With regular testing and following suggestions, Hawrelak’s criteria out of range items went from 9 , to 7, to 4. Suggestions appear to work (slowly). This is a follow up of prior posts, the bottom line is that with

• Jan 25,2022 A review of a ME/CFS Microbiome
• Jul 16,2022 Comparing 4 ME/CFS Samples with New Tool

I am going to start with the same comparison as I did in the prior post above, and then move on to do an analysis using the latest tools available.

Why Follow Up Posts are important

The first item is simple, does the model and suggestion appear to work. Everything is theoretically computed, not based on clinical practice or clinical studies. The second item is that these posts encourages people to try suggestions, or to do “self-serve” with the site.

Foreword – 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 appears to 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.

Comparisons between Samples

We have the latest test processed through both Ombre and Biomesight. This analysis will use Ombre because that is what was used in prior; latest one will use Biomesight so we can use the new special studies for suggestions

The high lights are:

• Sample quality is better than the prior samples, we see more bacteria reported
  • Ombre is reporting more (as we saw in a prior post)
• Improvement in the critical bacteria identified by Dr. Jason Hawrelak, we are down to just 4 bacteria outside of range for both (from prior 7 and 9)
• Similar with Medivere, MyBioma,Nirvana/CosmosId, and XenoGene ranges
• On the opposite side, we have more outside of Box-Plot-Whiskers, Lab Range (+/- 1.96SD) and Kaltoft-Moldrup – this is not unexpected because we have a lot more bacteria. The criteria improved are the criteria with a fix set of bacteria that are usually there in most samples.
• The number of extreme enzymes levels (using Ombre) have been significantly reduced. Compounds have no clear shift

Measure	8/22/2022 BIOMESIGHT	8/22/2022 OMBRE	6/15/2022	5/16/2022	3/15/2022	11/21/2021
Lab Read Quality	5	5	4.8	4.8	3.6	4.2
Bacteria Reported By Lab	657	765	515	669	593	473
Bacteria Over 99%ile	0	9	0	1	0	1
Bacteria Over 95%ile	15	45	4	22	21	9
Bacteria Over 90%ile	38	82	22	40	48	21
Bacteria Under 10%ile	168	35	43	112	23	87
Bacteria Under 5%ile	84	16	18	60	5	46
Bacteria Under 1%ile	24	3	0	9	0	2
Lab Read Quality	BiomeSight	Ombre	Ombre	Ombre	Ombre	Ombre
Pathogens	47	43	37	42	38	33
Outside Range from JasonH	4	4	7	7	9	9
Outside Range from Medivere	15	15	17	17	20	20
Outside Range from Metagenomics	8	8	8	8	7	7
Outside Range from MyBioma	4	4	8	8	10	10
Outside Range from Nirvana/CosmosId	20	20	23	23	22	22
Outside Range from XenoGene	4	4	8	8	10	10
Outside Lab Range (+/- 1.96SD)	16	14	2	7	6	2
Outside Box-Plot-Whiskers	135	118	42	71	72	25
Outside Kaltoft-Moldrup	155	209	113	148	143	91
Condition Est. Over 99%ile	0	0	0	0	0	0
Condition Est. Over 95%ile	0	0	0	0	0	0
Condition Est. Over 90%ile	0	0	0	0	1	0
Enzymes Over 99%ile	2	8	91	48	53	5
Enzymes Over 95%ile	48	78	599	305	182	147
Enzymes Over 90%ile	99	154	719	629	438	458
Enzymes Under 10%ile	175	75	70	71	38	169
Enzymes Under 5%ile	101	33	19	28	4	78
Enzymes Under 1%ile	20	3	2	0	0	0
Compounds Over 99%ile	31	36	6	93	143	19
Compounds Over 95%ile	131	265	186	277	190	89
Compounds Over 90%ile	371	380	303	435	220	118
Compounds Under 10%ile	212	282	321	528	333	133
Compounds Under 5%ile	54	186	195	378	310	100
Compounds Under 1%ile	23	62	0	118	267	42

The data suggests further improvement with the latest sample — in terms of numbers, dramatic!

Going Forward

We are going to use the Special Studies to generate the next set of suggestions. Remember that the numbers below are sensitive to the number of bacteria detected (i.e. lab quality). The latest sample had the highest quality which means that percentages may increase due to that alone.

	Percentage Matches	8/22/2022	7/21/2022	4/20/2022	2/22/2022	11/22/2021
1	Alcohol intolerance or Medication sensitivities	52	34	36	36	39
1	Allergic Rhinitis (Hay Fever)	33	31	35	35	36
0	Allergies And Food Sensitivity	30	32	32	32	34
0	Autism	38	28	31	31	44
1	Bloating	24	22	24	24	32
2	Brain Fog	28	32	39	39	26
2	Chronic Fatigue Syndrome (CFS/ME)	33	30	28	28	30
0	Cold Extremities	31	36	29	29	31
0	Constipation	17	18	15	15	29
2?	COVID19 (Long Hauler)	39	36	31	31	39
0	Depression	40	30	33	33	35
0	Easily irritated	28	31	24	24	27
2	General Fatigue	26	26	28	28	28
1	High Anxiety	28	26	25	25	26
1	Histamine or Mast Cell issues	28	24	27	27	32
0	Inflammatory bowel disease	43	48	28	38	43
0	irritable bowel syndrome	31	30	26	26	36
1	Intolerance of Extremes of Heat and Cold	32	30	24	24	36
0	ME/CFS with IBS	31	24	24	24	27
2	ME/CFS without IBS	30	25	23	23	28
0	Poor Gut Motility	25	37	31	31	35
2	Post-exertional malaise	22	24	23	23	26
0	SIBO	38	36	27	27	34
0	Tinnitus (ringing in ear)	32	34	24	24	28
2	Unrefreshed sleep	37	27	26	26	29

What surprised me, and delighted me, was the relative consistency of the numbers for the same person over time for many symptoms. This time, because of the special studies, we are going to focus on generating suggestions specific to the issues of greatest concerns (2) above.

• Brain Fog
• Chronic Fatigue Syndrome (CFS/ME)
• COVID19 (Long Hauler)
• General Fatigue
• ME/CFS without IBS
• Post-exertional malaise
• Unrefreshed sleep

Having high IBS or IBD values does not equate to ME/CFS with IBS — prior to my latter flares, I saw no gut issues at all.

The top Items are similar to each other:

• Pulses (Black Beans,Broad Beans,dry beans, dry broad beans, dry peas, chickpeas, cow peas, pigeon peas, lentils, Bambara beans, vetches, lupins), navy bean, pea (fiber, protein)
• symbioflor 2 e.coli probiotics,colinfant e.coli probiotics and d-ribose (which feeds e.coli)
• arabinoxylan oligosaccharides (prebiotic)
• lactulose
• green-lipped mussel
• levan
• fasting
• galacto-oligosaccharides (prebiotic)
• non-starch polysaccharides
• carob
• raffinose(sugar beet)
• wheat bran
• barley,oat
• sesame cake/meal
• Reduce choline (Beef, Chicken Eggs)

The top of the avoid list are many B-Vitamins. In prior posts, I speculated that the low vitamin B-levels seen in the blood of ME/CFS patients etc is because of greedy gut bacteria that prevents it being absorbed. I just did some literature browsing and this speculation appears to agree with some research.

Now, Wexler et al. show that some gut microbes may be able to pirate vitamin B12 from us as it passes through the digestive tract. Wexler et al. showed that a protein called BtuG on the surface of a type of gut bacteria called Bacteriodes grabs onto vitamin B12 with extraordinary strength. In fact, these bacterial proteins bind to vitamin B12 so strongly that they can even pry it away from our own vitamin B12 collecting protein.

Human gut Bacteroides capture vitamin B₁₂ via cell surface-exposed lipoproteins [2018]

This means that to avoid B-vitamins via food or supplements, despite having low blood level may be a rational approach. Getting Vitamin-B injections bypassing the gut bacteria may be a more effective approach to dealing with low vitamin-B. Choline is connected with B-Vitamins, see The B Vitamins and Choline: Overview and Methods [1998], hence the reduce choline suggestion above.

Probiotics

Escherichia coli was the top probiotic on the consensus. Using Ombre reading of the sample and the Kyoto Encyclopedia of Genes and Genomes, Escherichia coli is the top suggestion with items like Bacillus subtilis being 1/3 of contribution. The same results appear with the BiomeSight processing.

For flavonoids and polyphenols — it seems that supplementing with any should be avoided. The very few with a positive value has ‘equivalents’ being negative values. For amino acids: Conjugated Linoleic Acid, l-citrulline and proline (amino acid) are the top choices. Diet choices are low animal protein (which agrees with avoiding b-vitamins) and high fiber (which agrees with pulses above)

Bottom Line

Remember, these are not generic suggestion for anybody with ME/CFS. These are specific to this person’s microbiome. We see that the numbers for his microbiome has improved, but some items are still of concern. Our method of getting suggestions shifted over to using the Special Studies because he had a number of symptoms that were significant which were covered by the special studies, as well as his data being processed thru BiomeSight which we are using for special studies (apples to apples comparisons).

Again, the computations are based on the odds of items helping the microbiome to shift in the desired direction. Odds are just that, some will work, some will not — but ideally more will work than not. For the suggestions, remember ROTATION (Rotation — Essential for Changing the Microbiome), and pick items that work for you and your medical professional. The suggestions can be viewed as a series of dresses on a rack, you do not need to buy all of them to be fashionable. Use the ones that work for you.