lassesen 6:55 pm on November 18, 2017  

4 Biomes over 2 years — A time based analysis

A reader informed me that he has just gotten his 4th ubiome done. This is especially interesting because he recorded his Health Score when each one was done — thus we may be able to see patterns between the microbiome and the health score.

The Raw data

Date 10/29/2017 11/30/2016 3/7/2016 9/17/2015
Health Score 25% 45% 35% 65%
Diversity 56%ile 76%ile 81%ile 87%ile
Bifidobacterium 1.87 0 0 0
Lactobacillus 0 0.2 0.01 0
Akkermansis 0 1.15 1.12 0.73
 Firmicutes:Bacteroidetes ratio 1.3 1.7 3.1 2.1
Rare genus ( < 5%) Christensenella Georgenia none Anaerovorax
Alcaligenes
Meiothermus
Paucibacter
Shinella
Overgrowths Sutterella: 6.84 X Lachnospira: 3.31 X Intestinibacter: 10.70 X Intestinibacter: 4.92 X
Moryella: 5.90 X Parasutterella: 2.17 X Flavonifractor: 4.89 X Prevotella: 2.47 X
Bilophila: 4.42 X Marvinbryantia: 2.08 X Marvinbryantia: 3.96 X Mogibacterium: 2.16 X
Phascolarctobacterium: 4.04 X Terrisporobacter: 1.60 X Fusicatenibacter: 2.41 X Terrisporobacter: 1.82 X
Erysipelatoclostridium: 3.18 X Barnesiella: 1.58 X Terrisporobacter: 2.02 X Porphyromonas: 1.68 X
Collinsella: 2.77 X Sarcina: 1.52 X Hespellia: 1.73 X Anaerostipes: 1.59 X
Dorea: 2.38 X Phascolarctobacterium: 1.51 X Subdoligranulum: 1.69 X
Parabacteroides:  2.27 X Flavobacterium: 1.62 X
Anaerostipes: 2.04 X
Peptoclostridium: 1.71 X
Senegalimassilia: 1.55 X
By Order Burkholderiales:  6.48 X Burkholderiales:  1.33 X Flavobacteriales:  1.33 X Clostridiales:  1.16 X
Desulfovibrionales: 2.97 X Clostridiales:  1.07 X Clostridiales:  1.32 X  
Coriobacteriales: 2.69 X Bacteroidales: 1.02 X Coriobacteriales:  1.14 X
Selenomonadales: 2.25 X    
Erysipelotrichales: 1.88 X  
Bifidobacteriales: 1.16 X
Bacteroidales: 1.07 X

A Narrative

  • Best:
    • Firmicutes:Bacteroidetes ratio  2.1 (normal)
    • Overgrowth Orders: 1
    • Overgrowth Genus ( > 1.5): 6
  • 2nd Best
    • Firmicutes:Bacteroidetes ratio  1.7 (19% below)
    • Overgrowth Orders: 3
    • Overgrowth Genus ( > 1.5): 7
  • 3rd Best
    • Firmicutes:Bacteroidetes ratio  3.1 (47% above)
    • Overgrowth Orders: 3
    • Overgrowth Genus ( > 1.5): 8
  • Worst
    • Firmicutes:Bacteroidetes ratio  1.3 (39% above)
    • Overgrowth Orders: 7
    • Overgrowth Genus ( > 1.5): 11

It looked like Clostridiales overgrowth was the start, as it grew it made a friendly environment for two more to join: Flavobacteriales, and Coriobacteriales. This allowed the Burkholderiales to get established (eventually pushing out Clostridiales which has dropped  to just 71% in the last uBiome).  Burkholderiales foster the growth of many other orders as a result with the result massive drop in health status.

In short, we see an ongoing battle between the various bacteria-cartels!

Deep dive into the current uBiome example

A fresh ubiome sample is something that should be used to modify diet, supplements as soon as possible. As we have seen above, there are ‘bacteria wars’ between bacteria cartels so we have a moving target!

My immediate concern is Peptoclostridium, because it includes Peptoclostridium  difficile, the bacteria formerly known as Clostridium difficile!

Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.

Avoid

  • Amoxicillin-Clavulanate antibiotics
  • Animal-based diet
  • arabinoxylans
  • Barley
  • Berberine
  • Bifidobacterium adolescentis
  • Bifidobacterium longum.
  • Bile
  • BPA bottles
  • Butyrate producing probiotics
  • Canole Oil
  • Chicory root
  • Dairy
  • Glucose foods (fructose [fruit sugar] appears to be fine)
  • Helminth infections
  • Isoniazid-
  • Lactobacillus rhamnosus
  • Lingonberries
  • L-sorbose
  • Milk-derived saturated fat
  • Polydextrose
  • Proton-pump inhibitors (PPI)
  • Pyrazinamide
  • Raspberries
  • Rhubarb
  • Rifampin-
  • Saccharomyces boulardii
  • Sleepless nights
  • Soluble corn fiber
  • Stress
  • Walnuts
  • Wheat Breads
  • xylitol

Take

  • Acarbose
  • Capsaicin(chili peppers)
  • Chicory
  • Cranberry bean flour [parent]
  • Flaxseed
  • Fructooligosaccharides (FOS)
  • Fumarate
  • Galactooligosaccharides
  • Galactooligosaccharides (GOS)
  • Ketogenic diet
  • Lactobacillus kefiri
  • Lactobacillus paracasei
  • Lactobacillus plantarum
  • Lactobacillus reuteri
  • l-glutamine
  • Metronidazole antibiotics
  • Mutaflor (E.Coli Nissle 1917)
  • NSAIDs (see list here), I prefer aspirin as first choice.
  • Oral Iron Supplements
  • Polymannuronic acid
  • Pomegranate
  • Resveratrol (grape seed extract)
  • Sleep
  • Sodium chloride (Table Salt)
  • Streptococcus probiotics
  • Tea
  • Vitamin D3
  • β-glucan

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of CFS. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.