A reader wrote gave me access to their latest uBiome
“I’ve been following your probiotics protocol. I’ve been taking L. Reuterii, a mix of bifidobacterium and symbioflor 2.
Comparing the Before and Now Samples
Overall, there have been a significant improvement is the all profiles with Gout being the sole item with significant increase.
| All Profiles | 125 | 104 |
|---|---|---|
| Allergies | 6 | 5 |
| ADHD | 6 | 7 |
| Alzheimer’s disease | 5 | 5 |
| Autism | 9 | 9 |
| Autoimmune Disease | 3 | 3 |
| Chronic Fatigue Syndrome | 10 | 10 |
| Crohn’s Disease | 9 | 4 |
| Depression | 8 | 8 |
| Fibromyalgia | 1 | 1 |
| Gout | 3 | 7 |
| High Blood Pressure | 3 | 2 |
| Histamine Issues | 0 | 0 |
| Histamine Issues From Ubiome | 4 | 4 |
| Inflammatory Bowel Disease | 10 | 4 |
| Irritable Bowel Syndrome | 6 | 4 |
| Metabolic Syndrome | 7 | 4 |
| Mood Disorders | 4 | 3 |
| Rheumatoid arthritis | 7 | 7 |
| Schizophrenia | 0 | 0 |
| Systemic Lupus Erythematosus | 11 | 9 |
| Type 2 Diabetes | 8 | 6 |
| Ulcerative colitis | 5 | 2 |
Bacteria Shifts
Apart from two phylum (small populations usually), things have improved. As I have mentioned before — recovery is not a straight line recovery. It is moving from one island to the next until you back to your original harbor.
| (phylum)Actinobacteria | 0 % | 0 % |
| (phylum)Bacteroidetes | -25 % | 0 % |
| (phylum)Euryarchaeota | -44 % | 104979 % |
| (phylum)Fibrobacteres | 0 % | -99 % |
| (phylum)Firmicutes | 7 % | 0 % |
| (phylum)Lentisphaerae | 0 % | 3 % |
| (phylum)Proteobacteria | 35 % | 0 % |
| (phylum)Synergistetes | 0 % | -3 % |
| (phylum)Tenericutes | 0 % | 0 % |
| (phylum)Verrucomicrobia | -35 % | -33 % |
Class
Moving down to the class level, we see better clarity. Remember the criteria was to focus on items > 150%. All of them went down
| (class)Actinobacteria | 0 % | 0 % |
| (class)Alphaproteobacteria | -88 % | -30 % |
| (class)Bacilli | 0 % | 0 % |
| (class)Bacteroidia | -26 % | 0 % |
| (class)Betaproteobacteria | 202 % | -65 % |
| (class)Clostridia | 9 % | 0 % |
| (class)Deltaproteobacteria | 48 % | 271 % |
| (class)Epsilonproteobacteria | 0 % | -98 % |
| (class)Erysipelotrichia | 0 % | 0 % |
| (class)Fibrobacteria | 0 % | -99 % |
| (class)Flavobacteriia | 0 % | 0 % |
| (class)Gammaproteobacteria | -96 % | -90 % |
| (class)Lentisphaeria | 0 % | 9 % |
| (class)Methanobacteria | -43 % | 104979 % |
| (class)Mollicutes | 0 % | 0 % |
| (class)Negativicutes | 0 % | 59 % |
| (class)Synergistia | 0 % | 35 % |
Looking at High Family items we see that we succeed in reducing them.
| (family)Clostridiaceae | 180 % | 96 % |
| (family)Oscillospiraceae | 96 % | 0 % |
| (family)Sutterellaceae | 203 % | -83 % |
So where do we go next?
The latest result have good list of changes:
| Item | Action | Confidence value |
|---|---|---|
| coconut products | Take | 8.372 |
| antiseptics | Take | 5.107 |
| resveratrol | Take | 4.764 |
| gallic acid and tannins | Take | 4.242 |
| inulin prebiotics | Take | 3.764 |
| bacillus probiotics | Take | 3.606 |
| raffinose foods | Take | 3.376 |
| fodmap diet | Take | 3.276 |
| fruit | Take | 3.162 |
| lactobacillus kefiri probiotics | Take | 3.106 |
| bile supplements | Take | 2.983 |
| vitamin b3 niacin | Take | 2.517 |
| gluten free diet | Take | 2.373 |
| vitamin b7 biotin | Take | 1.815 |
| cranberry juice, flour or raw | Take | 1.811 |
| lactobacillus plantarum probiotics | Take | 1.684 |
| flaxseed | Take | 1.631 |
| enterococcus faecium probiotics | Take | 1.539 |
| gynostemma pentaphyllum herb | Take | 1.497 |
| whole grains | Take | 1.416 |
| glutamine amino acid | Take | 1.293 |
| chitosan supplements | Take | 1.078 |
| garlic | Take | 1.042 |
As well as avoids
| high fat diet | Avoid | -1.026 |
|---|---|---|
| olive oil | Avoid | -1.163 |
| bacillus subtilis probiotic | Avoid | -1.177 |
| high fiber diet | Avoid | -1.177 |
| black raspberries fruit | Avoid | -1.177 |
| aspirin | Avoid | -1.236 |
| dairy milk fats | Avoid | -1.301 |
| saccharin sugar | Avoid | -1.434 |
| low glycemic/sugar diet | Avoid | -1.508 |
| bifidobacterium pseudocatenulatum probiotic | Avoid | -1.737 |
| saccharomyces probiotics | Avoid | -1.748 |
| mediterranean diet | Avoid | -1.811 |
| nonsteroidal anti-inflammatory drug | Avoid | -2.013 |
| iron supplements | Avoid | -2.301 |
| barley | Avoid | -2.345 |
| berberine supplement | Avoid | -2.365 |
| walnuts nuts | Avoid | -2.719 |
| beta-glucan foods | Avoid | -2.786 |
| bisphenol a (bpa) plastic | Avoid | -2.944 |
| ethinylestradiol prescription | Avoid | -2.944 |
| no carbohydrate diet | Avoid | -4.604 |
It is interesting to note that bacillus probiotics is on the take list, but one specific one is on the avoid list: bacillus subtilis probiotic
Some concerns
Candidatus Saccharibacteria: 31x normal only (14.49% of Samples) phylum have this
Candidatus Saccharimonas 22x normal only (0.97% of Samples) genus
The only known item to reduce this are macrolides, for example azithromycin.
For the very high Methanobacteriaceae (35.75% of Samples) family, we see coconut (lauric acid and myristic acid) and bile are items that will decrease it
Bottom Line
It was nice to see objective improvement in the microbiome by following earlier suggestions. The suggestions were successful for reducing high bacteria (the specific goal sought).
The new analysis sight allows both high and low to be adjusted for. We will likely see in a few months what the latest recommendations caused to change.
REMEMBER: Adjust for one shift may induce other shifts.
This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.
CFS Remission 