Reader Notes

“My official diagnosis is ME/CFS from Stanford and I’ve tried a lot of different treatments including a year of Valcyte. I’ve gotten everything under the sun tested. Have such a high amount of Candida that a Gastro Doc said that I must have an autoimmune disease but found nothing.”

This all started when I was a Peace Corps Worker in Panama. I got really sick in the jungle where I was working and after one day in the river I started getting a tingling feeling in my out extremities. It then turned to burning sensation, fatigue, brain fog, restless legs, unable to sleep, tiredness, unrestful sleep, and IBS. Its been 5 years and I’ve a lot of treatments.

Standard Items:

• Lactobacillus: 0.01x
• Bifidobacterium: 0.88x
• Akkermansia:  1.06x
• Diversity:  79%ile
• Firmicutes to Bacteroidetes: 1.4:1 (Normal 2.1:1)

Uncommon Bacteria

High Bacteria

Reference

• Paraprevotella:https://cfsremission.wordpress.com/2017/11/28/decreasing-paraprevotella-genus/
• Parabacteroides: https://cfsremission.wordpress.com/2017/10/17/decreasing-parabacteroides-genus/
• Moryella: https://cfsremission.wordpress.com/2017/11/11/decreasing-moryella-genus/
• Peptococcus: https://cfsremission.wordpress.com/2017/11/28/decreasing-peptococcus-genus/
• Terrisporobacter: https://cfsremission.wordpress.com/2017/11/05/reducing-terrisporobacter-genus/
• Thalassospira: https://cfsremission.wordpress.com/2017/10/22/reducing-thalassospira-genus/

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
• Canola Oil
• Lactobacillus caseiLactobacillus paracasei
• Lactobacillus rhamnosus
• Lingonberries
• Proton-pump inhibitors (PPI)
• Resistant Starch
• Rhubarb
• Rice bran
• Saccharomyces boulardii
• Sleep Apnea
• Walnuts

Take

• Berberine
• Capsaicin(chili peppers)
• Cinnamon
• Cranberry
• Flaxseed
• Gallate (tea)
• High Fat Diet
• Lactobacillus reuteri
• Metronidazole antibiotics
• Palm kernel meal

Comment

This microbiome had many genus uncommon with CFS. Given that the onset was probably a tropical infection, and each infection alters the microbiome in distinctive manners, I suspect this was a contributory factor for the unusual genus appearing as well as  Bifidobacterium and Akkermansia being close to normal. In terms of general supplements from this post, these are likely the most important

• γ-Amino butyric acid (GABA)
• Trimethylamine
• Vitamin B12
• Acetylcholine

To the above, dairy should be added to increase the Firmicutes to Bacteroidetes ratio (see this post)

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. 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

INHIBITED BY

• Gallate [parent]
• Cranberry bean flour [parent]

ENHANCED BY

• Walnuts [parent]

PubMed Data

There are  690+ studies on PubMed

Disease

• “These included (increaased) Aggregatibacter (OTU id 4335776), Aggregatibacter segnis (A. segnis), Campylobacter, Capnocytophaga, Clostridiales, Dialister, Leptotrichia, Parvimonas, Peptostreptococcus, Peptococcus, Prevotella, Selenomonas, SR1, Tannerella, TM7-3 and Treponema in the Intra-oral halitosis  group. ” [2017]
• Infection of the foot with Peptococcus magnus [1977].
• “Mixed Peptococcus magnus infections involved the following sites: bone and joint (32 cases), soft tissue (57 cases), foot ulcers (29 cases), abdominal cavity (16 cases), and miscellaneous (17 cases).” [1980]

Diet

• “At the genus level, Peptococcuswere decreased in the cinnamon bark group.” [2017]

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

• Walnut

Take

• Gallate (tea)
• Cranberry
• Cinnamon

For updated information see Microbiome Prescription

DataPunk.Net Data

ENHANCED BY

• Cranberry bean flour [parent]

PubMed Data

There are 11+ studies on PubMed

Disease

• “early-stage primary biliary cirrhosis  were enriched in some bacterial taxa containing opportunistic pathogens, such as γ-Proteobacteria, Enterobacteriaceae, Neisseriaceae, Spirochaetaceae, Veillonella, Streptococcus, Klebsiella, Actinobacillus pleuropneumoniae, Anaeroglobus geminatus, Enterobacter asburiae, Haemophilus parainfluenzae, Megasphaera micronuciformis and Paraprevotella clara. ” [2016]
• “Substance Abuse Disorders… At the genus level, bacteria from Bacteroides (24.20% vs 33.97%), Faecalibacterium (5.62% vs 6.93%), Alistipes (1.21% vs 2.49%), Gemmiger(0.49% vs 1.68%), Clostridium XI (0.77% vs 1.83%), Escherichia/Shigella(0.99% vs 1.65%), Dialister (0.43% vs 0.98%), Paraprevotella (0.19% vs 0.72%), Megasphaera (0.23% vs 0.70%), Haemophilus (0.37% vs 0.80%), Parabacteroides (1% vs 1.29%), Barnesiella (0.26% vs 0.53%), and Blautia(0.44% vs 0.48%) were less abundant ” [2017]
• ” Liver disease whereas Akkermansia spp. (1 OTU), Alistipes spp. (29 OTUs), Barnesiella spp. (75 OTUs), Blautia spp. (1 OTU), Lactobacillus spp. (5 OTUs), Odoribacter spp. (73 OTUs), Parabacteroides spp. (2 OTUs), Paraprevotella spp. (21 OTUs), Parasutterella spp. (35 OTUs), Prevotella spp. (54 OTUs) were significantly decreased.” [2016]
• “at the genus level, bacteria from Bacteroides (26.62% vs 37.02%), Megamonas (5.27% vs 7.35%), Gemmiger (0.44% vs 2.06%), Escherichia/Shigella (1.10% vs 2.45%), Alistipes (1.17% vs 2.22%), Parabacteroides (1.07% vs 1.80%), Paraprevotella (0.23% vs 0.76%), Dialister (0.47% vs 1.00%), Haemophilus (0.50% vs 0.90%), Veillonella(0.57% vs 0.69%), Blautia (0.36% vs 0.55%), Megasphaera (0.25% vs 0.51%), Parasutterella (0.19% vs 0.47%), and Clostridium XlVa (1.05% vs 1.07%) were less abundant
• “At the level of genus, hypoxia resulted in significant greater values of Paraprevotella and Prevotella, and smaller ones of Odoribacter and Bacteroides (according to the Bacteroidetes Genera), and in the case of the Firmicutes genera, smaller abundances of Turicibacter, rc4-4, Oscillospira and Allobaculum, than the control group ” [2014]

Diet

• “Stool microbiome analysis from rice bran group showed significant genus level increases in Methanobrevibacter, Paraprevotella, uminococcus, and Bifidobacterium compared to the control group,”

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

• Cranberry
• Sleep Apnea
• Rice bran

Take

Web Site to do Analysis Coming

Over the Christmas holidays I am hoping to write a web site that will allow people to self-serve — with better algorithms where there is a conflict, and report symptoms with their ubiome results. Once that is up, I will discontinue these analysis unless one of great interest appears.

Reader Notes

• Leaky Gut –> IBS –> CFS with mild MCS –> remission –> atypical Crohn’s with fistulas and severe MCS
• None of the CFS symptoms (no brain fog, tiredness, etc)
• MCS
• Histamine issues

Standard Items:

• Diversity: 15%ile
• Lactobacillus:  0.0x
• Bifidobacterium: 0.01x
• Akkermansia: 0.01x
• Firmicutes:Bacteroidetes: 3.6:1 (Normal  2.1:1)

Most aspects of a CFS profile, but as with a prior review, diversity is at the opposite end of the spectrum

Uncommon Bacteria

High Bacteria

Reference

• Anaerostipes:   https://cfsremission.wordpress.com/2017/10/07/decreasing-anaerostipes-genus/
• Slackia: https://cfsremission.wordpress.com/2017/10/15/decreasing-slackia-genus/
• Barnesiella: https://cfsremission.wordpress.com/2017/10/15/decreasing-barnesiella-genus/
• Oscillospira: https://cfsremission.wordpress.com/2017/10/15/decreasing-oscillospira-genus/
• Gordonibacter: https://cfsremission.wordpress.com/2017/10/09/decreasing-gordonibacter-genus/
• Clostridium :  https://cfsremission.wordpress.com/2017/10/07/decreasing-clostridium-genus/
• Blautia:   https://cfsremission.wordpress.com/2017/10/29/reducing-blautia-genus/
• Anaerotruncus: https://cfsremission.wordpress.com/2017/11/19/reducing-anaerotruncus-genus/
• Parasutterella: https://cfsremission.wordpress.com/2017/10/19/decreasing-parasutterella-genus/
• Fusicatenibacter: https://cfsremission.wordpress.com/2017/11/03/decreasing-fusicatenibacter-genus/

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

• Arabinoxylans
• Aspirin (other NSAID’s are fine)
• Bacillus subtilis
• barley
• Berberine
• Bifidobacterium adolescentis
• Bifidobacterium catenulatum
• Bifidobacterium longum
• Bifidobacterium pseudocatenulatum
• Bifidobacterium animalis lactis
• brown rice
• Butyrate producing probiotics
• Chicory root
• Cholic acid
• CVS Maximum Strength Probiotic
• flavone
• Fluoroquinolone
• Glucose foods (fructose [fruit sugar] appears to be fine)
• Glutten
• high grain diet
• inulin
• Lactobacillus fermentum
• Lactobacillus plantarum
• Lactobacillus rhamnosus GG
• Lactobacillus salivarius
• L-sorbose
• Metformin
• Oligofructose
• Omega-3
• Pomegranate
• Raspberries
• Resistant starch (type II, IV)
• Rosemary
• Saccharomyces boulardii
• Safflower oil
• Sodium butyrate
• Vitamin K2
• Walnuts

Take

• Alchohol
• Bacillus licheniformis
• Bifidobacterium Breve
• Bile supplements
• Chitosan supplements
• Enzymatically modified resistant starch
• Flaxseed
• Gallate – Tea
• Grape seed polyphenols,/ Wine
• Have Chocolate!
• Lactobacillus Casei
• Lactobacillus Kefiri
• Lactobacillus Paracasei (24 BCFU/daily)
• Lactobacillus Rhamnosus
• Mutaflor (E.Coli Nissle 1917)
• Oranges (pectin/flavanones)
• Polymannuronic acid
• Prescript Assist
• Resistant starch (type II & IV)
• Streptococcus probiotics
• Vitamin D3
• Xylooligosaccharide (XOS) prebiotic

A Challenge with Probiotics:

Inulin is on the avoid list and it is unfortunately included with many probiotics.

CustomProbiotics.com do not add any prebiotics and provide single species, thus a source for:

• Lactobacillus Casei – 160 BCFU per serving
• Lactobacillus Kefiri – only one source at present (Italy), appears to be inulin free. 1 BCFU/serving
• Lactobacillus Paracasei – 300 BCFU per serving
• Lactobacillus Rhamnosus  –  160 BCFU per serving
• Streptococcus 320 BCFU per serving

• Xylooligosaccharide (XOS) prebiotic lozenges are available (AOR)    AOR Site

• Bacillus licheniformis appears to be only available in mixtures with Bacillus subtilis — so not feasible
• Polymannuronic acid – is in Sodium Alginate (a food thickening agent) – Amazon

Financials

Usually I do not look at the cost and advocate people do what they can

• Custom Probiotics: US$630 for 4 month supply or $157/month
• Mutaflor:  $80/month

So taking continuously, $250/month. Alternating in two sets: $125/month, 3 sets $85/month, or lower dosages of each.

After exhausting the probiotics above,  another uBiome should be done. The microbiome would likely have shifted and we want to know if we need to change things.

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

I recently did a post on blood pressures and the microbiome, a disturbance often seen with CFS/FM/IBS.  Hypothyroidism is also a common disturbance.

“autoimmune thyroid disease (AITD). The underlying mechanism comprises inherent genetic predisposition, abnormality of Th17 and Treg related biological molecules, and gut microbiota disorder. ” [2017]

“With a little help from my friends” – The role of microbiota in thyroid hormone metabolism and enterohepatic recycling [2017].

• “Functional thyroid disorders were associated with bacterial overgrowth and a different microbial composition. Although thyroid metabolism was apparently disregarded, the interference of microbiota on peripheral iodothyronine homeostasis is an intriguing issue. In this review we focused on the interactions of intestinal microbiota with thyroid-related micronutrients and with the metabolic steps of endogenous and exogenous iodothyronines.”

Does microbiota composition affect thyroid homeostasis? [2015]

• “real-time PCR showed obvious decrease of Bifidobacterium and Lactobacillus ((*) P < 0.05), and increase of Enterococcus ((*) P < 0.05) in the hyperthyroid group. ” [2014]

Grave’s Disease

• “Common risk factors for GD (gender, smoking, stress, and pregnancy) reveal profound changes in the bacterial communities of the gut compared to that of healthy controls but a pathogenetic link between GD and dysbiosis has not yet been fully elucidated.” [2017]
• ” Interestingly, all the environmental factors involved in Graves’ disease(GD) and Graves’ orbitopathy (GO) pathogenesis can alter the balance within the microorganisms located in the gut, and influence the immune system, in particular the proportions of regulatory Treg and inflammatory TH17 cells. It is hoped that investigating GD and GO pathogenesis from this novel aspect will identify new targets for prevention and treatment.” [2017]

Hashimoto’s thyroiditis

• “We observed the declined abundance of Prevotella_9 and Dialister, while elevated genera of the diseased group included Escherichia-Shigella and Parasutterella. The alteration in gut microbial configuration was also monitored at the species level, which showed an increased abundance of E. coli in HT. Therefore, the current study is in agreement with the hypothesis that HT patients have intestinal microbial dysbiosis.” [2017]
• Does the gut microbiota trigger Hashimoto‘s thyroiditis? [2014]
  “Further studies are clearly needed to test the hypothesis that the gut commensal microflora represents an important environmental factor triggering Hashimoto‘s thyroiditis.”
• “Components of several viruses such as hepatitis C virus, human parvovirus B19, coxsackie virus and herpes virus are detected in the thyroid of Hashimoto’s thyroiditis patients. ” [2010]
• “Similar changes have interestingly been detected in patients with Hashimoto’s thyroiditis (Cindoruk et al., 2002; Sasso et al., 2004), suggesting a pathogenic role of the leaky gut barrier in the development of Hashimoto’s thyroiditis.” [2012]

Bottom Line

Research is looking more and more at the microbiome aspect of thyroid dysregulation. (note all of the 2017 studies). We have had only a few studies done of the shifts. We see that the same low lactobacillus and bifidobacterium pattern is seen as with CFS/IBS/FM.  Enterococcus and Parasutterella  are overgrowth that I have already covered:

• Enterococcus: https://cfsremission.wordpress.com/2017/10/29/reducing-enterococcus-genus/
• Parasutterella: https://cfsremission.wordpress.com/2017/10/19/decreasing-parasutterella-genus/

This hints some of the following actions may be useful in reducing the microbiome shift

Avoid

• High fat diet
• Bile
• Sesame cake/meal
• Esculin
• Red wine
• Navy bean (Cooked)
• Berbine
• Metformin
• Vitamin K2
• Bifidobacterium pseudocatenulatum
• Bifidobacterium catenulatum

Take

• Lactobacillus Plantarum
• Lactobacillus Fermentum (ME3  or   CECT5716)
• Triphala (see this post)
• Hyperiform (St. John’s Wort)
• Glycyrrhizic acid (a.k.a. Licorice)
• Resistant starch (type IV)
• Propolis (from bees)

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