Gut Bacteria Testing: Part 2 – what CFSer have gotten back from the labs

This page is an attempt to merge citizen science with professional science to paint a better perspective on how the gut bacteria is altered in CFS. This is a technical page which may cause information overload (even without CFS!)

My model is that 70-90% of the CFS symptoms are directly related to the dysfunction bacteria in the gut. Different symptoms, different bacteria. Same symptoms, likely similar bacteria. Since CFSer have different symptoms, I expect some common dysfunction and some dysfunction which will only occur for some people.

I attach my detail tables as here. Below are what I have identified as common across the data. As data grows, more patterns may appear. There are likely data errors in my transcriptions which I will correct over time.

I would suggest opening to help understand where each item belongs. If you look up a specific item in Wikipedia, the hierarchy is usually shown on the right side, as shown below:


I will not attempt to interpret the meaning of the dysfunction in this post — strictly present the raw data!

Common Results from Ubiome

Although there are only two results share at the moment (and a few folks are waiting to receive their), there appear to be some commons shifts.

The following are limited to where BOTH results have a factor of 10x shift in the same direction from normal readings. All of the shifts were negative (i.e. much much less of these bacteria)

Red Labs

Above we see a recurring pattern of major decrease of families and genus of bacteria. Going over to the single report from Red Labs, I see almost all of the references is almost a steady stream of “<  N”, in other words  it is focused on detecting OVERGROWTH and not undergrowth (with just 4 with > N ),.   In my analysis of the results (in the spread sheet attached), I assumed that a report of “0” in this scernario indicated undergrowth (Low). I am not completely happy with having to make that assumption and would prefer to see Red Labs amend their labs with ranges.

Of the four testing explicitly for undergrowth ( > N), we had three positives:

  • Bifidobacterium (Bifidobacteriaceae) – seen in all Ubiome results that I had for this (1), Reported in 1998 Study
  • Asaccharobacter (Coriobacterineae) – one slight up, one slight down with Ubiome
  • Ruminococcus (Ruminacoccaceae) – seen in 1 /2 of Ubiome results


Just one sample reports from one person.

  • Coliforms (E.Coli) Low
  • Aerobe High
  • Streptococcus High
  • Clostridium High


  • Both sample reports reported low Beneficial E.Coli
  • Other results in disagreement between reports

Older Studies [1998]

These personal results appear to be in agreement.

  • Enterococcus reported low for CFS (Enterococcus/Enterococcaceae/Lactobacillales) – Only Ubiome report on this  had -67 x decrease. Red Labs had Zero reported
  • Lactobacillus reported low for CFS – One Ubiome reported -26 x Decrease, and Red Lab reported Zero
  • E.Coli reported low for CFS – Red Labs reported Escherochia only and found Zero. Genova low (or none). BioScreen low.

Bottom Line

With our very small sample, we have replicated the 1998 results as well as identify other families of bacteria that also show the very low characteristics.

We need more reports – with uBiome being the clear winner for usefulness. If you have not order uBiome or AmericanGut kits, and wish to contribute $100 to CFS research — seriously consider doing so and forwarding your results to me. I am hoping that both uBiome and AmericanGut will enable a complete download of the data so that sharing and analysis will become much easier with less chance of typographical mistakes.