Walking in the void of no studies

For a microbiome review recently I wrote:

I was curious about Actinomadura because of the differences. It appears to occur in about 3% of samples, hence to get a reasonable sample to get relationships from, a clinical study would need to have 30/3% = 1000 participants and use a 16s processor that detects this bacteria (many do not). Worst yet, because of this rarity, we know of nothing that impacts it from clinical studies.

What to do when there is no information on changing a bacteria!!!

This actually opens the door to using bacteria-to-bacteria associations. We have 111 of them!

Seen when display level is increased.

Looking at one with the highest positive associations, Desulfofarcimen, we see some items that will increase this bacteria (and by increasing that bacteria, Actinomadura should increase): cranberry polyphenols, Goji (berry,juice), walnuts, saccharin. Using all of the 111 interactions, we found only one thing that shows up as increasing Actinomadura (and many things to decrease), choline deficiency (i.e. reduce choline in diet). Items to avoid would be:

  • jatropha curcas linn. (euphorbiaceae)
  • nigella sativa seed (black cumin)
  • oplopanax horridus(Devil’s Club)
  • hypericin(St. John’s Wort)
  • kefe cumin (laser trilobum l.)
  • foeniculum vulgare (Fennel)
  • lactobacillus bulgaricus (probiotics)

The only likely item would be yogurt containing lactobacillus bulgaricus).

Trying a test of what it predicts as modifiers

I decided to use Lactobacillus: NCBI 1578, it is very well studied. I tried to see what it predicts. The results are below. All of the significant factors were items that reduces it (negative). Below each is the number of studies.

  • thyme Herb or Spice -39
  • vitamin b3 (niacin) Vitamins, Minerals and similar -39.1
    • 1 Studies report Decreases
  • N-Acetyl Cysteine (NAC), flavonoids, polyphenols etc -39.2
    •  1 Studies report Decreases
  • cranberry (flour, polyphenols) flavonoids, polyphenols etc -39.7
    • 6 Studies report Decreases
  • sulfites food additives Miscellaneous, food additives, and other odd items -40
    • 2 Studies report Decreases
  • bacillus laterosporus (probiotic) Probiotics -40.3
    •  2 Studies report Decreases
  • glycyrrhizic acid (licorice) Herb or Spice -44.7
    • 1 Studies report Decreases
  • sucralose Sugar and similar -45.8
    • 2 Studies report Decreases
  • stevia Sugar and similar -46.6
    •  2 Studies report Decreases
  • magnesium-deficient diet Diet Style -46.6
    • 1 Studies report Decreases
  • high-fat diets Diet Style -66.5
    •  6 Studies report Decreases
  • saccharin Sugar and similar -71.3
    •  4 Studies report Decreases
  • Hesperidin (polyphenol) flavonoids, polyphenols etc -72.4
    •  4 Studies report Decreases

A 100% agreement is actually better than I expected and appears to validate this approach. I will be adding these forecasts to bacteria that lack clinical studies in the next week or so.