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.com/Library/GutModifiers

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

• algae supplements : ascophyllum nodosum chondrus crispus laminaria digitata laminaria hyperborea sarcodiotheca gaudichaudii
• almonds : almond almonds almonds/ almond skins
• aloe vera : aloe vera
• alpha-glucosidase inhibitor (prescription) : a-glucosidase inhibitors
• aminoglycosides antibiotics : 6 n netilmicin amikacin aminoglycoside apramycin astromicin dibekacin gentamicin gentamicin b gentamincin b isepamicin kanamycin lividomycinneomycin netilmicin paromomycin ribostamycin sisomicin spectinomycin spectomycin streptogramin a streptogramin b streptomycin tobramycin
• anise herb : anise
• arabinogalactan (gums) : arabinogalactan gum arabic mastic gum
• arabinoxylan : arabinoxylan arabinoxylans xylan
• arginine amino acid : l-arginine
• ashwagandha herb : ashwagandha withania somnifera root
• aspartame sugar : aspartame
• aspirin : aspirin
• bacillus licheniformis probiotics : bacillus licheniformis
• bacillus probiotics : bacillus bacillus coagulans bacillus licheniformis bacillus natto bacillus subtilis natto bacitracin paenibacillus polymyxa (prescript assist)

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

• bacillus
• bacillus coagulans
• bacillus licheniformis
• bacillus natto
• bacillus subtilis natto
• bacitracin
• paenibacillus polymyxa (prescript assist)

The following are impacted

Picking an original citation

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

bacillus subtilis natto

• bacillus probiotics
• bacillus subtilis natto probiotic
• bacillus subtilis probiotic

The following are impacted

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

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

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.

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.