at the distribution by frequency, we see an over-population of bacteria with low levels.

The Bacteria over 90% and Bacteria under 10% are a simple statistic to understand. If you have 188 different genus and true randomness then you would expect around 19 in each group. We has 12 over 90%, close, but a whopping 61 under 10% — that 32% of all bacteria, not 10%!!! In other words, we have a massive number of different bacteria at low levels. It is not a problem of a few bacteria being too high.

Percentile	Genus	Species
0 – 9	61	76
10 – 19	20	16
20 – 29	14	16
30 – 39	9	8
40 – 49	15	20
50 – 59	14	14
60 – 69	16	20
70 – 79	10	22
80 – 89	17	22
90 – 100	12	21

Looking at Dr. Jason Hawrelak Recommendations for levels, he was at the 99.7%ile and the very few misses for being ideal.. they were border line.. (i.e. 15.1 versus 15; 0 versus 0.0001). In short, almost an ideal microbiome by that criteria.

Going Forward

Doing the usual 3 suggestions sets, we

•  Standard Lab Ranges (+/- 2 Std Dev) – 9 bacteria
•  Box Plot Whisker – 43 bacteria
•  Kaltoft-Moltrup Normal Ranges – 85 bacteria

The list of top suggestions look very close to what I was taking for my own remission (pre-microbiome analysis days).

• rosmarinus officinalis (rosemary)
• thyme (thymol, thyme oil)
• peppermint (spice, oil)
• lactobacillus paracasei (probiotics)
• lemongrass oil
• Human milk oligosaccharides (prebiotic, Holigos, Stachyose)
• neem
• syzygium aromaticum (clove)
• Sumac(Rhus coriaria)
• cinnamon (oil. spice)
• Ajwain (trachyspermum ammi)
• Curcumin
• lactobacillus casei (probiotics)
• thiamine hydrochloride (vitamin B1)
• aloe vera
• ashwagandha (withania somnifera)
• garlic (allium sativum)
• olea europaea (olive leaf)

Looking at the to-avoid

• vsl#3 (probiotics)
• walnuts
• lactulose
• amaranth
• barley, oat
• arabinoxylan oligosaccharides (prebiotic)
• fish oil
• saccharomyces cerevisiae (probiotics)
• low protein diet : typically seen when B-vitamins are wanted.

The full details are below

Going over to the Food Site we see:

• Chicken and Turkey Liver being at the top of the list

mg per 100 grams	Significant amount	Nutrient
25800	Significant	Protein
13.925	Significant	Niacin
12.9	Significant	Iron, Fe
4.293	Significant	Retinol
2.313	Significant	Riboflavin
0.84	Significant	Pyridoxine (Vitamin B6
0.56	Significant	Folic acid
0.02113	Significant	Vitamin B-12

Pass 2 — Looking at Prescription items

One non-prescription showed up near the top, an item that I have used with good effect: monolaurin. The top antibiotics list include:

• piperacillin-tazobactam (antibiotic)s [Penicillin]
• benzylpenicillin sodium (antibiotic) [Penicillin G]
• hyoscyamine (l),(prescription) – “It can treat muscle cramps in the bowels or bladder. it can treat symptoms of irritable bowel syndrome (IBS), colitis, and other digestive problems.” [Src]
• minocycline (antibiotic)s [Tetracycline] – used by many ME/CFS physician, and also by me. It has many good characteristics (neuroprotective, cross body-brain barrier, etc)
• tobramycin (antibiotic)s – usually only used for eye infections
• ampicillin (antibiotic)s [Penicillin]

The above have various risks, and should be review carefully. My own preferences would be minocycline first, then hyoscyamine [because IBS is a factor for this patient]. I should note that using a different algorithm without consensus (Special Reports for your MDs) reports contrary results.

Feedback on Antibiotics

Another freak incident that resulted in a five month remission. In 2011, I had one tonsil that became huge. The other remained completely normal. Doctors were suspect of cancer, and both were removed. Thankfully, it was not cancer. So they didn’t look any further to determine the cause.

But at 49 year old, this was no picnic. Rough surgery and recovery, but it followed with probably the most significant remission of all. It was an amazing turn around, all symptoms backed off, energy returned to nearly normal. After 5 months though, symptoms began to return, and within the year I was back to my previous state

I was on amoxicillin for several weeks after the surgery. When the symptoms began to return, we became suspect that it was the amoxicillin that had done something. My doctor put me back on it, but there was no improvement. Whatever had taken place, was a random-chance occurrence. Maybe the amoxicillin was responsible, by creating a shift in bacteria balance.

I found that Cecil Jadin’s protocol is what I tend to advocate. One of the key reason is that it was it was tuned from many years of clinical experience at the Pasteur Institute for Tropical Medicine for what they termed as an “Occult Rickettsia” infection. The basis of it is rotating different families of antibiotics. The mathematics are simple — first round may eliminate 90% of the issues with 10% being resistant. A different antibiotic usually require a different type of resistance, so 90% of the remaining 10% is eliminated.. leaving just 1%. Doing a third round, takes us down to 0.1%

I speculate that the few survivors from your first round of amoxicillin slowly rebuild . Because these bacteria were the survivors, those with resistance genes. The repopulated gut was largely resistant, hence no effect from this antibiotic later. Think of it as a boxing match. You landed a good punch — but instead of landing more punches, the opponent was able to recover and block the same punch later.

Later, discussion of this story with a well-meaning gastrologist, he had me do a week of xifaxan. He felt certain, based on my story, it would get me back to the previous gains. It made me horrid sick, lasting for weeks after stopping it. There was no improvement.

My preference is not to pick antibiotics by symptoms (or what worked for the prior patient), but from the bacteria results that are desired. Results are not guaranteed — rather, IMHO this approach has higher probability of being successful.

Looking at Probiotics

First, using KEGG data: as is typical for most ME/CFS people (and consistent with the ME/CFS conference reports from 1998): Escherichia coli (Symbioflor-2 or Mutaflor). The next common one is Bacillus subtilis (natto), Clostridium butyricum, Lacticaseibacillus casei, Enterococcus faecalis.

From the consensus list we see a good overlap and have in order:

• lactobacillus paracasei (probiotics)
• lactobacillus casei (probiotics)
• lactobacillus casei shirota (probiotics) – Yakult
• bacillus subtilis natto (probiotics)
• symbioflor 2 e.coli probiotics

bacillus subtilis natto is the source for a supplement called nattokinase, which dissolves fibrin deposits and also an anti-inflammatory [2021]. It is also available not as a probiotic, but in a Japanese Dessert Food called Natto. Natto is an acquired taste.

My probiotic suggestions would be the following (at sufficient dosage, see this page):

• 2 weeks of Bacillus subtilis (perhaps 10 BCFU daily)
• 2 weeks of lactobacillus casei (perhaps 48 BCFU daily)
• 2 weeks of one of the E.Coli probiotics (Mutaflor: 4 capsules per day, starting at 1 and slowly increasing)

Then repeat. Note that some probiotics are strong avoid, for example: saccharomyces cerevisiae / saccharomyces boulardii.

Taking Herbs

There are a large number of herbs cited above. In keeping with my philosophy of avoiding resistance, take some of herbs for 2 weeks and then change to others herbs for the next two weeks. The question is how to take it? I know that some will claim that tinctures are more effective; IMHO, tinctures are very effective for reducing back accounts!

My personal practice is to take herbs in one of two ways:

• Buying them in bulk, organic and making our own 000 capsules. Most store purchased herb capsules do not appear to be organic, often with additional ingredients “to make them better” – which is often marketing hype.
  • We take them immediately prior to meals so that the stomach acid produced to handle the meal, also dissolves the active ingredients from the herbs.
• Taking them as a hot tea. Some herbs are horrible tasting… those tend to end up as capsules.

Many, but not all, herbs have documented dosages with links to studies (which can be informative for how to take). For example: Neem: 120 mg/day, Olive Leaf: 700 mg/day, Curcumin: 3 gm/day. My general rule of thumb is one 000 capsule with each meal.

Questions

Q: Curious to know, do you think there may be an advantage of using this method with probiotics, to deliver past the stomach, farther down the gut?

A: I know this common belief, but have not seen any clinical studies demonstrating it. What I have seen is probiotics delivered as a liquid in water, are documented to persist for weeks after a single dose. That is, the specific strain delivered was not detected before but was detected in subsequent weeks. This indicates that this belief is very questionable. Personally, I tend to use single documented strains of probiotics from Custom Probiotics and follow their directions. I do keep food at least a hour away from taking probiotics so stomach acid production will be quiet.

On a related issue, remember that the gut is downstream from the mouth and nasal passages. The source of bad bacteria may be there and may account for repopulation over time. One probiotic that has been shown effective for the nasal passages etc is Symbioflor-1. There are a few hard tablet probiotics out there (for example, Miyarisan — Clostridium butyricum). I have often just put them in my mouth and let them dissolve there.

NOTE: I will be doing a follow up post on The oral microbiome, coming soon!

This post started out seeking to confirm or debunk the claim located here.

The method was very simple because we have a continuous stream of samples from before COVID, before the COVID vaccination and after the majority of people uploading samples would have been vaccinated. If this massive change is happening then the pre-COVID bifidobacterium count (by lab) would be much higher than the post-COVID vaccination bifidobacterium counts.

My results: there was no statistical significance between the averages

• Pre 2020-01-01: Average Count 20380 on 118 samples, Std Dev 98300
• Post 2022-06-01: Average Count 26111 on 406 samples, Std Dev 72700

That is a 28% increase when a decrease was expected from the above talk.

I am open data, so you can pull the data and check the calculations:

Volatility of Numbers

I was also curious to see if there was any apparent month by month pattern, so I pulled the statistics for biidobacterium, shown below. It is illuminating to a statistician like me, perhaps confusing or concerning to people with poor understanding of statistics (who would expect the numbers from month to month to be similar).

		Thryve			BiomeSight
Year	Month	Average	Std Dev	Obs	Average	Std Dev	Obs
2020	7	32438	131646	24	27929	35826	14
2020	8	25456	43405	21	7683	8948	9
2020	9	13410	19329	17	18501	22566	14
2020	10	84056	148144	18	4370	7390	20
2020	11	18598	34049	9	4926	8197	13
2020	12	10078	17108	16	1841	2718	29
2021	1	68152	172405	20	12436	20675	32
2021	2	101600	163980	30	17289	55509	45
2021	3	57957	103248	17	14482	33774	33
2021	4	21979	42967	30	7700	24436	46
2021	5	24693	51744	56	14257	33608	38
2021	6	28166	84491	39	21465	85762	51
2021	7	47023	105209	39	22620	67229	51
2021	8	60283	82398	43	18427	79784	37
2021	9	62438	92929	28	12002	19635	41
2021	10	13121	29924	24	5922	8565	38
2021	11	11515	27095	57	9996	24966	58
2021	12	28582	80191	17	11498	29919	63
2022	1	15114	28760	38	7076	15149	50
2022	2	24816	59069	32	11707	27202	52
2022	3	10486	23995	33	20243	51539	47
2022	4	10207	21580	57	7916	18288	69
2022	5	33471	82497	80	10304	23719	81
2022	6	23861	60126	53	8053	21994	235
2022	7	26797	109435	40	10709	20439	62
2022	8	67707	132108	60	8085	17190	85
2022	9	13926	17622	28	12635	21332	92
2022	10	9090	14049	45	9627	21171	89
2022	11	10296	19034	39	7293	12150	61
2022	12	3186	6194	21	10887	21390	42
2023	1	10224	18215	41	13302	21612	89
2023	2	10604	22883	52	9103	19781	72
2023	3	65953	78173	30	13566	34256	57

My conclusion is that you need to have two things to get good results:

• All of the samples should be processed by the same lab at the same time. Different batches of reagents may cause different results.
• You need good sample sizes, at least 100+
• You need to be very very careful not to cherry pick data (example below)

An example from Thryve/Ombre data above, with a sample size of 30, the average was 101600. Later a sample size of 21 reported just 3186. Conclusion: going back to school caused family bifidobacterium to tank!

On sample size of 100 issue:

This is an update of my 2016 post: Low Iron – A Gut Bacteria Connection. One key addition is that Vitamin A supplementation may have significant positive impact.

The microbiota shifts the iron sensing of intestinal cells [2016]. “The amount of iron in the diet directly influences the composition of the microbiota. Inversely, the effects of the microbiota on iron homeostasis have been little studied….Commensal organisms (Bacteroides thetaiotaomicron VPI-5482 and Faecalibacterium prausnitzii A2-165) and a probiotic strain (Streptococcus thermophilus LMD-9) led to up to 12-fold induction of ferritin in colon.”

Probiotics to Take

• Probiotic strain Lactobacillus plantarum 299v increases iron absorption from an iron-supplemented fruit drink: a double-isotope cross-over single-blind study in women of reproductive age[ 2015 ].[2017] [2019] [2020] [2021]
• Effects of Lactobacillus casei on Iron Metabolism and Intestinal Microflora in Rats Exposed to Alcohol and Iron.[2022]
• “No significant differences were found between the two yogurts (one with live  cultures and the other without) in terms of their effects on serum iron, AST and ALT levels.” [2013] – so only certain  bacteria are involved. Most lactobacillus do not have an effect [2007]
• Oral administration of Bifidobacterium longum CECT 7347 ameliorates gliadin-induced alterations in liver iron mobilisation [2013].
• “we show that a panel of probiotics are not able to respond to increased iron availability, and identify an isolate of Streptococcus thermophilus NCIMB 41856 that can increase growth rate in response to increased iron availability.” [2011]
• Vitamin A modulates the expression of genes involved in iron bioavailability [2012] [2019]
• Heat-Killed Lactococcus lactis subsp. cremoris H61 Altered the Iron Status of Young Women: A Randomized, Double-Blinded, Placebo-Controlled, Parallel-Group Comparative Study [2022]

Likely No or Negative Effect

• “Bifidobacterium bifidum.. decreased amounts of calcium and iron released from bread.” [2012]
• Probiotics Lactobacillus reuteri DSM 17938 and Lactobacillus casei CRL 431 modestly increase growth, but not iron and zinc status, among Indonesian children aged 1-6 years [2013].
• “we show that a panel of probiotics are not able to respond to increased iron availability, and identify an isolate of Streptococcus thermophilus NCIMB 41856 that can increase growth rate in response to increased iron availability.” [2011]
• Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron [2013]. “Thus, iron availability impacts S. Typhimurium growth, and E. coli Nissle reduces S. Typhimurium intestinal colonization by competing for this limiting nutrient.” – So E.Coli probiotics and iron deficiency may not play well together.
  • ” Intestinal bacteria compete for the essential nutrient iron, leading to replacement of pathogenic Salmonella by the probiotic Escherichia coli Nissle, which is better equipped with iron acquisition systems, and resolution of infectious colitis.” [2013]

This is a person as in this prior set of posts, A Microbiome Trek Continues thru the land of ME/CFS.

There are two key differences that needs to be understood

• Difference in numbers reported (of bacteria and percentiles)
• Will the suggestions change?

Comparison of Results: Thorne to Biomesight

The samples were only a few weeks apart, so similar data. The ratio of bacteria reporting is 6x more for Thorne than Biomesight, so the expectation would be similar shifts for most of the others.

Key Difference: Bacteria Percentiles come from Thorne, the other percentiles are computed against a composite of other samples (until we get sufficient samples). The Conditions, Enzymes and Compound estimates are likely unreliable (we compare against all tests and not other samples from the same procession) and we will ignore in this analysis.

Many of the criteria are identical between tests: Outside Range for JasonH, Medivere, Metagenomics , MyBioma, Nirvana/CosmosId and XenoGene. So for people using those criteria — there is no difference between the tests.

The Bacteria over 90% and Bacteria under 10% are a simple statistic to understand. 10% should be under 10% and 10% above the 90%ile to have a balance microbiome.

With Thorne we have 3226 bacteria and true randomness then you would expect around 322 in each group. We find 239 over 90%, close, but a whopping 1577 under 10% — that 48% of all bacteria, not 10%!!! In other words, we have a massive number of different bacteria at low levels. It is not a problem of a few bacteria being too high (which is a common belief about gut dysfunction), but many only have token amounts.

For Biomesight, we have 503, and thus would expect 50 and 50. For over 90%ile, we have just 25, and for under 10%, 108 bacteria. The high %ile is just 50% of expected and 200% of expected for low with Biomesight; Thorne is just 75% of expected for high, but a massive 489% of expected for low.

Criteria	Thorne Sample	Biomesight
Bacteria Reported By Lab	3226	503
Bacteria Over 99%ile	193	10
Bacteria Over 95%ile	212	18
Bacteria Over 90%ile	239	25
Bacteria Under 10%ile	1577	108
Bacteria Under 5%ile	1411	44
Bacteria Under 1%ile	1106	3
Different Labs – Items Skipped
Pathogens	162	34
Outside Range from JasonH	6	6
Outside Range from Medivere	16	16
Outside Range from Metagenomics	7	7
Outside Range from MyBioma	5	5
Outside Range from Nirvana/CosmosId	17	17
Outside Range from XenoGene	35	35
Outside Lab Range (+/- 1.96SD)	189	8
Outside Box-Plot-Whiskers	685	27
Outside Kaltoft-Moldrup	1753	91
Condition Est. Over 99%ile	6	6
Condition Est. Over 95%ile	15	7
Condition Est. Over 90%ile	24	10
Enzymes Over 99%ile	93	10
Enzymes Over 95%ile	673	118
Enzymes Over 90%ile	1131	647
Enzymes Under 10%ile	312	150
Enzymes Under 5%ile	262	75
Enzymes Under 1%ile	183	12
Compounds Over 99%ile	230	100
Compounds Over 95%ile	498	463
Compounds Over 90%ile	684	606
Compounds Under 10%ile	1350	599
Compounds Under 5%ile	1336	580
Compounds Under 1%ile	1324	569

Comparison of Results: Thorne to Ombre

The Bacteria over 90% and Bacteria under 10% are a simple statistic to understand. If you have 3226 bacteria and true randomness then you would expect around 322 in each group.

• For Ombre we would expect 59 over 90%ile and under 10%ile. close. We have 22 or 37% of expected for low %ile and 117 or 200% of expected for low percentile.

Many of the criteria are identical between tests: Outside Range for JasonH, Medivere, Metagenomics , MyBioma, Nirvana/CosmosId and XenoGene. So for people using those criteria — there is no difference between the tests.

Criteria	Thorne Sample	Ombre
Bacteria Reported By Lab	3226	588
Bacteria Over 99%ile	193	2
Bacteria Over 95%ile	212	10
Bacteria Over 90%ile	239	22
Bacteria Under 10%ile	1577	117
Bacteria Under 5%ile	1411	67
Bacteria Under 1%ile	1106	6
Different Labs – Items Skipped
Pathogens	162	34
Outside Range from JasonH	7	7
Outside Range from Medivere	14	14
Outside Range from Metagenomics	5	5
Outside Range from MyBioma	8	8
Outside Range from Nirvana/CosmosId	18	18
Outside Range from XenoGene	46	46
Outside Lab Range (+/- 1.96SD)	189	5
Outside Box-Plot-Whiskers	685	34
Outside Kaltoft-Moldrup	1753	129
Condition Est. Over 99%ile	6	0
Condition Est. Over 95%ile	15	0
Condition Est. Over 90%ile	24	0
Enzymes Over 99%ile	93	0
Enzymes Over 95%ile	673	9
Enzymes Over 90%ile	1131	101
Enzymes Under 10%ile	312	165
Enzymes Under 5%ile	262	65
Enzymes Under 1%ile	183	2
Compounds Over 99%ile	230	38
Compounds Over 95%ile	498	236
Compounds Over 90%ile	684	332
Compounds Under 10%ile	1350	248
Compounds Under 5%ile	1336	159
Compounds Under 1%ile	1324	33

My personal opinion is that Thorne is better because the more bacteria reported, the greater the statistical significance of over and under representation. On the positive side, all three samples agree on the shifts of bacteria patterns

Analysis

The distribution continues to match a common pattern with ME/CFS microbiomes, an over abundance of low percentile bacteria. This is also seen with the prior Biomesight sample. This shift is made much stronger with Thorne because more genus and species are reported. It also emphasis the shifts seen above.

Percentile	Genus	Species
0 – 9	417	628
10 – 19	85	82
20 – 29	60	85
30 – 39	42	69
40 – 49	34	32
50 – 59	59	339
60 – 69	26	60
70 – 79	16	28
80 – 89	15	31
90 – 99	21	142

Percentile	Genus	Species
0 – 9	24	33
10 – 19	32	37
20 – 29	15	23
30 – 39	9	11
40 – 49	9	16
50 – 59	8	14
60 – 69	8	9
70 – 79	10	17
80 – 89	7	15
90 – 99	6	10

Treatment Dilemma

The usual algorithm is to increase bacteria with low percentiles and decrease those with high percentiles. When you have a huge numbers of low percentile then the question arises: Do you really want to increase these, or do you want to eliminate them entirely to get them off the radar? It is a valid question, but to do that, we have to make increase/eliminate suggestions on 417 genus. That is not practical (given the sparseness of data and limited knowledge of so many genus). My working hypothesis is that keeping to the usual algorithm is the best way to go. Let the bacteria make the determination of winners and losers.

Going Forward

I am going to build two consensus reports. One for Thorne and one for the latest Biomesight, then use the “Uber Consensus” report on the Multiple Samples tab. The purpose is to see whether there are really significant differences in suggestions between the two sample reports.

We are going to do 4 basic suggestions for each:

•  Standard Lab Ranges (+/- 2 Std Dev) Thorne: 53 bacteria,BiomeSight: 8 bacteria
•  Box Plot Whisker Thorne: 86 bacteria,BiomeSight: 21 bacteria
•  Kaltoft-Moltrup Normal Ranges Thorne: 215 bacteria,BiomeSight: 70 bacteria
•  Percentile in top or bottom 10% Thorne: 1508 bacteria,BiomeSight: 130 bacteria

The results had 581 suggestions. I did a Pivot tables of Take Counts against Avoid Counts to visualize the similarities between each set of suggestions going into the uber suggestions. I read the pivot table below as indicating that the suggestions were equivalent with 73 items being to Take with no Avoid, and a further 72 items with just 1 avoid. We have lots of choices in agreement

Counts	Takes
Avoid	0	1	2	3	4	5	6	7	8
0		4	5	16	23	1	1	1	22
1	3	2	3	7	11	6		72
2	3	3	11	10	19	5	29
3	20	6	9	11	5	47
4	15	18	9	4	29	1		1
5	12	10	1	44		1
6	3	2	25			1
7		37
8	13

What are some of the top suggestions?

• bacillus subtilis (probiotics)
• whole-grain barley
• high fiber diet
• Cacao
• noni
• dates
• aspartame (sweetner) — which is always a tricky one to suggest
• Taxifolin
• Sriracha sauce
• wasabi
• Cilantro

As with the prior reports, Escherichia coli probiotics is at the top of the KEGG computed probiotics, typical for ME/CFS. From the consensus, we have:

• bacillus subtilis (probiotics)
• bifidobacterium infantis,(probiotics)
• bifidobacterium pseudocatenulatum,(probiotics)
• clostridium butyricum (probiotics),Miya,Miyarisan
• lactobacillus reuteri (probiotics) – which produces a powerful natural antibiotic, Reuterin
• bifidobacterium pseudocatenulatum li09,bifidobacterium catenulatum li10 (probiotics)

The absence of most Lactobacillus is not surprising because they are hostile to Escherichia Coli. My pivot conference report from 1998 had this bacteria being low in ME/CFS patients. With Thorne, we can get actual numbers (16s numbers for Escherichia Coli are questionable). This person Thorne Results is at the 27%ile for Escherichia and 29%ile for Escherichia Coli, which is consistent with that conference report and the KEGG computation for probiotics.

Out of interest, I looked for the %ile on the Thorne results of the consensus suggested probiotics:

• bacillus subtilis (probiotics) – 66%il1
• bifidobacterium infantis,(probiotics) – 0%ile
• bifidobacterium pseudocatenulatum,(probiotics) – 16 %ile
• clostridium butyricum (probiotics),Miya,Miyarisan – 92%ile
• lactobacillus reuteri (probiotics) – 32%ile

Having the actual percentiles for the strains used in probiotics allows us to tune the suggestions. In this case, we should skip any probiotics with bacillus subtilis or clostridium butyricum. There is no point in taking them. On the other side, you have confirmation that the suggested probiotics are likely to have an impact. I give the Thorne results a big 👍 because you can actually determine the probiotics that you likely not benefit from. The 16s results only report a few probiotic species (with questionable accuracy).

The Extras from the Thorne Results

This person did not see the next data on Thorne’s Web Site — but it was in the data CSV file to upload. The virus count with a few having percentiles. The ones without percentiles are rare ones without data.

And Fungi too!

For both of these sets of data, values over 90% should be researched. Fungi are of special concern because they can both be treated often and may also indicate a mold issue around the person.

User Feedback

Thanks Ken! .. and yikes . Mold is my nemesis. I’ve been trying to figure if I’ve had mold / moldy house for years. I did an ermi for the entire house and got a 2 which is really low. Recently I did an air test all around the house and it was pretty low minus a car which I knew was an issue and I’ve been trying to avoid. I’m trying to decipher if it’s a past issue and I can’t detox or current 

Attached is my air test.

Question: yellow highlights on Thorne. Those were 90%+ , there were some non highlighted 90% + results. Should I only research the ones you highlighted?

I should have a new mold urine test result coming too which I’ll send your way once I get it!

Answers: As a general and very rough rule, count the number of items reported (Virus: 35, Fungi:50). Take this number and multiple by a percentile – say 99%ile, and round up. For Virus and Fungi it is 1. This is the number of false positives that would be expected with 99% or higher.

You appear to have an issue. Your mold test fortunately identifies the genus and where it is located. The HVAC and washing machine hints that it is brought into the house, likely on clothes. The attic appears free of the ones that you are high in. I noticed that Malassezia is not reported in the mold test.

Bottom Line

IMHO, getting a Thorne sample is a definite should do at least once. Why? some of your issues may be fungi or virus related. The difference for suggestions of using Thorne, BiomeSight or Ombre is slight. The differences are reasonable given the sparseness of the data that we have for suggestions.

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.