uBiome: A reader results 2016-10-15

A reader allowed me access to his uBiome results for me to review. I have done other patients 2014-10-30, 2014-10-27, 2014-03-16.

I should remind the reader that while these results can give insight to the issues, taking action to correct the issues can often exceed our current knowledge.


Over prior 3 months, the reader had taken Align, Yakult, SymbioFlor-2, Miyarisan, Prescript Assist. No herbs or antibiotics.

The Familiar Ones

See the 1998 Alison Hunter Memorial Foundation Report for what was found then.  We have the same pattern of CFS for this patient.

  • Bifidobacterium: just 15% of normal
  • Lactobacillus: 24% of normal
  • Enterobacter: 184% of normal

Some items that were unexpected:

Other Families

First a visual where you can see significant overgrowth/undergrowth of different phylum (largest classification).


  • Diversity:  97%ile — good news, the reader has more different types of bacteria than most people. This is not typical of CFS and I suspect Prescript Assist was a factor here.Reader reported: ” I tend to think my high biome diversity is a function of not living in North America, but rather on a ***** farm in rural ***** for the past twenty years. We grow and eat all our own fruits and vegetables.”
  • Akkermansia: 170% of normal, this is associated with weight gain and inflammation.

Major differences seen across all uBiome reports for all readers

Other families were high with one individual and low with the next. This is expected because the fine details are unique to each individuals, with a group of shift being very common.

Increasing Bacteroidetes

This Phylum consists of many classes


  • Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. [2016]
  • “Dairy intake was positively associated with the Firmicutes:Bacteroidetes ratio,”[2016] i.e. reduce dairy intake to increase Bacteroidetes
  • “Inflammatory bowel disease (IBD) includes a spectrum of diseases from ulcerative colitis (UC) to Crohn’s disease (CD). Many studies have addressed the changes in the microbiota of individuals affected by UC and CD. A decrease in biodiversity and depletion of the phyla Bacteroidetes and Firmicutes has been reported, among others.”[2016]

Decreasing Proteobacteria

  • “human milk oligosaccharides… results in a reduction in relative abundance of Firmicutes and Proteobacteria.[2016]
  • ” Specifically, vitamin D, mono-unsaturated fat, cholesterol, and retinol(Vitamin A) were associated with relative increases in Proteobacteria… saturated fat, vitamin E, and protein were associated with relative decreases in Proteobacteria.” [2016]

Suggestions for reader to discuss with their Medical Professional

  • Increase of Vitamin E
  • Stop taking Vitamin A (if they were taking it), reduce foods high in vitamin A
  • Depending on Vitamin D levels, reduce supplementation
  • Increase animal fat in their diet (but not milk fat)
  • Reduce milk and milk products (perhaps drop Yakult)
  • Add General Biotics Equilibrium to their probiotics list, rotate Prescript Assist more often
  • Continue rotation with:  SymbioFlor-2 (take SymbioFlor-1 with it – they cross support each other), Miyarisan, Prescript Assist.