MicrobiomePrescription Site Revision – Stage 1

This week I have taken off from work to do some serious refactoring on the recommendation site. The first phrase is to simplify recommendations and make items clearer for the brain fogged. At present we have 6,977 different relationships for modifying bacteria in our database.

Example:

  • One of the recommendations was for  naringenin. This is mainly found in grapefruit fruit . Very few of my readers would discover this.
  • Often the same item would have multiple names, common name, scientific name or the dominant chemical in it.

The apparent change in Stage 1 is on a single item “Modifiers”, http://microbiomeprescription.azurewebsites.net/Library/GutModifiers

Stage1

You will see that the old items are clustered into groups.

Picking an aggregate

You will see what they appear to impact overall. Often we lack appropriate studies — but ‘similar items’ can be inferred to have similar effects. This allows us to make a reasonable guess when we lack studies.

bacillus probiotics

The following are impacted

Taxonomy Rank Effect Citations Links
Betaproteobacteria class Decreases Studies Also modified by
Acidaminococcaceae family Decreases Studies Also modified by
Bacillaceae family Increases Studies Also modified by
Bacteroidaceae family Increases Studies Also modified by
Clostridiaceae family Decreases Studies Also modified by
Lachnospiraceae family Increases Studies Also modified by
Methanobacteriaceae family Decreases Studies Also modified by
Pasteurellaceae family Increases Studies Also modified by
Rikenellaceae family Decreases Studies Also modified by
Ruminococcaceae family Increases Studies Also modified by
Veillonellaceae family Increases Studies Also modified by
Verrucomicrobiaceae family Increases Studies Also modified by
Acidaminococcus genus Decreases Studies Also modified by
Akkermansia genus Increases Studies Also modified by
Alistipes genus Decreases Studies Also modified by
Bacillus genus Increases Studies Also modified by
Bacteroides genus Increases Studies Also modified by
Clostridium genus Decreases Studies Also modified by
Faecalibacterium genus Increases Studies Also modified by
Haemophilus genus Increases Studies Also modified by
Megamonas genus Increases Studies Also modified by
Methanobrevibacter genus Decreases Studies Also modified by
Roseburia genus Increases Studies Also modified by
Methanobrevibacter smithii species Decreases Studies Also modified by

Picking an original citation

This shows the various aggregations that it has been placed into and the specifics..

bacillus subtilis natto

The following are impacted

Taxonomy Rank Effect Citations Links
Betaproteobacteria class Decreases Studies Also modified by
Clostridiaceae family Decreases Studies Also modified by
Rikenellaceae family Decreases Studies Also modified by
Alistipes genus Decreases Studies Also modified by
Clostridium genus Decreases Studies Also modified by

Studies

Clicking Studies, shows where this information came from.

  1. Effect of Feeding Bacillus subtilis natto on Hindgut Fermentation and Microbiota of Holstein Dairy Cows.
    Asian-Australasian journal of animal sciences (Asian-Australas J Anim Sci ) Vol: 27 Issue 4 Pages: 495-502
    Pub: 2014 Apr Epub:

    • Song DJ
    • Kang HY
    • Wang JQ
    • Peng H
    • Bu DP

Links

This takes you to other things that modifies the bacteria.

In the example below, we see high fat diet increases and low fat diets decreases (results from different studies agreed). BUT we also see that  ketogenic diet  has a contrary effect — possibly due to the low carbohydrate component. (The ketogenic diet is a high-fat, adequate-protein, low-carbohydrate diet that in medicine is used primarily to treat difficult-to-control epilepsy in children. The diet forces the body to burn fats rather than carbohydrates.Wikipedia)

Betaproteobacteria

General Specific Effect
bacillus probiotics bacillus subtilis natto Decreases
bacillus subtilis natto probiotic bacillus subtilis natto Decreases
bacillus subtilis probiotic bacillus subtilis natto Decreases
cellulose carboxymethyl cellulose Increases
emulsifiers (additives) polysorbate 80 Increases
fraxinus angustifolia herb fraxinus angustifolia Increases
high fat diet high fat diet Increases
ketogenic diet Decreases
low fat diet low fat diets Decreases
polymannuronate hydrolase supplement polymannuronic acid Decreases
pulse / legumes navy bean Increases
taurine amino acid l-taurine Decreases
walnuts nuts walnuts Decreases

On the above, if you click the links under effect,

ketogenic diet

Decreases

You will again be taken to the list of studies

  1. tion
    Acta neurobiologiae experimentalis (Acta Neurobiol Exp (Wars) ) Vol: 77 Issue 1 Pages: 18-30
  2. Effects of diet on gut microbiota profile and the implications for health and disease.
    Bioscience of microbiota, food and health (Biosci Microbiota Food Health ) Vol: 32 Issue 1 Pages: 1-12
  3. Short-term impact of a classical ketogenic diet on gut microbiota in GLUT1 Deficiency Syndrome: A 3-month prospective observational study.
    Clinical nutrition ESPEN (Clin Nutr ESPEN ) Vol: 17 Issue Pages: 33-37
  4. Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice.
    Nutrients (Nutrients ) Vol: 9 Issue 7 Pages:
  5. Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy.
    World journal of gastroenterology (World J Gastroenterol ) Vol: 23 Issue 33 Pages: 6164-6171
  6. Gut Microbiome-Induced Shift of Acetate to Butyrate Positively Manages Dysbiosis in High Fat Diet.
    Molecular nutrition & food research (Mol Nutr Food Res ) Vol: 62 Issue 3 Pages:
  7. Curated database of commensal, symbiotic and pathogenic microbiota
    Generative Bioinformatics (Center of Excellence in Generative Medicine ) Vol: Issue
  8. Influence of diet on the gut microbiome and implications for human health.
    Journal of translational medicine (J Transl Med ) Vol: 15 Issue 1 Pages: 73
  9. Sodium butyrate attenuates high-fat diet-induced steatohepatitis in mice by improving gut microbiota and gastrointestinal barrier
    World Journal of Gastroenterology (World J Gastroenterol ) Vol: 23 Issue 1 Pages: 60-75

Bottom Line

This is stage 1, reorganizing the data. Stage 2 will be adding a second recommendations choice to use the reorganized data.  The second phrase will be on the “Other Lab Analysis” reports to test that the results are similar.

OtherLabs

The third phrase will be applying it to the uBiome data.

Quality Assurance Needed!

I have done my  best guess at aggregations. I may be missing some or have some incorrect. Please email me at Ken /at/ lassesen.com with recommendations/corrections.