A reader reminded me of A short ME/CFS/MCS remission with microbiome samples [2019], which used uBiome. The toolset has changed a lot since those days, so I thought it would be a good learning activity to look at the samples with the new tools.

The person had a short remission from ME/CFS after:

• 19th-22nd Amoxicillin And Clavulanate
• 22-24th VSL#3

Analysis

The table below shows about the same number of bacteria identified but with an increase in the number of bacteria at extreme values. Condition Est. had a dramatic drop which would agree with the remission. We also see a dramatic drop in extreme Enzymes and Compounds.

In my humble opinion, it suggests that reducing extremes of enzymes and compounds is a desired objective goal.

Criteria	Current Sample	Old Sample
Lab Read Quality	9.1	8.1
Bacteria Reported By Lab	327	303
Bacteria Over 99%ile	8	5
Bacteria Over 95%ile	38	22
Bacteria Over 90%ile	70	56
Bacteria Under 10%ile	38	21
Bacteria Under 5%ile	24	11
Bacteria Under 1%ile	8	5
Lab: uBiome
Rarely Seen 1%	3	1
Rarely Seen 5%	26	4
Pathogens	26	24
Outside Range from JasonH	7	7
Outside Range from Medivere	16	16
Outside Range from Metagenomics	8	8
Outside Range from MyBioma	11	11
Outside Range from Nirvana/CosmosId	16	16
Outside Range from XenoGene	31	31
Outside Lab Range (+/- 1.96SD)	16	17
Outside Box-Plot-Whiskers	122	78
Outside Kaltoft-Moldrup	156	102
Condition Est. Over 99%ile	0	0
Condition Est. Over 95%ile	0	1
Condition Est. Over 90%ile	1	11
Enzymes Over 99%ile	0	0
Enzymes Over 95%ile	50	32
Enzymes Over 90%ile	148	94
Enzymes Under 10%ile	80	246
Enzymes Under 5%ile	45	50
Enzymes Under 1%ile	6	1
Compounds Over 99%ile	3	182
Compounds Over 95%ile	16	465
Compounds Over 90%ile	27	535
Compounds Under 10%ile	81	319
Compounds Under 5%ile	76	237
Compounds Under 1%ile	72	70

Spot Checking Specific Bacteria Shifts

The more extreme bacteria shifts are shown below. The drop of Faecalibacterium levels was likely due to the drop of lactic acid produced by Lactobacillus [Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria 2020]. Given that the person has a ME/CFS diagnosis, my thoughts point to the massive reduction of Lactobacillus caused by Amoxicillin and Clavulanate resulting in a drop of lactic acid (see Lactic Acidosis in ME/CFS). While the bacteria producing lactic acid may be killed, it takes time for the system to clear it. Some sources cite a half life of 18 hours in the body[src]. The VSL#3 may be incidental or may have contributed to the remission ending.

Bacteria	Newest Percentile(Percentage)	Older Percentile(Percentage)
(genus) Alistipes	31 (0.9%)	89 (5.7%)
(genus) Anaerococcus	97 (1.8%)	62 (0.08%)
(genus) Bifidobacterium	87 (3.6%)	96 (7.3%)
(genus) Erysipelatoclostridium	99 (3.9%)	69 (0.7%)
(genus) Faecalibacterium	19 (3.9%)	51 (12.1%)
(genus) Finegoldia	99 (3.5%)	68 (0.1%)
(genus) Intestinibacter	79 (0.4%)	97 (2.4%)
(genus) Klebsiella	91 (1.3%)	none
(genus) Kluyvera	89% (1.8%)	none
(genus) Lactobacillus	67 (0.01%)	97 (3.5%)
(genus) Megasphaera	96 (2.6%)	76 (0.01%)
(genus) Parabacteroides	95 (7.0%)	81 (3.5%)
(genus) Streptococcus	99 (7.3%)	13 (0.003%)

Bottom Line

Short term remission causes are often difficult to identify the cause. In this patient, the evidence appears to be for a model of Amoxicillin and Clavulanate being effective against existing lactic acid producing species (i.e. Lactobacillus). It takes time for the lactic acid to clear the body. On the flip side, the lactobacillus would start regrowing and producing lactic acid (thus ending the remission).

A compounding factor is “Antibiotic Resistance of LACTOBACILLUS Strains [2019]”

For the subset of people with ME/CFS that improves on antibiotics and then regress; it is likely because the antibiotic suppress (but does not eliminate) lactic acid bacteria which then regrows…