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)

• Role of Rickettsiae and Chlamydiae in the Psychopathology of Chronic Fatigue Syndrome (CFS) Patients by Philippe Bottero
• Common Clinical and Biological Windows on CFS and Rickettsial Diseases by C. L. Jadin
• Role of Mycoplasmal Infections in Fatigue Illnesses by G.L. Nicolson

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 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.