Standard Measures

Firmicutes to Bacteroidetes: 0.4: 1 (Average ratio is 2.1 to 1 – a 5 fold shift)
- 2x as many Bacterioidetes compared to reference
- 40% of Firmicutes compared to reference
Akkermansia: NONE (0.00%)
Bifidobacterium: 0.16x (16%)
Lactobacillus 0.02 (2%)
E.Coli proxy: Proteobacteria -> Gammaproteobacteria -> Enterobacteriales -> Enterobacteriaceae (< 0.01X)-> Escherichia -> Escherichia coli

All of the standard shifts seen with CFS

Rare Bacteria Genus

Just one < 5%. This has little information and it is a sibling to Aldercreutzia

Bacteria name	Rank	% of Samples
Paraeggerthella	Genus	0.5%

Over grown Bacteria Genus

Bacteria	Ratio
Parasutterella:	13.92 X
Adlercreutzia:	6.84 X
Bilophila:	6.36 X
Butyricimonas:	5.28 X
Oscillibacter:	3.69 X
Intestinimonas:	3.36 X
Odoribacter:	3.20 X
Flavonifractor:	3.10 X
Alistipes:	3.03 X
Moryella:	2.04 X
Bacteroides:	1.77 X
Dorea:	1.72 X
Dialister:	1.55 X

References to literature that I am working off:

Parasutterella: https://cfsremission.wordpress.com/2017/10/19/decreasing-parasutterella-genus/
Adlercreutzia: https://cfsremission.wordpress.com/2017/10/14/decreasing-adlercreutzia-genus/
Bilophila: https://cfsremission.wordpress.com/2017/10/14/decreasing-bilophila-genus/
Butyricimas: https://cfsremission.wordpress.com/2017/10/14/decreasing-butyricimonas-genus/
Oscillospira: https://cfsremission.wordpress.com/2017/10/15/decreasing-oscillospira-genus/
Intestinimonas: https://cfsremission.wordpress.com/2017/11/05/reducing-intestinimonas-genus/
Odoribacter: https://cfsremission.wordpress.com/2017/10/19/decreasing-odoribacter-genus/
Flavonifractor: https://cfsremission.wordpress.com/2017/11/05/reducing-flavonifractor-genus/
Alistipes: https://cfsremission.wordpress.com/2017/10/09/decreasing-alistipes-genus/
Moryella: https://cfsremission.wordpress.com/2017/11/11/decreasing-moryella-genus/
Bacteroides: https://cfsremission.wordpress.com/2017/10/20/decreasing-bacteroides-genus/
Dorea : https://cfsremission.wordpress.com/2017/10/18/reducing-dorea-genus/
Dialister: https://cfsremission.wordpress.com/2017/11/05/reducing-dialister-genus/

I have highlighted the extreme overgrowth associated suggestions in red

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

Bold — applies to HIGHEST, Italic to lowest

Allergens
Animal-based diet
Bacillus probiotics
Barley
Berbine
Bifidobacterium Animalis subsp. Lactis BB-12
Bifidobacterium catenulatum
Bifidobacterium longum.
Bifidobacterium pseudocatenulatum
Bile
Broad beans and lupin seeds
Clostridium butyricum
Fermented Korean soybean paste
Fish Oil
Fructo-oligosaccharides
Gallic acid
Gum arabic
Helminth infections
High animal protein/meat diet
High Fat Diet
High meat diet
Lactobacillus fermentum
Lactobacillus Reuteri
L-citrulline
Low fat diets
Lysine supplements and foods
Metformin
Milk-derived saturated fat
pomegranate juice
Proton-pump inhibitors (PPI)
Saccharin
Saccharomyces boulardii
Stevia
stress
Tannic acid
Walnuts (and likely pomegranates)

Take

Bold — applies to HIGHEST, Italic to lowest

Bifidobacterum Bifidum
Bifidobacterum Infantis
Cellobiose
Chicory
Cranberry bean flour (or fresh cranberries)
E.Coli Probioitics
Enzymatically modified resistant starch
Faecalibacterium prausnitzii
Flaxseed
Galactooligosaccharides
Gallate – green tea
Garlic
Grapes (table) – Resveratrol (grape seed extract)
Inulin
Lactobacillus Casei
Lactobacillus kefiri
Lactobacillus plantarum
Lactobacillus rhamnosus GG
Lactobacillus salivarius
L-glutamine
Oligosaccharide prebiotics
Oral Iron Supplements
Polymannuronic acid
Resistant starch (type II & IV)
Sucralose (Splenda)
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.

Hana 9:10 am on November 11, 2017

Thank you very much, abdominal swelling and fatigue are predominant factors.
The onset of the disease was due to digestive problems, with swollen abdomen, nausea, abdominal pain and discomfort.
- lassesen 4:31 pm on November 11, 2017
  
  If you think you can persuade your MD to look at your results and they may be willing to prescribe antibiotics, I would be glad to research and document(i.e. studies) suggested antibiotic candidates for your three highest overgrowth.
  
  I usually avoid giving any antibiotic recommendation — but with 14x overgrowth of one genus and a 5 fold shift in the F:B ratio — it should be considered if there is a willing MD
  - Hana 2:36 am on November 12, 2017
    
    Thanks, I think I can try to have my doctor check for overgrowth and prescribe an antibiotic.
  - Hana 7:43 am on November 13, 2017
    
    Ken was treated years ago with RIFAXIMINA six days a month the digestive symptoms improved, but in a short time it was bad again. Never combine it with prebiotics and probiotics, I think if that would be an adequate path.
Rosa Entrealmendros (Rosi Morales) 8:27 am on November 12, 2017

Hana, me alegro mucho de que ya tengas una camino a seguir, ken esta haciendo una labor maravillosa con nosotros. Te deseo mucha suerte con tu inmersión el el mundo del microbioma.

Hana, I’m glad you already have a route to follow, Ken is doing a wonderful job with us. I wish you good luck with your immersion in the microbiome world.
- Hana 7:35 am on November 13, 2017
  
  Thank you Rosa, it will take time to learn but it will be achieved. The work that Ken does is fantastic, if it were not for his informative work and his studies he would never have had a new hope.
  - Hana 7:36 am on November 13, 2017
    
    Gracias Rosa, va a llevar tiempo aprender pero se lograra. El trabajo que hace Ken es fantastico, si no es por su labor divulgativa y sus estudios nunca habria podido tener una nueva esperanza.
Gary 10:47 am on November 12, 2017

Hi Ken,
My Ubiome showed up high Bacterioidetes and explains why i am quiet thin and can’t gain weight. Is there a way to do the opposite and swing the ratio from Bacterioidetes to Firmicutes?
- lassesen 3:53 pm on November 12, 2017
  
  Yes, my basic approach is to reduce the high bacteria genus. Once those are reduced, there are some bacteria genus associated with weight gain. then it would be encouraging those.
  
  Are you able to use my list here (https://cfsremission.com/2017/10/08/update-and-recap/) to sort out probable changes of diet etc? Are there any deep dives of a specific genus that are missing in that list. If not send me your login and I will do a post using it.
  - Gary 9:43 pm on November 12, 2017
    
    Thanks Ken.
    Yes the diet i am able to follow and by the looks of it, am already consuming those foods. I sent my login details about a month ago,but will send you a PM with the login details.
    For some reason my name is coming up as Gary,but it’s Jason. Some kind of glitch from my end.
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