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

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!

• Sutterella: https://cfsremission.wordpress.com/2017/10/13/decreasing-sutterella-genus/
• Moryella: https://cfsremission.wordpress.com/2017/11/11/decreasing-moryella-genus/
• Bilophila:   https://cfsremission.wordpress.com/2017/10/14/decreasing-bilophila-genus/
• Phascolarctobacterium: https://cfsremission.wordpress.com/2017/11/12/decreasing-phascolarctobacterium-genus/
• Erysipelatoclostridium: https://cfsremission.wordpress.com/2017/11/14/decreasing-erysipelatoclostridium-genus/
• Collinsella: https://cfsremission.wordpress.com/2017/10/10/decreasing-collinsella-genus/
• Dorea :  https://cfsremission.wordpress.com/2017/10/18/reducing-dorea-genus/
• Parabacteroides: https://cfsremission.wordpress.com/2017/10/17/decreasing-parabacteroides-genus/
• Anaerostipes:   https://cfsremission.wordpress.com/2017/10/07/decreasing-anaerostipes-genus/
• Peptoclostridium: https://cfsremission.wordpress.com/2017/11/18/reducing-peptoclostridium-genus/
• Senegalemassilia: https://cfsremission.wordpress.com/2017/11/18/reducing-senegalemassilia-genus/

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.

For updated information see Microbiome Prescription

DataPunk.Net Data

ENHANCED BY

• Partial Sleep Deprivation [parent]

PubMed Data

There are 1+ studies on PubMed.

“This bacterium was isolated from the feces of a healthy Senegalese patient. It is a Gram-positive, anaerobic, indole-negative coccobacillus. ” [2013]

Disease

Diet

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

Take

• Lots of sleep!

For updated information see Microbiome Prescription

Includes Clostridium difficile (Peptoclostridium difficile)

DataPunk.Net Data

INHIBITED BY

• Cranberry bean flour [parent]

PubMed Data

There are 10+ studies on PubMed

Disease

Diet

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

Take

• Cranberry bean flour [parent]

Symptoms:

Extreme fatigue,brain fog,adrenal fatigue/low cortisol,high th2,constipation alternating to loose stools,bloating,depression,underweight. High levels of klebsiella pneumoniae found in stool test. All of the the typical CFS symptoms.

Standard Elements

•  Lactobacillus 0x
• Bifidobacterium 0x
• Diversity:  2%  (unusually low)

Overgrowths of Bacteria Genus

Reference Deep Dives

• Alistipes: https://cfsremission.wordpress.com/2017/10/09/decreasing-alistipes-genus/
• Bacteroides: https://cfsremission.wordpress.com/2017/10/20/decreasing-bacteroides-genus/
• Parabacteroides: https://cfsremission.wordpress.com/2017/10/17/decreasing-parabacteroides-genus/
• Sutterella: https://cfsremission.wordpress.com/2017/10/13/decreasing-sutterella-genus/
• Barnesiella: https://cfsremission.wordpress.com/2017/10/15/decreasing-barnesiella-genus/

Rare Bacteria Genus

Nothing below 5%

Bottom Line

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
• Aspirin (other NSAID’s are fine)
• Bacillus probiotics
• Bacillus subtilis
• Bifidobacterium Animalis subsp. Lactis BB-12
• BPA bottles
• Broad beans  and lupin seeds
• Canole Oil
• Cranberry
• Fructo-oligosaccharides
• Gallic acid
• Glutten
• Gum arabic
• High meat diet
• Lactobacillus casei
• Lactobacillus acidophilus La-5
• Lactobacillus Fermentum
• Lactobacillus paracasei
• Lactobacillus rhamnosus GG
• Lactobacillus plantarum
• L-citrulline
• Lingonberries
• Low fat diets
• Melatonin
• Oligofructose
• Pea Fibre
• Proton-pump inhibitors (PPI)
• Red wine, Grape Seed Extract
• Resistant starch (type IV)
• Resveratrol (Grapes, wine)
• Rhubarb
• Saccharin
• Stevia
• Tannic acid

Take

• Bacillus licheniformis
• Bacillus subtilis natto (or nattokinease supplements)
• Bifidobacterum Bifidum
• Bifidobacterum Infantis
• Bifidobacterum Longum
• Bile supplements
• Capsaicin  (chili peppers)
• Dairy Products
• Faecalibacterium prausnitzii
• Garlic
• High Fat diet
• Lactobacillus kefiri LKF01
• Metronidazole antibiotics
• Polymannuronic acid
• Sucralose (Splenda)
• Tannin and Gallate   — green tea see this web page.
• Walnuts
• Whole-grain barley
• Xylitol
• β-Glucan

The Compounded Probiotic Dilemma!

The reader asked about taking Megaspore (which he just received). Checking my post for Bacillus probiotics that I know about, we find that it is the only one containing

• Bacillus licheniformis [TAKE]

But it also contain

• Bacillus subtilis [AVOID]

This leaves us with a dilemma which people will resolve different ways. Being aware of patients financials and that probiotic potency decreases over time, I would proceed for myself as follows:

• Use the Megaspore but do not reorder. Keep one week supply for a re-trial later.
• While not doing other changes, slowly ramp up and see if it has any impact

Once exhausted (except for the one week retrial amount) stay off it for at least 6 weeks and see if there are any changes from stopping it.  Do a retrial of it for a week and see if the earlier changes repeat or not. Re-evaluate based on your actual experience.

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.

A year ago, several readers shared their ubiome for me and I did a series of post looking for patterns. See this post on the Genus Numbers.

It is time that I do deep dives for these early sharers.

Results B

• Sure, I got sick with ME after an infection I probably picked up on the airplane back from Asia. Probably lived in mold a few years prior to that that probably took my immune system down too, before the final straw with the infection. Major symptoms: fatigue, unable to do much physically, brainfog, get tired of concentrating too much and being social, my head “shuts down”, joint pain, muscle pain, headaches, swollen lymph nodes, feeling like a flu is coming on very frequently, everything is made worse by too much exertion I do not think I did much probiotics before the sample was done actually…
  • 4/12/2014

Deep Dive References

• Intestinimonas: https://cfsremission.wordpress.com/2017/11/05/reducing-intestinimonas-genus/
• Thalassospira: https://cfsremission.wordpress.com/2017/10/22/reducing-thalassospira-genus/
• Alistipes: https://cfsremission.wordpress.com/2017/10/09/decreasing-alistipes-genus/
• Bilophila:   https://cfsremission.wordpress.com/2017/10/14/decreasing-bilophila-genus/
• Oscillospira: https://cfsremission.wordpress.com/2017/10/15/decreasing-oscillospira-genus/
• Acetitomaculum: https://cfsremission.wordpress.com/2017/11/14/decreasing-acetitomaculum-genus/
• Butyricimas: https://cfsremission.wordpress.com/2017/10/14/decreasing-butyricimonas-genus/
• Clostridium :  https://cfsremission.wordpress.com/2017/10/07/decreasing-clostridium-genus/
• Lachnospira: https://cfsremission.wordpress.com/2017/11/03/reducing-lachnospira-genus/
• Blautia:   https://cfsremission.wordpress.com/2017/10/29/reducing-blautia-genus/
• Sarcina: https://cfsremission.wordpress.com/2017/10/12/decreasing-sarcina-genus/
• Collinsella: https://cfsremission.wordpress.com/2017/10/10/decreasing-collinsella-genus/
• Dialister:  https://cfsremission.wordpress.com/2017/11/05/reducing-dialister-genus/
• Erysipelatoclostridium: https://cfsremission.wordpress.com/2017/11/14/decreasing-erysipelatoclostridium-genus/

Bottom Line Suggestions

The items from each of the deep dives aligned very nicely for this microbiome, for example, Inulin was listed many times.

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

• Clostridium butyricum
• Bacillus subtilis
• Barley
• Berberine
• Bifidobacterium longum
• Bifidobacterium animalis
• Brown rice
• Cholic acid
• Dairy
• Flavone
• Fluoroquinolone
• Generic Bacillus probiotics
• High animal protein/meat diet
• High grain diet
• Isoniazid-
• Lactobacillus fermentum
• Lactobacillus plantarum
• Lactobacillus Reuteri
• Lysine supplements and foods
• Metformin
• Milk-derived saturated fat
• omega-3
• Pyrazinamide
• Rifampin-
• Rosemary
• Saccharomyces boulardii
• Safflower oil
• Sleepless nights
• Sodium butyrate
• Starch
• Vegetables
• Walnuts
• Wheat breads

Take

• Bacillus licheniformis
• Bifidobacterium Breve
• Bifidobacterum Bifidum
• Bifidobacterum Infantis
• Cellobiose
• Chicory
• Chitosan supplements
• Cranberry bean flour (or fresh cranberries)
• Coli Probioitics
• Enterococcus  faecalis probiotics
• Faecalibacterium prausnitzii
• Fennel
• Flaxseed
• Gluten free diet
• Grape seed polyphenols,/ Wine
• Green or black tea
• Chocolate
• High resistance starch
• Inulin
• Ketogenic diet
• Lactobacillus Casei
• Lactobacillus acidophilus
• Lactobacillus paracasei (24 BCFU)
• Low calories High protein diet
• L-glutamine
• lychee, rambutan, guarana, korlan, pitomba, Spanish lime and ackee. [fam-Sapindaceae]
• NSAIDs (see list here), I prefer aspirin as first choice.
• oral iron supplements
• Oranges (pectin/flavanones)
• Polymannuronic acid
• pomegranate (walnuts is likely helpful too)
• Prescript Assist
• Streptococcus Probiotics
• Sunflower seeds and oil
• Thiamine

Vitamin D3

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.