Reader’s microbiome changes following suggestions.

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.

I get an improvement in my brain fog and cognition, my bowel movements have become much smaller and I’m over all way more constipated. Any theories on why this might be happening? I have been taking them for months, so it’s not an adjustment period. 
I’ve tried taking them on their own. Symbioflor on it’s own doesn’t do much for me. L. Reuterii on it’s own still gives me constipation, same with the bifidobacterium.” 
The older recommendations he followed was focused on reducing high bacteria only.

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.