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.

A reader forwarded me a link to new probiotic that he is trying. Lactobacillus fermentum CECT5716 .  I post about Lactobacillus Fermentum ME3 – earlier

“Lactanza ^® hereditum ^® is a dietary supplement based on Lactobacillus fermentum Lc40 (CECT5716), a strain found naturally in breast milk. It is the first probiotic that contributes to the balance of the mammary flora.

The administration of Lactobacillus fermentum Lc40 (CECT5716) reduces the bacterial concentration of Staphylococcus in the mammary flora and helps to restore its balance, allowing a more comfortable and healthy lactation, and reducing the recurrence rate in mastitis ^31,32 . This helps to maintain lactation since mastitis is the main medical cause of premature and unwanted abandonment of breastfeeding ²³ .”

PubMed Literature

There are 20+ studies on this specific strain on PubMed ranking it as one of the most studies probiotic at the strain level.

• A synbiotic composed of Lactobacillus fermentum CECT5716 and FOS prevents the development of fatty acid liver and glycemic alterations in rats fed a high fructose diet associated with changes in the microbiota [2017].
• [Lactobacillus fermentum CECT5716 – probiotic from human milk with interesting properties] [2016].
• Lactobacillus fermentum CECT 5716 Reduces Staphylococcus Load in the Breastmilk of Lactating Mothers Suffering Breast Pain: A Randomized Controlled Trial. [2015]
• “Long-term administration of probiotics reduced systolic blood pressure.” [2015]
• The viability of Lactobacillus fermentum CECT5716 is not essential to exert intestinal anti-inflammatory properties [2015].
• Human milk probiotic Lactobacillus fermentum CECT5716 reduces the incidence of gastrointestinal and upper respiratory tract infections in infants [2012].
• Oral intake of Lactobacillus fermentum CECT5716 enhances the effects of influenza vaccination. [2007]
• Two Lactobacillus strains, isolated from breast milk, differently modulate the immune response [2007].
• “Therefore, in general, the effect of Lact. fermentum CECT5716 is immunostimulatory in contrast to the anti-inflammatory effect of Lact. salivarius CECT5713.” [2007]
• “Pretreatment with L. fermentum CECT 5716 attenuates trinitrobencene sulfonic acid  colitis, an effect that seems to be due to its antioxidant abilities. When administered after trinitrobencene sulfonic acid , this probiotic is also effective in accelerating colitis recovery, and this is associated with an enhanced Toll-like receptor function.” [2009]

• Lactobacillus plantarum CECT7315 and CECT7316 stimulate immunoglobulin production after influenza vaccination in elderly [2012]

Bottom Line

This is human sourced, like Lactobacillus Fermentum ME3 , and appear to have similar characteristics. It is well studies.

It is available on Amazon.co.uk , Amazon.es,, Amazon.it  but not US or Canadian sites.

Reader Summary

“I am a 56 year old female with a long history of illnesses followed by partial recovery for 5-7 years until the next thing hits me.  I was diagnosed with IBS and had multiple repeat infections in my teens (respiratory, bladder and yeast infections), mid 20’s I had a severe EBV infection (titers 10,240) and was hospitalized, followed by CFS with brain fog and severe fatigue causing me to spend 14 hrs a day in bed.  I recovered slowly over the next three years, but then in my late 30’s was diagnosed again, this time with Fibromyalgia with the primary issues being joint pain and hypersensitivity to many things.  I mostly recovered and was able to work normally, although I fatigued faster than most people and had to be very careful about what I ate and drank and ensure I rested as much as possible.  

In my late 40’s I started getting sick again, but my doc thought it was mostly related to hormone issues, so treated symptomatically until I had another bad respiratory infection which resulted in being diagnosed again with Fibromyalgia and CFS.  I’m on a multitude of treatments but still don’t have my life back yet almost 2 years later.  Symptoms include major sleep issues, pain, brain fog, and joint/body pain.  I have also been diagnosed with Hashimoto’s but have not noticed any difference with thyroid treatment.  “

Standard Items:

• Diversity: 2%ile
• Lactobacillus:  0.23x
• Bifidobacterium: 0.55x
• Akkermansia: 0x
• Firmicutes:Bacteroidetes: 0.4:1 (Normal  2.1:1)

Typical CFS profile

Uncommon Bacteria

Many many uncommon

• Anaerobacillus Genus 0.1%
• Ureaplasma Genus 0.8%
• Aerosphaera Genus 1.0%
• Jonquetella Genus 1.1%
• Mycoplasmataceae Family 1.3%
• Mycoplasmatales Order 1.3%
• Anaeroglobus Genus 1.4%
• Aerococcus Genus 1.6%
• Actinobaculum Genus 1.8%
• Ochrobactrum Genus 1.9%

High Bacteria

Reference

Several of the unusual overgrowths for CFS are associated with bacteria involved with the mouth which raises issues about oral health.

• Eisenbergiella: https://cfsremission.wordpress.com/2017/11/25/reducing-eisenbergiella-genus/
• Bacteroides: https://cfsremission.wordpress.com/2017/10/20/decreasing-bacteroides-genus/
• Subdoligranlum: https://cfsremission.wordpress.com/2017/10/10/decreasing-subdoligranlum/
• Odoribacter: https://cfsremission.wordpress.com/2017/10/19/decreasing-odoribacter-genus/
• Erysipelatoclostridium: https://cfsremission.wordpress.com/2017/11/14/decreasing-erysipelatoclostridium-genus/
• Catenibacterium: https://cfsremission.wordpress.com/2017/11/18/reducing-catenibacterium-genus/
• Dorea :  https://cfsremission.wordpress.com/2017/10/18/reducing-dorea-genus/
• Granulicatella: https://cfsremission.wordpress.com/2017/11/25/reducing-granulicatella-genus/
• Actinomyces: https://cfsremission.wordpress.com/2017/11/25/reducing-actinomyces-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

• Allergens
• Animal-based diet
• Bacillus subtilis
• Barley
• Berberine
• Bifidobacterim Breve
• Bifidobacterium animalis subsp. lactis
• Bifidobacterium catenulatum
• Bifidobacterium pseudocatenulatum
• BIO-THREE
• Broad beans  and lupin seeds
• Dairy
• Enterococcus faecium
• fermented Korean soybean paste
• Fructo-oligosaccharides
• Gallic acid
• gum arabic
• Helminth infections
• High meat diet
• Isoniazid-
• Italian-style gluten-free diet
• Lactobacillus acidophilus
• Lactobacillus rhamnosus
• Lactobacillus salivarius
• Lactobacillusplantarum
• lacto-ovo-vegetarian diet
• L-citrulline
• Low fat diets
• Macrolides
• Navy bean (Cooked)
• Omega 3
• Partial Sleep Deprivation [parent]
• pomegranate juice
• Proton-pump inhibitors (PPI)
• Pyrazinamide
• Red wine, Grape Seed Extract
• Resistant starch (type IV)
• Rifampin-
• Saccharin
• Saccharomyces boulardii
• Sleepless nights
• Stevia
• stress
• Stress
• Sucrose (ordinary sugar)
• Tannic acid
• Walnuts (and likely pomegranates)

Take

• Bacillus licheniformis
• Bifidobacterium longum
• Flaxseed
• Galactooligosaccharides
• Garlic
• Good Dental Health
• Inulin
• Ketogenic diet
• Lactobacillus fermentum
• Lactobacillus gasseri
• Lactobacillus rhamnosus
• Lactobacillus kefiri LKF01
• l-glutamine
• Maltitol
• Oats
• Oligosaccharide prebiotics
• Oral Iron Supplements
• Polymannuronic acid
• Sucralose (Splenda)
• Vegetable/fruit juice-based diets
• Whole Grains
• β-Glucan

Personal Note

This is an outlier to the usual CFS Microbiome:

• Diversity at 2% (versus 98% often seen)
• Bifidobcaterium is not low, just low average
• Lactobacillus is not low, just low average

That there is a microbiome dysfunction is clear! The microbiome just does not match the usual pattern seen with CFS.

• Extremely low diversity — to improve, I would suggest these
  • Prescript Assist
  • Equilibrium
• No apparent need to recommend bifidobacterium
• The four above Lactobacillus should be beneficial
• Flaxseed with Oats and other whole grain for breakfast with fruit using Sucralose for sweetening may be a good diet change

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.