Another uBiome Analysis

I am making good progress on an automated analysis site (list of symptoms is evolving — check them out and catch any omissions), and waiting for some technical data. I hope to have it working (at least using DataPunk.Net data, my deep dive data has to be manually re-entered).
A reader was desperate for an analysis, so I am doing another one manually. This turned our to be interesting because it bought in 68 new taxonomy units to the existing 509 from other uBiome samples; I also had to do another deep dive.

After posting, reader responded: “followed the Jaden protocol Now I see why it did not work” — Explanation: many of the overgrowth bacteria are resistant to tetracycline antibiotics (the workhorse for both Jadin and many Lyme protocols)

Standard Items:

  • Lactobacillus: 0.05x
  • Bifidobacterium: 2.01x – identified by species
  • Akkermansia:  0x
  • Diversity:  80%ile
  • Firmicutes to Bacteroidetes:  2.4:1 (Normal 2.1:1)

Uncommon Bacteria

Bacteria name Rank % of Samples
Synergistes Genus 0.5%
Mitsuokella Genus 2.9%
Parvibacter Genus 4.1%

High Bacteria

Slackia: 3.67 X
Collinsella: 2.95 X
Mitsuokella: 2.38 X
Desulfovibrio: 2.24 X
Peptococcus: 2.15 X
Senegalimassilia: 1.91 X
Streptococcus:  1.83 X
Faecalibacterium:  1.77 X
Phascolarctobacterium: 1.71 X
Dorea: 1.54 X


Bottom Line Suggestions For New Ones

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.

I have done a x # to indicate items that results from multiple bacteria genus.


  • Animal-based diet
  • Bacillus subtilis
  • Barley
  • Berberine x3
  • Bifidobacterium adolescentis  Probiotics
  • Bifidobacterium animalis  subsp. lactis
  • Bifidobacterium longum
  • Bifidobacterium pseudocatenulatum
  • Enterococcus probiotics
  • Helminth infections
  • High Fat Diet
  • High Fiber Diet
  • Hospital Food
  • Jerusalem artichoke, Inulin, Chicory x2
  • Lactobacillus rhamnosus
  • Polydextrose
  • Proton-pump inhibitors (PPI) x2
  • red wine (or grape seed extract or reservatol)
  • Rifaximin
  • Saccharomyces boulardii x2
  • Soluble corn fiber
  • Stress
  • VSL#3 Probiotics
  • Walnut x3
  • Wheat


  • Acarbose
  • Aloe vera
  • Bacillus clausii
  • Bacillus Coagulans
  • Bile salts
  • Black cumin Seed
  • Chinese Ginger, FreshGinger
  • Chitosans
  • Cinnamon x2
  • Coleus forskohlii, Plectranthus barbatus, Indian Coleus
  • Coptis chinensis, Chinese gold thread
  • Cranberry
  • Eucalyptus globulus, Tasmanian bluegum
  • Figs
  • Flaxseed [parent]
  • Fructooligosaccharides (FOS)
  • Fumarate
  • Galactooligosaccharides (GOS) x 3
  • Gallate (Green or black tea) x4
  • Garlic (allicin)
  • Gluten-free diet
  • Gooseberry
  • High Protein Diet x3
  • Hyocyamine
  • Lactobacillus Casei x3
  • Lactobacillus paracasei x3
  • Lactobacillus plantarum
  • Lactobacillus salivarius
  • Larreatridentata, chaparral, gobemadora, greasewood, creosote bush
  • Lemongrass oil
  • l-glutamine
  • Licorice
  • Lots of sleep!
  • Low fiber diet
  • Magnolia Bark
  • Navy bean (Cooked) x2
  • NSAIDs (see list here), I prefer aspirin as first choice.
  • Olive Leaf
  • Omega 3 fatty acids (600 mg of omega-3 daily for 14 days cited in studies )
  • Oral Iron Supplements x3
  • Peppermint oil
  • Polymannuronic acid
  • Pomegranate
  • Propionibacterium freudenreichii
  • Resistant starch (type II & IV)
  • Salvia officinalis, Common Sage
  • Sodium chloride (Table Salt)
  • Stevia
  • Thyme x2
  • Triphala
  • Turmeric
  • Turnera diffusaDamiana
  • Vitamin D x2
  • Withania somnifera (Ashwangdha)
  • xylooligosaccharide prebiotic
  • β-glucan

Comment: Despite the many genus, we find many items associated with gluten in the Avoid list, and Gluten-Free diet in the take list.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.