Revisiting old data/post with latest tool set

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:


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.

CriteriaCurrent SampleOld Sample
Lab Read Quality9.18.1
Bacteria Reported By Lab327303
Bacteria Over 99%ile85
Bacteria Over 95%ile3822
Bacteria Over 90%ile7056
Bacteria Under 10%ile3821
Bacteria Under 5%ile2411
Bacteria Under 1%ile85
Lab: uBiome
Rarely Seen 1%31
Rarely Seen 5%264
Outside Range from JasonH77
Outside Range from Medivere1616
Outside Range from Metagenomics88
Outside Range from MyBioma1111
Outside Range from Nirvana/CosmosId1616
Outside Range from XenoGene3131
Outside Lab Range (+/- 1.96SD)1617
Outside Box-Plot-Whiskers12278
Outside Kaltoft-Moldrup156102
Condition Est. Over 99%ile00
Condition Est. Over 95%ile01
Condition Est. Over 90%ile111
Enzymes Over 99%ile00
Enzymes Over 95%ile5032
Enzymes Over 90%ile14894
Enzymes Under 10%ile80246
Enzymes Under 5%ile4550
Enzymes Under 1%ile61
Compounds Over 99%ile3182
Compounds Over 95%ile16465
Compounds Over 90%ile27535
Compounds Under 10%ile81319
Compounds Under 5%ile76237
Compounds Under 1%ile7270

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.

BacteriaNewest Percentile(Percentage)Older Percentile(Percentage)
(genus) Alistipes31 (0.9%)89 (5.7%)
(genus) Anaerococcus97 (1.8%)62 (0.08%)
(genus) Bifidobacterium87 (3.6%)96 (7.3%)
(genus) Erysipelatoclostridium99 (3.9%)69 (0.7%)
(genus) Faecalibacterium19 (3.9%)51 (12.1%)
(genus) Finegoldia99 (3.5%)68 (0.1%)
(genus) Intestinibacter79 (0.4%)97 (2.4%)
(genus) Klebsiella91 (1.3%)none
(genus) Kluyvera89% (1.8%)none
(genus) Lactobacillus67 (0.01%)97 (3.5%)
(genus) Megasphaera96 (2.6%)76 (0.01%)
(genus) Parabacteroides95 (7.0%)81 (3.5%)
(genus) Streptococcus99 (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…

2 thoughts on “Revisiting old data/post with latest tool set

  1. Do VSL#3 strains produce biogenic amines? Perhaps there’s infection or other problem causing inflammation which is aggrevated by histamin.

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