For updated information see Microbiome Prescription

Most studies were done with cattle.

DataPunk.Net Data

INHIBITED BY

• Flaxseed [parent]

ENHANCED BY

• Partial Sleep Deprivation [parent]

PubMed Data

There are 3+ studies on PubMed

Disease

• Gout ..being up-regulation of opportunistic pathogens, such as Bacteroides, Porphyromonadaceae Rhodococcus, Erysipelatoclostridium and Anaerolineaceae. [2017]
• “Our data also showed that Erysipelatoclostridium, Gemella, Granulicatella,
  Mogibacterium, Rothia, and Streptococcus increased dramatically in Crohn’s Disease patients,” [2017]
• “Erysipelatoclostridium (0.77% vs 2.04% in the healthy infants, q-value < 0.05) ..in

  bronchiolitis” [2017]

• “Whereas in individuals with other neurological diseases, increase of bacterium Erysipelatoclostridium ramosum”[2016]

Diet

• “Dairy intake was positively associated with the Firmicutes:Bacteroidetes ratio, and in particular Erysipelatoclostridium spp.,” [2016]
• “ketogenic diet exposure also induced a decrease in Erysipelatoclostridium (by 8.67% ..)” [2017]
• “

Prebiotic

Probiotics

Antibiotics

• “Interestingly, increases (as opposed to decreases) in bacterial taxa due to isoniazid-rifampin-pyrazinamide treatment were limited to genus Erysipelatoclostridium (and genus Eggerthia in the naïve versus TB + HRZ comparison).” [2017]

Bottom Line

Avoid

• Sleepless nights
• Isoniazid-
• Rifampin-
• Pyrazinamide
• Dairy

Take

• Flaxseed
• Ketogenic diet

For updated information see Microbiome Prescription

Most studies were done with cattle.

DataPunk.Net Data

INHIBITED BY

• Flaxseed [parent]

ENHANCED BY

• Walnuts [parent]
• Saccharomyces boulardii [parent]

PubMed Data

There are 10+ studies on PubMed

Disease

Diet

• “Sunflower Oil addition decreased the relative abundance of Rikenellaceae_RC9 and Acetitomaculum. Starch increases” [2013]
• Xylan increases [1994]

Prebiotic

Probiotics

Antibiotics

Bottom Line

Avoid

• Walnuts
• Saccharomyces boulardii 
• Starch

Take

• Flaxseed
• Sunflower seeds and oil

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 C:

• Diagnosis: ME/CFS, POTS, MCAS, IBS-C, mold illness. No probiotics before test. I changed environments and had some health improvement between tests.
  • C1 10/1/2013
  • C2 9/13/2015
  • C3 6/23/2016

Deep Dive References

• Akkermansia: https://cfsremission.wordpress.com/2017/10/14/decreasing-akkermansia-genus/
• Bilophila:   https://cfsremission.wordpress.com/2017/10/14/decreasing-bilophila-genus/
• Alistipes: https://cfsremission.wordpress.com/2017/10/09/decreasing-alistipes-genus/
• Eggerthella: https://cfsremission.wordpress.com/2017/10/19/decreasing-eggerthella-genus/
• Intestinimonas: https://cfsremission.wordpress.com/2017/11/05/reducing-intestinimonas-genus/
• Odoribacter: https://cfsremission.wordpress.com/2017/10/19/decreasing-odoribacter-genus/
• Bacteroides: https://cfsremission.wordpress.com/2017/10/20/decreasing-bacteroides-genus/
• Flavonifractor: https://cfsremission.wordpress.com/2017/11/05/reducing-flavonifractor-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

• Akkenmansia muciniphila probiotic (when it becomes available)
• Allergens
• Animal-based diet
• Arginine supplements
• Bacillus subtilis
• Barley
• Bifidobacterium Animalis subsp. Lactis BB-12
• Bifidobacterium catenulatum
• Bifidobacterium pseudocatenulatum
• Bile
• Broad beans  and lupin seeds
• Capsaicin (Chili Peppers)
• Daesiho-tang (DSHT)
• fermented Korean soybean paste
• Fructo-oligosaccharides
• gum arabic
• Heme
• High animal protein/meat diet
• High meat diet
• High protein diet
• L. casei
• Lactobacillus acidophilus
• Lactobacillus fermentum
• L-citrulline
• Lingonberries
• Low fat diets
• Low processed foods diet
• Lysine supplements and foods
• Melatonin
• Metformin
• Milk-derived saturated fat
• Pomegranate ellagitannins
• pomegranate juice
• Resveratrol
• Rhubarb
• Saccharin
• Stevia
• Stress
• Tannic acid

Take

• Bacillus licheniformis
• Bacillus subtilis natto
• Bifidobacterum Bifidum
• Bifidobacterum Infantis
• Chicory
• Faecalibacterium prausnitzii
• Flaxseed
• Garlic
• Inulin
• Lactobacillus kefiri LKF01
• Lactobacillus plantarum
• Oligosaccharide prebiotics
• Omega 3 fatty acids
• Polymannuronic acid
• Sucralose (Splenda)
• Tea Tree Oil
• Vitamin D
• Walnuts
• Whole-grain barley
• 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.

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 D:

• IBS. No CFS
  • D2 1/16/2015
  • D1  3/26/2015

Deep Dive References

• Dorea :  https://cfsremission.wordpress.com/2017/10/18/reducing-dorea-genus/
• Clostridium :  https://cfsremission.wordpress.com/2017/10/07/decreasing-clostridium-genus/
• Blautia:   https://cfsremission.wordpress.com/2017/10/29/reducing-blautia-genus/
• Enterorhabdus: https://cfsremission.wordpress.com/2017/11/05/reducing-enterorhabdus-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

• Animal-based diet
• Bacillus subtilis
• barley
• Berberine.
• Bifidobacterium longum
• Bifidobacterium animalis
• brown rice
• Cholic acid
• flavone
• Fluoroquinolone
• Helminth infections
• high grain diet
• Lactobacillus plantarum
• Lactobacillus salivarius
• Metformin
• omega-3
• Resistant starch (type II, IV)
• Rosemary
• Saccharomyces boulardii
• Safflower oil
• Sodium butyrate
• Stress
• Walnuts (and likely pomegranates)

Take

• Bacillus licheniformis
• Bifidobacterium Breve
• Bile acid
• Chitosan supplements
• Coconut Oil, Monolaurin (Lauric Acid)
• Flaxseed
• Galactooligosaccharides
• Grape seed polyphenols,/ Wine
• Have Chocolate!
• Lactobacillus casei
• Lactobacillus paracasei  24 billion viable  daily
• l-glutamine
• Oral Iron Supplements
• Oranges (pectin/flavanones)
• Polymannuronic acid
• Prescript Assist
• Smoking (!?!)
• Streptococcus Probiotics
• Vitamin D3
• Xylooligosaccharide
• 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.

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 A

• ME/CFS for 20 years, 90-100% functional for years 2-8, 60 – 80% functional for years 9-16, 10% – 70% functional for years 16-20 Currently about 50%-60% again. Main symptoms, fatigue, lack of energy, feeling crappy (flu-like), get sick easily and stay sick for months (I have 2 kids 8 – 10 now so they kept bring home infections) no brain fog now, but currently issues with a tired brain, IBS or dysbiosis, Urinary Issues
  • A1 – 9/18/2015
  • A2 3/17/2016

Deep Dive References

• Intestinimonas: https://cfsremission.wordpress.com/2017/11/05/reducing-intestinimonas-genus/
• Flavonifractor: https://cfsremission.wordpress.com/2017/11/05/reducing-flavonifractor-genus/
• Marvinbryantia: https://cfsremission.wordpress.com/2017/11/06/decreasing-marvinbryantia-genus/
• Terrisporobacter: https://cfsremission.wordpress.com/2017/11/05/reducing-terrisporobacter-genus/
• Hespellia: https://cfsremission.wordpress.com/2017/11/05/reducing-hespellia-genus/
• Phascolarctobacterium: https://cfsremission.wordpress.com/2017/11/12/decreasing-phascolarctobacterium-genus/

• Subdoligranlum: https://cfsremission.wordpress.com/2017/10/10/decreasing-subdoligranlum/

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

• Berberine
• Bifidobacterim Breve
• High Fat Diet
• Lactobacillus salivarius
• Lysine supplements and foods
• Minocycline
• Omega 3
• Penicillin
• Polydextrose
• Saccharomyces boulardii
• Soluble corn fiber
• Walnuts (and likely no  pomegranate – both are high urolithin)

Take

• Acarbose
• Cranberry bean flour
• Flaxseed
• Fumarate
• Galactooligosaccharides (GOS)
• High Protein Diet
• Inulin
• Lactobacillus kefiri LKF01
• Lactobacillus paracasei
• palm kernel meal
• Resistant starch (type II)
• Sodium chloride (Table Salt)
• Tea

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.