lassesen 9:27 am on December 10, 2023
Tags: CFS, Chronic Fatigue Syndrome ( 4 ), chronic-fatigue ( 2 ), chronic-illness ( 4 ), fatigue, health ( 9 ), long-covid ( 2 )

Review of Recent ME/CFS Research, Dec 2023

The vast majority of papers were repeats of prior research (earlier research was in 1992 for some topics). The following were more interesting:

Understanding, diagnosing, and treating Myalgic encephalomyelitis/chronic fatigue syndrome – State of the art: Report of the 2nd international meeting at the Charité Fatigue Center [2023]
An Explainable Artificial Intelligence Model Proposed for the Prediction of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and the Identification of Distinctive Metabolites [2023]
- “The metabolomics of C-glycosyltryptophan, oleoylcholine, cortisone, and 3-hydroxydecanoate were determined to be crucial for ME/CFS diagnosis.”
- The items identified are associated with other conditions too (see links). Prediction is not treatment.
DNA Methylation Changes in Blood Cells of Fibromyalgia and Chronic Fatigue Syndrome Patients [2023]
- “Methylomes of the blood cells of patients with FM and CFS in three independent studies have shown methylation changes that appear to be implicated in the pathogenesis of these syndromes.”
- Well known, see MEPedia, treatment based on this hypothesis has not been effective for most
Myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes [2023]
People with Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Exhibit Similarly Impaired Vascular Function [2023]
- ” both long COVID and ME/CFS patients exhibit similarly impaired endothelial function, indicating potential vascular involvement in the pathogenesis of these post-viral illnesses. The significant reduction in flow-mediated dilation values suggests an increased cardiovascular risk”
Increased gut permeability and bacterial translocation are associated with fibromyalgia and myalgic encephalomyelitis/chronic fatigue syndrome: implications for disease-related biomarker discovery [2023]
- “Biomarkers of intestinal barrier function and inflammation were associated with autonomic dysfunction assessed by COMPASS-31 scores in FM and ME/CFS respectively. Anti-β-LGB antibodies, ZO-1, LPS, and sCD14 may be putative predictors of intestinal barrier dysfunction in these cohorts.”
- Well known from prior studies, causality not explored.
Brain-regional characteristics and neuroinflammation in ME/CFS patients from neuroimaging: A systematic review and meta-analysis [2023]
- “Regional alterations were most frequently identified in the cerebral cortex, with a notable focus on the frontal cortex. However, our meta-analysis data revealed a significant hypoactivity in the insular and thalamic regions, contrary to observed frequencies. These abnormalities, occurring in pivotal network hubs bridging reason and emotion, disrupt connections with the limbic system, contributing to the hallmark symptoms of ME/CFS.”
- This is a repeat of prior research going back to 1992
Many studies with “Some patients …” with specific abnormalities
A Quick and Practical Approach to Secure a Chronic Fatigue Syndrome Diagnosis: The Novel Functional Limitation Index [2023]
- “The Functional Limitation Index (FLI) could provide an easy and accurate diagnosis of this condition in both genders in a one-day assessment.”
Effects of traditional Chinese mind-body exercises for patients with chronic fatigue syndrome: A systematic review and meta-analysis[2023]
- “In patients with CFS, TCME probably reduces post-intervention fatigue, depression, and anxiety and may improve sleep quality and mental function compared with passive control, but has limited long-term effects. “
Frontiers in chronic fatigue syndrome research: An analysis of the top 100 most influential articles in the field [2023]
- “The prospective research directions in this field include the search for biological markers, with a particular focus on immunology; the advancement of diagnostic techniques; the screening of risk genes associated with CFS; and the conduct of epidemiological investigations.”
- So treatment does not seem to be an active dimension.
Onset Factors:
- Increased risk of chronic fatigue syndrome following infection: a 17-year population-based cohort study [2023]
  - “infection with common pathogens, including bacteria, viruses, is associated with an increased risk of developing CFS.”
  - This matches my model that ME/CFS is a post-infection persistent microbiome dysfunction.
- Genetic risk factors for severe and fatigue dominant long COVID and commonalities with ME/CFS identified by combinatorial analysis [2023]
  - Genetics have long been identified as a factor
- Typing myalgic encephalomyelitis by infection at onset: A DecodeME study [2023]
- There is an overlap between long covid and ME/CFS.[2023]
Is there a role for traditional and complementary medicines in managing chronic fatigue? a systematic review of randomized controlled trials [2023]
- “recommendations of T&CMs in treating CFS remain inconclusive. To develop better quality evidence about T&CMs for CFS, future studies should employ more objective diagnosis standards and outcome measurements, larger sample size, and better bias control, and ensure the compliance with the corresponding reporting guidelines”
- I have seen this constantly in studies: too small sample size, poor statistical analysis, spinning results to “find something”.
Treatment:
- Successful treatment of myalgic encephalomyelitis/chronic fatigue syndrome using hydrogen gas: four case reports [2023]
  - “In conclusion, since this was a case study based on self-assessments by a small number of patients and not a clinical study”
  - Hydrogen is a gas used by bacteria (illustrated by SIBO testing for Hydrogen), this approach is likely to influence the microbiome. Looking at the data on Microbiome Prescription, we found that ME/CFS patients microbiome has a significantly higher consumption of Hydrogen — thus the extra hydrogen may alter the microbiome.
- B-vitamins, related vitamers, and metabolites in patients with quiescent inflammatory bowel disease and chronic fatigue treated with high dose oral thiamine [2023]
  - Glucan (or foods containing it: Barley etc) is a very frequent suggestion from Microbiome Prescription when a ME/CFS microbiome was processed through microbiome prescription.
- Repetitive transcranial magnetic stimulation ameliorates symptoms in patients with myalgic encephalomyelitis (chronic fatigue syndrome) [2023]
  - Some symptoms improved: “orthostatic intolerance with the inability to complete the 10-min standing test was resolved in 10 (83%) out of 12 patients, and disequilibrium was resolved in 15 (88%) out of 17 patients. “
- Yeast Beta-Glucan Supplementation with Multivitamins Attenuates Cognitive Impairments in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Randomized, Double-Blind, Placebo-Controlled Trial [2023]
  - Beta-Glucan (or foods containing it: Barley etc) is a very frequent suggestion from Microbiome Prescription when a ME/CFS microbiome was processed through microbiome prescription.
  - “significantly improved cognitive fatigue (assessed with FIS-40 scores) after the 36-week treatment

lassesen 7:25 am on December 10, 2023
Tags: CFS, Chronic Fatigue Syndrome ( 4 ), chronic-illness ( 4 ), chronic-pain ( 4 ), Fibromyalgia ( 2 ), health ( 9 ), journey-to-wellness

The Remission Biome Project: Tess Falor

For more information on this project see Health Rising post. Both participants has granted me to do a review with their real names. For information about Tess see the Wired Story: How Chronic Illness Patients Are ‘Hacking’ Their Wearables (See Objective evidence — the smart watch dimension for my take). This is the first of a series of posts on this project.

The earliest use of antibiotics for treating ME/CFS that I am aware of, dates from the late 1990’s with articles in Journal of Chronic Fatigue Syndrome (and conference reports prior)

My remission from ME/CFS was done by combining C.L. Jadin protocol with Dave Berg anticoagulant protocol.

Overview of results

First, let us show the numbers and then talk about them. It is clear that there are significant changes. There are a lot of dimensions to consider.

Criteria	2-Mar	9-Mar	21-Mar	3-Apr	16-Jun
Shannon Diversity Index (Percentile)	85.2	79.0	99.8	72.4	16.0
Simpson Diversity Index (Percentile)	72.6	63.4	64.4	77.0	91.4
Chao1 Index (Percentile)	65.7	31.2	77.2	62.9	7.9
Lab Read Quality	8.9	8.7	6	4.5	4.4
Bacteria Reported By Lab	654	533	725	585	389
Bacteria Over 99%ile	2	4	30	11	24
Bacteria Over 95%ile	13	10	70	33	38
Bacteria Over 90%ile	25	23	103	63	55
Bacteria Under 10%ile	287	213	123	113	140
Bacteria Under 5%ile	253	173	66	48	96
Bacteria Under 1%ile	219	135	17	8	46
Lab: BiomeSight
Rarely Seen 1%	13	1	38	5	6
Rarely Seen 5%	28	9	107	17	29
Pathogens	36	31	50	40	36
Outside Range from JasonH	6	6	9	9	8
Outside Range from Medivere	15	15	22	22	22
Outside Range from Metagenomics	7	7	9	9	9
Outside Range from MyBioma	5	5	6	6	6
Outside Range from Nirvana/CosmosId	26	26	18	18	15
Outside Range from XenoGene	28	28	46	46	42
Outside Lab Range (+/- 1.96SD)	6	8	56	17	27
Outside Box-Plot-Whiskers	44	36	124	70	67
Outside Kaltoft-Moldrup	233	169	207	137	170
Condition Est. Over 99%ile	0	0	13	10	48
Condition Est. Over 95%ile	1	0	24	35	75
Condition Est. Over 90%ile	2	2	34	55	84
Enzymes Over 99%ile	0	0	347	606	957
Enzymes Over 95%ile	7	0	635	970	1145
Enzymes Over 90%ile	24	28	746	1159	1228
Enzymes Under 10%ile	506	515	561	237	245
Enzymes Under 5%ile	378	360	422	143	174
Enzymes Under 1%ile	194	166	120	52	94
Compounds Over 99%ile	0	0	225	215	617
Compounds Over 95%ile	2	0	355	410	732
Compounds Over 90%ile	8	11	441	520	778
Compounds Under 10%ile	1243	986	1105	902	822
Compounds Under 5%ile	1156	926	1032	856	796
Compounds Under 1%ile	1115	875	936	828	767

Next are the percentages by percentile which I noticed tend to have over representation with ME/CFS and Long COVID in the 0-9 percentile. We see this pattern at the start, with improvement and then a bounce back to high numbers.

	2-Mar	2-Mar	9-Mar	9-Mar	21-Mar	21-Mar	3-Apr	3-Apr	16-Jun	16-Jun
Percentile	Genus	%	Genus	%	Genus	%	Genus	%	Genus	%
0 – 9	65	40%	51	36%	28	15%	29	19%	35	36%
10-19	13	8%	16	11%	36	19%	23	15%	9	9%
20 – 29	11	7%	16	11%	20	11%	23	15%	14	14%
30 – 39	5	3%	9	6%	17	9%	17	11%	4	4%
40 – 49	13	8%	10	7%	14	8%	11	7%	5	5%
50 – 59	12	7%	8	6%	10	5%	8	5%	3	3%
60 – 69	12	7%	9	6%	6	3%	14	9%	1	1%
70 – 79	12	7%	3	2%	10	5%	6	4%	5	5%
80 – 89	10	6%	10	7%	15	8%	9	6%	7	7%
90 – 99	11	7%	8	6%	30	16%	15	10%	15	15%
Total	164		140		186		155		98

	2-Mar	2-Mar	9-Mar	9-Mar	21-Mar	21-Mar	3-Apr	3-Apr	16-Jun	16-Jun
Percentile	%	Species	%	Species	%	Species	%	Species	%	Species
0 – 9	41%	94	43%	79	13%	40	17%	36	21%	31
10-19	6%	14	9%	16	15%	44	13%	28	9%	13
20 – 29	8%	18	9%	16	13%	39	12%	27	15%	22
30 – 39	3%	7	5%	10	10%	29	10%	22	8%	11
40 – 49	7%	17	4%	7	7%	20	8%	17	6%	9
50 – 59	9%	21	5%	9	7%	22	6%	12	5%	7
60 – 69	6%	14	8%	14	3%	10	6%	14	6%	9
70 – 79	8%	18	4%	7	6%	19	7%	15	6%	9
80 – 89	6%	13	8%	15	8%	23	8%	17	10%	14
90 – 99	5%	12	6%	11	19%	57	13%	29	14%	21
Total		228		184		303		217		146

The Events Around the above Samples

2023-03-02 (baseline)
2023-03-09 (during a stomach bug)
2023-03-21 (during a “Level 1” remission while taking Amoxiclav. Level 1 = all symptoms gone. Felt great. Had started Amoxiclav on the morning of 3/20, this sample was taken after 3 doses around 3pm)
2023-04-03 (4 days after stopping Amoxiclav, was on Doxycycline)
2023-06-16 (During 2nd round of Amoxiclav when I felt really bad)

The microbiome results definitely reflected the Level 1 remission on 3-21. The low percentile genus and species percentage almost made it to the target level of 10% from the prior 40%! The Shannon Diversity Index was awesome (the higher the better!).

I have often described correcting the microbiome as being similar to sailing a sailboat along a coast line. Depending on wind and tide, there may be a lot of course changes required. I am curious on the ranking of Amoxiclav[amoxicillin] and Doxycycline with these samples. The numbers below suggests that going on to Doxycycline may have been a poor choice. On the 2nd round of Amoxiclav, it was at just 35% of the highest value recommendation versus 70% on the 1st round.

Criteria	2-Mar	9-Mar	21-Mar	3-Apr	16-Jun
Amoxicillin	280	159	210	560	384
Doxycycline	3.7	67	260	-27	-141
Highest	402	354	1010	912	1050
Best Antibioitic	rifaximin	triclosan	rifampicin	imipenem	imipenem

Note that rifaximin and rifampicin are in the same family and used by some ME/CFS specialists. Imipenem shows up often with ME/CFS samples — but since it is intravenous, not the easiest to get on an ongoing basis.

Take Away and Reflections

This project main purpose was to show that remission can be triggered by antibiotics to another generation of people suffering from ME/CFS. The remission on 21-Mar demonstrates this to be correct both subjectively and objectively (Microbiome data — specifically Shannon Diversity Index and Percentages in different percentiles for Species and Genus). I should emphasis that both of these measures are multi-bacteria measures and do not support the common myth that ME/CFS is caused by a single bacteria.

The critical issue is maintaining remission. How do keep the microbiome where it should be. I often use analogies of cities because we are talking about a city of bacteria. To stop riots and looting in the streets you send in the National Guard (antibiotic). The city is back to normal. The causes of the the riots are still there. Typically lack of opportunities, neglect, etc. in these same ghettos. You must address these other issues. A repeat of sending in the National Guard may have the same effect as the first time OR very different effects – the same can be said for using the same antibiotics.

With bacteria we have two “radical organizations in the ghetto” — The Antibiotic resistant and the Resistors. For example, the bacteria that survive learnt how to avoid the National Guard and proceed to share that skill to other bacteria. Instead of a wall of shields pushing the rioters back, Molotov cocktails rain down on the troops from above.

Another analogy is that the gut is a pendulum. The antibiotics, probiotics and other items pushes the gut towards the equilibrium position! There is great joy! The gut is centered… At this point, many people go down the wrong reasoning path — “Keep doing more of the same to stay in remission!“. Remission is lost and the momentum pushes the guts out to the other side!!! You pushed out one devil and seven more devils return! (Math 12:43-45)

The key is to dampen down the swing so there is less and less swing. My personal opinion is that Cecile Jadin’s protocol using antibiotics for only 7 days each month is a very effective way of dampening the pendulum gained from decades of experience.

My approach with Microbiome Prescription is to try to address the whole city. Before taking action, we get intelligence on the nature of the city and decide on the appropriate action for a period of time (typically 4-10 weeks). We then update our intelligence (i.e. microbiome test) and pick the next course of action. Actions may include “food kitchens”, “safe injection sites”, “training programs”, “home repairs”, “on the beat policing”, etc.

There are many people who will state that antibiotics gave me ME/CFS. I do not disagree. Antibiotics can also trigger remission — the problem is WHICH antibiotics. Since every person’s microbiome is unique, there can be no universal “best antibiotic” for ME/CFS. Antibiotics must be selected based on the individuals microbiome (which is the path that Microbiome Prescription took) for the best odds of making the right choice.

My Suggestions Going Forward

I am working with C.L. Jadin, M.D., on documenting her current protocol from almost 30 years of experience using antibiotics for ME/CFS. It will be out soon. I am hoping to have that available within a month. One key aspect of her protocol has been pulsing antibiotics using two at a time. There are a few studies showing that pulsing is more effective. Pulsing often means 7 days on and 21 days off.

Looking at Tess’s last sample, I would propose the following to be considered (items that I picked from the consensus suggestions):

Take a 3 week break from antibiotics (Ideally at the end take another sample)
Do a single course of gentamicin or ciprofloxacin
Take the following probiotics (rotating them every week)
- lactobacillus reuteri (at least 10 BCFU/day)
- clostridium butyricum AKA Miyarisan (500-1000 mg/day)
Take the following herbs
Have barley porridge with walnuts each day

In terms of things to stop (if doing)

Use the Dosages for Supplements for guidance on dosages!

The Human Behavior Problem

A common pattern of people is “Just give me a pill to fix me, I want to keep my current life style and I am not prepared to make significant life style and diet changes”. My impression is that making those changes is often required. Inertia is a real maintainer of ME/CFS, especially the pendulum inertia when trying to heal.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I can compute items to take, those computations do not provide information on rotations etc.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

lassesen 7:24 am on December 10, 2023
Tags: CFS, Chronic Fatigue Syndrome ( 4 ), chronic-illness ( 4 ), chronic-pain ( 4 ), Fibromyalgia ( 2 ), health ( 9 ), long-covid ( 2 )

The Remission Biome Project: Tamara Romanuk

For more information on this project see Health Rising post. Both participants has granted me to do a review with their real names. This is the second of a series of posts on this project, the first one was on The Remission Biome Project: Tess Falor.

Connected with review, you may wish to read Dr. Jadin’s Current Protocol for ME/CFS – Microbiome Prescription Blog, parts are being consider for incorporation into the Remission Biome Projects

The earliest use of antibiotics for treating ME/CFS that I am aware of, dates from the late 1990’s with articles in Journal of Chronic Fatigue Syndrome (and conference reports prior)

My remission from ME/CFS was done by combining C.L. Jadin protocol with Dave Berg anticoagulant protocol.

A big thanks to BiomeSight.com for donating some testing kits to the project. If interested in using their kits, there is a discount code (“micro”).

Overview of results

First, let us show the numbers and then talk about them. It is clear that there are significant changes. There are a lot of dimensions to consider. Some highlights:

The number of bacteria with abnormally high representation has gone from 123 down to 29
The number of bacteria with abnormally low representation has gone from 222, dropping down to as low as 19, before rebounding to 162 (still better than the start)
Most measure showed great improvement and then some relapse.

Criteria	7-Mar	23-Mar	15-Apr	22-Apr	29-Apr
Shannon Diversity Index	33.8	78.0	97.1	76.5	77.1
Simpson Diversity Index	0.7	65.1	58.6	60.3	73.4
Chao1 Index	91.3	61.6	72.0	89.4	14.8
Chi-Square (Lower is better)	55	47	46	50	30
Lab Read Quality	8.6	7.1	5.4	2.2	6.9
Bacteria Reported By Lab	755	638	628	765	461
Bacteria Over 99%ile	27	11	13	56	5
Bacteria Over 95%ile	72	25	30	105	18
Bacteria Over 90%ile	132	46	63	178	29
Bacteria Under 10%ile	222	218	62	19	162
Bacteria Under 5%ile	191	195	18	12	144
Bacteria Under 1%ile	177	179	0	3	112
Lab: BiomeSight
Rarely Seen 1%	8	4	3	66	2
Rarely Seen 5%	22	24	27	128	14
Pathogens	39	32	33	31	29
Outside Range from JasonH	8	8	8	8	8
Outside Range from Medivere	18	18	16	16	16
Outside Range from Metagenomics	9	9	6	6	6
Outside Range from MyBioma	10	10	6	6	6
Outside Range from Nirvana/CosmosId	18	18	12	12	12
Outside Range from XenoGene	52	52	39	39	39
Outside Lab Range (+/- 1.96SD)	43	15	17	36	7
Outside Box-Plot-Whiskers	146	51	83	227	43
Outside Kaltoft-Moldrup	251	189	105	212	158
Condition Est. Over 99%ile	1	5	0	0	3
Condition Est. Over 95%ile	2	14	0	5	13
Condition Est. Over 90%ile	11	28	2	11	21
Enzymes Over 99%ile	7	68	5	19	37
Enzymes Over 95%ile	22	281	209	123	250
Enzymes Over 90%ile	58	435	361	317	409
Enzymes Under 10%ile	219	354	59	48	201
Enzymes Under 5%ile	173	265	34	24	144
Enzymes Under 1%ile	138	94	13	12	79
Compounds Over 99%ile	3	44	1	13	16
Compounds Over 95%ile	15	186	82	68	87
Compounds Over 90%ile	27	297	154	153	183
Compounds Under 10%ile	882	889	985	987	875
Compounds Under 5%ile	862	859	959	963	841
Compounds Under 1%ile	845	802	935	952	820

As with Tess, the percentages by percentile which I noticed tend to have over representation with ME/CFS and Long COVID in the 0-9 percentile. We see this pattern at the start, with improvement and then a bounce back to high numbers in the last sample

Tamara suggested that I convert the tables below to charts. Both are now available on the site.

Pretty Pictures

Tamara suggested that I convert the tables below to charts. Both are now available on the site.

First, an old sample that she happened to have where we see Chi-Square at 6. The first of the recent samples had it jumping to 55, A normal microbiome is expected to have a Chi-square < 13. A higher value indicates a statistically significant, abnormal microbiome.

The next three show the changes with antibiotics. Chi-square went from 46 to 50 with a dramatic shift and then drifted down to 30.

The latest sample increased upward again, with the pronounced spikes that are common with ME/CFS being there.

The raw numbers are also shown. I will spare your eyes by omitting them.

The Events Around the above Samples

7 Mar – Before
23 Mar – Day 4 AmoxClav
15 Apr – More
22 Apr – Final Day of AmoxClav (30 days of AC)
- This sample has a low Lab Read Quality, this may account for the number of spikes in its report.
29 April – After 3 days of Aprepitant + Erythromycin (this was a BIG difference from Tess and was the intervention that seemed to give me the baseline increase this time).

As with Tess, let us see how these items rank in each sample. As with Tess, imipenem is the most common best suggestion.

Criteria	7-Mar	23-Mar	15-Apr	22-Apr	29-Apr	22-May
Amoxicillin	-104	95	276	296	432	402
Erythromycin	59	253	340	236	222	228
Aprepitant	393	297	260	320	280	80
Highest	632	497	635	610	650	594
	cefaclor hydrate	imipenem	imipenem	imipenem	cefoxitin	cefoxitin

Going Forward

As a result of a conference call with some of the Remission Biome Project, and Dr. Jadin’s Current Protocol for ME/CFS. I annotated all of the antibiotics used in studies for ME/CFS, Lyme, and related conditions with [CFS]. This allows us to quickly see the “consensus” antibiotics (i.e. used in studies and suggested by microbiome prescription algorithms).

The top ones are shown before (Just enter “CFS” in the Search dialog)

Only two of these were negative for her (doxycycline and ampicillin) with docycline sibling, minocycline being just 21).

I would suggest using this list to pick 2 antibiotics to do a one week course and then take a 3 week break. After the course, then do some of these probiotics. I am inclined to omit L.Casei because the strain used in Yakult is a negative. Thus we end up with these three as top suggestions. P.S.

bacillus subtilis (probiotics) : 342 @ 1 – 10 BCFU/day
bifidobacterium breve (probiotic) :328 @ 2-15 BCFU/day
bifidobacterium infantis,(probiotics): 292 @ 1 – 10 BCFU/day

Note the weight of these are above many of the antibiotics above. I usually advocate single species. The Bifido is available from Custom Probiotics with their recommended dosages above the amount listed above.

Part Deux — More Samples!

Her description of subjective changes: generally keep improving in terms of PEM, function etc. (was definitely a dip around the 2nd ‘constipation’ sample)

1st, [2023-06-14] in the series just a temporal sample, no additional treatments
2nd, [2023-07-15] in the series I had a major episode of constipation – wanted to catch that
3rd, [2023-07-20]last one was was post my 2nd treatment of aprepitant+erythromycin

Sample Comparison

We include the prior one above for easy reference). The key change items are:

The new Anti inflammatory Bacteria Score has seen a dramatic increase from 17%ile to 73%ile. The four prior samples were 7.6%ile, 8.2%ile, 3.9%ile and 6.9%ile
Outside Kaltoft-Moldrup is dropping. In terms of %age of reported: 32% -> 28% -> 29% ->16%
The high and low Enzymes also seem to be dropping
The last sample had a Chi-Square of 9, that is a probability of 0.54 instead of the .9999999… for all other samples. Unfortunately, the poor read quality makes this fuzzy.
Note: The last sample has a low read quality (thus less bacteria types are being reported)

Criteria	22-May	14-Jun	15-Jul	22-Jul
Shannon Diversity Index	69.4	29.20	43.00	15.00
Simpson Diversity Index	54.7	7.60	27.50	60.00
Chao1 Index	72.4	0.87	21.40	8.30
Anti inflammatory Bacteria Score	17.0	30.90	43.60	73.20
Chi-Square Score	49	51	32	9
Lab Read Quality	7.2	10.9	6.6	2.3
Bacteria Reported By Lab	659	752	512	375
Bacteria Over 99%ile	10	12	1	4
Bacteria Over 95%ile	22	24	2	20
Bacteria Over 90%ile	45	41	13	39
Bacteria Under 10%ile	199	229	189	19
Bacteria Under 5%ile	186	208	184	3
Bacteria Under 1%ile	167	165	166	0
Lab: BiomeSight
Rarely Seen 1%	25	13	0	0
Rarely Seen 5%	49	37	7	1
Pathogens	32	34	36	21
Outside Range from JasonH	4	7	7	4
Outside Range from Medivere	14	19	19	14
Outside Range from Metagenomics	6	7	7	6
Outside Range from MyBioma	4	6	6	4
Outside Range from Nirvana/CosmosId	18	19	19	18
Outside Range from XenoGene	33	34	34	33
Outside Lab Range (+/- 1.96SD)	11	12	1	13
Outside Box-Plot-Whiskers	56	75	23	50
Outside Kaltoft-Moldrup	209	212	150	61
Condition Est. Over 99%ile	0	0	1	0
Condition Est. Over 95%ile	0	0	1	0
Condition Est. Over 90%ile	1	0	3	0
Enzymes Over 99%ile	62	1	5	2
Enzymes Over 95%ile	130	3	18	11
Enzymes Over 90%ile	215	12	99	33
Enzymes Under 10%ile	429	211	171	304
Enzymes Under 5%ile	310	146	142	211
Enzymes Under 1%ile	152	85	73	47
Compounds Over 99%ile	31	0	3	1
Compounds Over 95%ile	64	2	9	11
Compounds Over 90%ile	106	7	48	24
Compounds Under 10%ile	959	1096	1009	1015
Compounds Under 5%ile	909	1041	981	971
Compounds Under 1%ile	860	1009	956	922

Since we had a symptom of constipation, let us see how well the samples match that reported from Studies on PubMed — there were no matched. When we went to our Special Studies, we see that the microbiome followed the reported symptoms. We then look at the top value from Special Studies — which was Long COVID for all samples. We see the lost of ground around the constipation and then regaining the progress.

Criteria	22-May	14-Jun	15-Jul	22-Jul
Special Studies	7%ile	14%ile	15%ile	7%ile
Top Item Long COVID	35 %	44 %	41 %	36 %

Next we go and look at aprepitant and erythromycin

Criteria	22-May	14-Jun	15-Jul	20-Jul
Aprepitant	80.4	113.7	205.8	169.9
Erythromycin	227.5	-76.8	226.7	194
Best CFS antibiotic Priority / Max Priority	metronidazole 430 /549	lymecycline 176 /307	amoxicillin 424 / 527	amoxicillin 351 / 484

The Percentage of Percentile show quite a shift — unfortunately, it is unclear if this is a temporary after effect of constipation, poor lab read quality, or the above aprepitant and erythromycin. The next sample may resolve this issue.

Is the Project working — YES

We are seeing both subjective improvement and object improvements.

Personally, I like what appears to be a shift towards Cecile Jadin’s approach — not continuous antibiotics but a course (7-10 days) followed by a break (ideally 3 weeks). Often I find that ME/CFS people tend to be impatient and just want to keep pressing on hard… which I have observed often result in tripping and rolling down the hill to where they were (or worst).

Postscript – and Reminder

I can compute items to take, those computations do not provide information on rotations etc.

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.

lassesen 5:21 pm on February 9, 2014
Tags: CFS, Diagnosis, Machine Learning

Key CFS Symptoms — the Big Data answer

I had been thinking about doing a post on CFS symptoms (i.e. creating a checklist to track your status). This morning I found the perfect article in International Journal of Machine Learning and Computing which is available in full for free. If you have not worked professional as a data scientist or statistician, you may find it geek (fortunately I have).

Samuel P. Watson, Amy S. Ruskin, Valerie Simonis, Leonard A. Jason, Madison Sunnquist, and Jacob D. Furst, “Identifying Defining Aspects of Chronic Fatigue Syndrome via Unsupervised Machine Learning and Feature Selection,” International Journal of Machine Learning and Computing vol.4, no. 2, pp. 133-138, 2014.

The bottom line is that they found 54 symptoms that predicted better if a person had CFS then any of the current research definitions.

The top 15 (in order of importance are below)

Fatigue/extreme tiredness
Next day soreness or fatigue after non-strenuous, everyday activities
Minimum exercise makes you physically tired
Physically drained or sick after mild activity
Dead, heavy feeling after starting to exercise
Feeling unrefreshed after waking up in the morning
Problems remembering things
Muscle weakness
Difficulty finding the right word to say or expressing thoughts
Only able to focus on one thing at a time
Pain or aching in your muscles
Difficulty paying attention for a long period of time
Mentally tired after the slightest effort
Absent-mindedness or forgetfulness
Sensitivity to noise

I am hoping to be able to balance the rest of them (as well as create a program that uses this information)… stay tune.

I find this to be a very important list because:

If you have none of these and have a CFS diagnosis — your diagnosis is probably very wrong.
If you have all of them (as I have had during CFS periods), your diagnosis is likely correct.
Some only — I am waiting to get more information to build a program that would calculate those odds.

lassesen 11:25 pm on November 11, 2012
Tags: CFS, Microflora, Probiotic

Role of Microflora in CFS / FM / IBS

A few years ago, a section on the gut for CFS and its bacteria would have been just a sentence and not a chapter. The involvement of the gut would likely be a description of poor absorption of nutrients only. Recent studies have suggested that the gut’s bacteria or microfloras may play a major, possibly dominant role, in CFS. Microbiota has a role in immune regulation, and changes in gut microbiota may be the basis for an increased incidence of autoimmune diseases and asthma in developed countries[663]. microfloras do impact stress response.

A 2010 study alters the relationship between microfloras and disease greatly. The study found that metabolic profiles based on bacterial structural components and metabolites are disease-specific. In other words, the pathogens determine different microfloras mixtures. The mixture is almost a fingerprint for the pathogen! Each microfloras produces different mixtures of amino acids, inflammatory chemicals, etc. Some specific microfloras convert food more efficiently than others and thus have been associated with obesity[665] [666]. Other microfloras impact the respiratory immune system and appear to be seeded by the birth process (quasi-inherited). Fecal transplants are most successful when the donor is a blood relative.

Of special interest to CFS patients, is the association of microfloras changes with sleep disorders, as well as behavioral changes in IBS. 92% of CFS patients in one study had IBS. We are not talking about minor changes of microfloras, but large shifts in microfloras populations.

Each person has a unique microfloral signature

We should note that we are talking about a lot of different types and species of bacteria. A total of 947 Bacteroides and 745 Clostridium strains were isolated from 67 healthy and 94 anti-microbial treated children in one study. For each family, over a thousand strains may be seen. Eliminating the harmful ones and encouraging the helpful ones is a task for researchers for decades to come. Shift of strains percentage in a species may be a significant factor that has only been lightly explored. There are more than a 1000 species that commonly live in and on the healthy human body. Each person harbors around 150 species, mostly in the gut (Nature, Volume 464, p. 56,18 March 2010). This unique profile is being investigated as equivalent (or better) than a fingerprint (New Scientist, Volume 215, no. 2875, p. 36, 28 Jul 2012). Identical twins who can rarely be distinguished by DNA are easily distinguished by the use of skin bacteria. A very old Dr.Who episode, used as a story-device, a scanner that determined who was the last person holding an object. This was science fiction then; today it has been demonstrated that a skin bacteria fingerprint will remain, and be detected for up to two weeks on computer mice, keyboards, and tables (Proceeding of the National Academy of Science, Volume 107 p. 6477).

CFS microfloras

Our current knowledge on CFS microfloras is limited, but there are many shifts of families of microfloras from those seen in controls.

High Enterobacter species (240%)
High Fungi
High Gram positive D/L lactate producing bacteria
High Klebsiella/Enterobacter
High Streptococcus
Low Escherichia coli[698](50% less) in 62% of CFS Patients
Low Bacteroides species in 25% of CFS Patients
Low Bifidobacterium species (30%)
Low Lactobacillus species.

This was done from a sample of CFS patients, and these individuals are expected to have different shifts depending on their pathogens (and their genes). This simple model explains the wide variety of laboratory manifestations and symptoms seen in CFS. The pathogens, microfloras, and genes determine the clinical manifestations.

Microfloras encourages pathogens

The triggering event for CFS may be changes of the microfloras that ended up activating pathogens altering microfloras further. Consider a change of microfloras that decreases lysine and increases arginine production: this combination is known to reactivate some herpes viruses. Over production of trypsin reactivates influenza viruses. microfloras and pathogens are a two way street. Pathogens alter microfloras; microfloras reactivates pathogens.

A second route arises from a surprising finding about the high incidence of viral RNA found in stomach samples compared to controls. The viral RNA becomes incorporated with your native microfloras, producing harmful mutations.

Probiotics can be deadly

Probiotics are not a zero risk treatment, contrary to popular belief.

“There is an urgent need to better define their appropriate clinical use, especially as probiotics are not always benign. There are many reports of probiotics causing infections, and in particular there is an increased risk of invasive infection in patients with in dwelling intravenous noeters. Probiotic use can even turn deadly: in one clinical trial examining probiotics for pancreatitis, the trial had to be stopped early because the probiotic group actually fared much worse. There were 24 deaths in the probiotic group and 9 in the control group, and 9 cases of bowel ischemia reported in the probiotic group, whereas none were seen in the control group. The results of this trial provide a good illustration of how we still do not entirely understand the complex mechanisms of action of probiotics, and of the urgent need to better determine the scientific basis for their function. This clinical trial used rigorously-tested probiotics, so it is not difficult to imagine the additional potential dangers lurking in probiotics of inadequately controlled quality. Fortunately, probiotic use is generally safe and it shows much promise for clinical efficacy in many gastrointestinal disorders, but we still have a long way to go. Ongoing research in this area, and a better understanding of host-microbial interactions through ongoing research on the human microbiome, will undoubtedly lead to further advances in this important field of Gl research”.

Elaine O. Petrof, Probiotics and Gastrointestinal Disease: Clinical Evidence and Basic Science

Probiotics can also cause inflammation for some conditions.

In my next post I will look at the probiotics that have been documented to help these conditions. Stay tune!

CFS Remission

Striving for true remission of CFS, chronic Lyme, FM, IBS etc

Tag Archives: CFS

Review of Recent ME/CFS Research, Dec 2023

The Remission Biome Project: Tess Falor

Overview of results

The Events Around the above Samples

Take Away and Reflections

My Suggestions Going Forward

The Human Behavior Problem

Postscript – and Reminder

The Remission Biome Project: Tamara Romanuk

Overview of results

Pretty Pictures

The Events Around the above Samples

Going Forward

Part Deux — More Samples!

Sample Comparison

Is the Project working — YES

Postscript – and Reminder

Key CFS Symptoms — the Big Data answer

Role of Microflora in CFS / FM / IBS

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Overview of results

The Events Around the above Samples

Take Away and Reflections

My Suggestions Going Forward

The Human Behavior Problem

Postscript – and Reminder

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Overview of results

Pretty Pictures

The Events Around the above Samples

Going Forward

Part Deux — More Samples!

Sample Comparison

Is the Project working — YES

Postscript – and Reminder

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