Author Archives: lassesen

Unknown's avatar lassesen 6:20 pm on November 19, 2017  

A reader with a litany of conditions

Reader Summary

I have a blepharitis, chalazion in right eye, repetitive urine infections, inflammation of the digestive system .. EBV, MYCOPLASMA, UREPLASMA, CANDIDA, PARASITES, NATURALL KILLERS VERY LOWS, DIGESTIVE PROBLEMS: CONSTIPATION, GASTRITIS, REFLUX, I can not take it anymore, lyme positive in germany, coinfections , circulation problems, inflammation, brain fog, and endless symptoms., i m only 34 years and i.m ill since i was eleven years. Recently Microscopic colitis was added to my diagnosis.

Standard Measures

  • Biodiversity: 41%ile
  • Bifidobacterium < 0.01x
  • Lactobacillus 0.07x
  • Firmicutes:Bacteroidetes ratio: 0.5 : 1 (normal 2.1:1)
  • Akkermansia: 0%

The microbiome appears to reflect the severity that is described above (see this post of 4 ubiomes on the same person), the reference person was at 25% when the ratio went down to 1.3:1, this is a far greater shift!

Overgrowth Bacteria Order

Bacteria
Ratio
Burkholderiales:  10.40 X
Enterobacteriales: 1.78 X
Bacteroidales:  1.53 X
Erysipelotrichales: 1.13 X

Overgrowth Bacteria Genus

Sutterella: 11.02 X
Barnesiella: 4.16 X
Pseudobutyrivibrio: 3.11 X
Odoribacter: 2.91 X
Butyricimonas: 2.18 X
Kluyvera: 1.91 X
Bacteroides:  1.64 X

Rare Bacteria Genus

Johnsonella Genus 0.5%
Ureaplasma Genus 0.8%
Brevundimonas Genus 2.0%
Succiniclasticum Genus 4.0%
AnaerobacterGenus Genus 3.0%

Reference

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
  • Aspartame (Nutrasweet)
  • Aspirin (other NSAID’s are fine)
  • Bacillus subtilis
  • Bifidobacterium Animalis subsp. Lactis BB-12
  • Bifidobacterium catenulatum
  • Bifidobacterium pseudocatenulatum
  • Black Tea
  • BPA bottles
  • Broad beans  and lupin seeds
  • Clostridium butyricum (i.e. Miyarisan) probiotics
  • Cranberry
  • fermented Korean soybean paste
  • Fructo-oligosaccharides
  • Gallic acid
  • Glutten
  • gum arabic
  • High meat diet
  • Inulin (common in many probiotics)
  • Lactobacillus casei
  • Lactobacillus acidophilus
  • Lactobacillus Fermentum
  • Lactobacillus plantarum
  • L-citrulline
  • L-Glutamic acid ( monosodium glutamate – MSG) and possibly gluten
  • Low fat diets
  • L-Proline
  • L-Serine
  • Melatonin
  • Oligofructose
  • Pea Fibre
  • Pomegranate
  • Resveratrol, Red wine, Grape Seed Extract
  • Resistant starch (type IV)
  • Saccharin
  • Saccharomyces boulardii
  • Stevia
  • Stress
  • Tannic acid
  • Walnuts

Take

  • Bacillus licheniformis
  • Bifidobacterium Longum
  • Bifidobacterium  Infantis,
  • Bifidobacterium  bifidum,
  • Bifidobacterium  adolescentis
  • Bifidobacterium   breve
  • Bile supplements
  • Capsaicin (Chili peppers)
  • Dairy
  • E.Coli Probioitics
  • Flaxseed
  • Garlic
  • High Fat diet
  • Lactobacillus paracasei
  • Lactobacillus kefiri LKF01
  • Lactobacillus salivarius
  • L-glutamine
  • L-Phenylalanine (Good sources of phenylalanine are eggs, chicken, liver, beef, milk, and soybeans.[5])
  • Oligosaccharide prebiotics
  • Polymannuronic acid
  • Sucralose (Splenda)
  • Whole-grain barley
  • Xylitol
  • β-Glucan

Post Script

Given the complexity of conditions and overgrowths, I would suggest you discussion with your physician the follow approach. Remember above is an ADDITION/CUSTOM TUNING  of the general advice — keep taking B12, Folate, Vitamin D3, Magnesium etc.

  • Week 0:
    • Eliminate everything on the Avoid list, especially: Gluten, Black Tea,  Saccharomyces boulardii
  • Week 1:
    • Breakfast: Cooked (Oats) porridge with Flaxseed, sweeten with Xylitol or Sucralose
    • Reduce sugar and use Xylitol or Sucralose when practical
    • Lunch/Dinner: eggs, chicken, liver — use fresh garlic when practical
  • Week 2:
    • Add L-Glutamine supplements
    • Bile supplements
    • Take one or more of the Bifidobacterium at bed time, only with water.
  • Week 3: Add one of the following every 3 days… it you herx keep on what is causing the herx and pause adding more until the herx is gone
    • E. Coli probiotics
    • Lactobacillus kefiri LKF01
    • Other Lactobacillus probiotics listed above

The reasoning is to avoid severe herx and a gradual shift. Dairy and Chili Peppers will help correct the severe Firmicutes:Bacteroidetes ratio you have.

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.

Unknown's avatar lassesen 1:55 am on November 19, 2017  

Blood Pressure and the Microbiome

Symptoms can be caused by microbiome shifts. Treatment for the symptoms are likely to also cause microbiome shifts. This is one of a planned series dealing with specific symptoms. I have already touched on Blood Pressure is some previous posts:

Literature

  • “several human studies showing that the human gut microbiome in patients with hypertension harbours lower microbial diversity and an increased Firmicutes:Bacteroidetes ratio accompanied by decreases in acetate-producing and butyrate-producing bacteria2,3. ” [Nature]
  • “These data indicate that non-obese and hypertensive rats harbor a different gut microbiota from obese rats and that exercise training alters gut microbiota from an obese and hypertensive genotype background.” [2014]
  • “Opportunistic pathogenic taxa, such as, Klebsiella spp., Streptococcus spp., and Parabacteroides merdae were frequently distributed in hypertensive gut microbiome,” [2017]
  • Restoration of A Healthy Intestinal Microbiota Normalizes Portal Hypertension In A Rat Model of Nonalcoholic Steatohepatitis. [2017]

High Blood Pressure

  • “In modern era, Ocimum sanctum Linn. (Tulsi) has been shown to be effective against diabetes mellitus, hypertension,” [2013]
  • “Several diseases have been linked to vitamin D deficiency, such as hypertension, diabetes, depression, Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, and chronic pain syndromes such as fibromyalgia. ” [2013]
  • “cardiovascular effects of probiotics Lactobacillus fermentum CECT5716 (LC40), or L. coryniformis CECT5711 (K8) plus L. gasseriCECT5714 (LC9) (1:1) …exert cardiovascular protective effects in genetic hypertension ” [2015]
  • “A meta-analysis of 9 randomized trials showed a significant decrease in both the systolic BP (SBP) and diastolic BP (DBP) in patients who consumed a daily dose of ≥1011 CFU of Lactobacillus helveticus (Khalesi et al., [2014]. “
  • Herbal Medicine for the Treatment of Cardiovascular Disease Clinical Considerations 1998
    • “The root of R serpentina (snakeroot), the natural source of the alkaloid reserpine, has been a Hindu Ayurvedic remedy since ancient times.
    • “Stephania tetrandra is an herb sometimes used in traditional Chinese medicine to treat hypertension. “
    • “The root of Lingusticum wallichii is used in traditional Chinese medicine as a circulatory stimulant, hypotensive drug, and sedative.”
    • “Uncaria rhynchophylla is sometimes used in traditional Chinese medicine to treat hypertension.”
    • Evodia rutaecarpa (wu-chu-yu) is a Chinese herbal drug that has been used as a treatment for hypertension.
  • ” Interventions such as oral antibiotic treatment2,5 and a high-fibre diet6 have been shown to attenuate high blood pressure and rebalance the dysbiotic gut microbiome in various hypertensive rodent models.” [Nature]
  • “We observed a significant increase in Gram-positive Streptococcus genus and Streptococcaceae family in the gut of the spontaneously hypertensive rat , both belonging to the order of Lactobacillales (lactic acid–producing bacteria) and the phylum of Firmicutes (Figure 6C, in red). This was consistent with changes we had previously observed in the Ang II–infusion hypertensive rodent model.22 Furthermore, we observed a significant decrease in the Bifidobacterium genus and the related Bifidobacteriaceae family of Actinobacteria phyla (Figure 6C, in green), a Gram-positive bacterium with probiotic properties.35,36 We also observed a decrease in several bacterial genera of the Bacteroidetes phyla.” [2017]
  • “All these genera were decreased in enterotype 1 as compared with enterotype 2 (Additional file 4: Figure S2b). Eight out of them were directly linked to Prevotella, while the other four, including Oscillibacter, Faecalibacterium, Butyrivibrio, and Roseburia, were indirectly linked to Prevotella. These findings highlighted the possibility of Prevotella as a key genus associated with pre-hypertension (pHTN) and  hypertension(HTN). The difference in gut enterotype distribution revealed profound changes of the intestinal microbiome structure in both pHTN and HTN, implying the significance of gut microbes in the development of HTN.”2016
  • “The present meta-analysis suggests that consuming probiotics may improve BP by a modest degree, with a potentially greater effect when baseline BP is elevated, multiple species of probiotics are consumed, the duration of intervention is ≥8 weeks, or daily consumption dose is ≥1011 colony-forming units.” [2014] – 100 MCFU or 0.1 BCFU.
  • “Licorice root, whose active ingredient, glycerrhetinic acid (GA), inhibits renal 11β-HSD2, and thereby causes hypertension in some individuals. Bacterially derived glucocorticoid metabolites may cause hypertension in some patients by a similar mechanism. ” [2017]

Low Blood Pressure

  • “Black licorice induced hypertension is an uncommon cause of hypertension in modern times because newer types of licorice rarely use the active ingredients in licorice root in large quantities. ” [2015]
  • “Post-treatment with magnolol (Magnolia officinalis, Magnolia Bark) significantly attenuated the deleterious haemodynamic changes (e.g., hypotension and bradycardia) caused by lipopolysaccharide. ” [2010]

Bottom Line

Including information from Decreasing Prevotella genus

Avoid

  • Lactobacillus casei
  • Lactobacillus gasseri
  • Lactobacillus rhamnosus GG.
  • Lactobacillus salivarius
  • Rosemary

Take

  • Bifidobacterium bifidum strain Bb probiotics
  • Chicory
  • E.Coli probiotics
  • Grape seed extract (Resveratrol)
  • Inulin
  • Jerusalem artichoke
  • Lactobacillus Brevis
  • Lactobacillus Fermentum ME3 (Reg’Activ) has both documented impact on BP and the standard capsule contains > 1 BCFU.
  • Lactobacillus Reuteri
  • Lactobacillus Helveticus
  • Low carbohydrate diet
  • Resistant starch (type IV)
  • Streptococcus probiotics
  • Tulsi Tea
  • Vitamin D3 — typically 10,000-20,000 IU/Day is needed to get someone up to the top quarter for Vitamin D3, the area needed to see impact
  • Whole-grain barley
Unknown's avatar lassesen 11:35 pm on November 18, 2017  

After Cancer treatment, CFS occured — the uBiome

In the past I have personally (physically) meet with several people that had CFS that went into remission when they started cancer treatment. Today, I got access to a uBiome of a reader that had Cancer treatment and then develop CFS.

It is unclear if this person matches the CFS microbiome or would qualify with symptoms for an official diagnosis. What is clear is that there is a dysfunction in their microbiome

Basic Measures

  • Diversity: 93%ile   (a lot of CFS ubiomes are clustered around this value!)
  • Firmicutes:Bacteroidetes:  2.1 (Normal is 2.1)
  • Akkermansia:  0x
  • Bifidobacterium:  1.36x (None match the species they tested for)
  • Lactobacillus:  0.01x
  • Rare Bacterias:
    • Succinivibrio,
    • Anaerovorax,
    • Parvibacter,
    • Christensenella,
    • Gardnerella

Overgrowth of Bacteria Orders

Bacteria
Ratio
Aeromonadales: 6.42 X
Erysipelotrichales: 4.62 X
Selenomonadales:  2.82 X
Oligosphaerales: 2.00 X
Coriobacteriales:  1.83 X
Desulfovibrionales: 1.81 X
Flavobacteriales:  1.25 X

Overgrowth of Bacteria Genus

Bacteria
Ratio
Catenibacterium: 4.36 X
Succinivibrio: 4.07 X
Dialister: 3.39 X
Desulfovibrio: 1.83 X
Dorea: 1.71 X
Collinsella: 1.59 X
Megasphaera: 1.51 X

The main overgrowth, Catenibacterium genus, is an uncommon overgrowth in CFS. Megasphaera is also uncommon.

References

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

  • Animal-based diet
  • Bacillus subtilis
  • Barley
  • Berberine
  • Bifidobacterium longum
  • BIO-THREE
  • Cashews
  • Enterococcus faecium  probiotics
  • Ginkgo
  • Helminth infections
  • High Meat Diet
  • Lactobacillus Reuteri
  • Lactobacillus rhamnosus
  • Navy bean (Cooked)
  • Partial Sleep Deprivation [parent]
  • Proton-pump inhibitors (PPI)
  • Stress
  • Thiamine supplements
  • Walnuts
  • Wheat
  • Xylans

Take

  • Cellobiose
  • Flaxseed [parent]
  • Galactooligosaccharides
  • Green or black tea
  • Lactobacillus plantarum
  • Lactobacillus acidophilus
  • L-glutamine
  • NSAIDs (see list here), I prefer aspirin as first choice.
  • Oral Iron Supplements
  • Polymannuronic acid
  • pomegranate
  • Saccharomyces boulardi
  • 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.

Unknown's avatar lassesen 11:13 pm on November 18, 2017  

Reducing Megasphaera genus

For updated information see Microbiome Prescription

Megasphaera elsdenii NCIMB 41125 is used as a probiotic with cattle

DataPunk.Net Data

ANTIBIOTIC RESISTANCE

PubMed Data

There are 400+ studies on PubMed.

Disease

  • “We identified links between rosacea and several changes in gut microbiota: reduced abundance of Peptococcaceae family unknown genus, Methanobrevibacter (genus), Slackia (genus), Coprobacillus (genus), Citrobacter (genus), and Desulfovibrio (genus), and increased abundance of Acidaminococcus (genus), Megasphaera (genus), and Lactobacillales order unknown family unknown genus. ” [2017]
  • ” Bifidobacterium, Megasphaera, Haemophilus and Streptococcus; and five genera enriched in infants with eczema: Escherichia/Shigella, Veillonella, Faecalibacterium, Lachnospiraceae incertae sedis ” [2016]

Diet

  • “The levels of Selenomonas ruminantium, Anaerovibrio lipolytica, Ruminobacter amylophilus, Succinivibrio dextrinosolvens and Megasphaera elsdenii were increased by ginkgo extract supplementation, possibly contributing to the higher propionate production.” [2017]

Prebiotics

Probiotics

  • “Dietary supplementation with B. subtilis resulted in increased (P < 0.05) cecal counts of Megasphaera elsdenii.” [2015]

Antibiotics

Bottom Line

Avoid

  • Ginkgo
  • Bacillus  subtilis

Take

Unknown's avatar lassesen 10:41 pm on November 18, 2017  

Reducing Catenibacterium genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 14+ studies on PubMed.

Disease

  • ” morbidly obese insulin resistant group had a significant increase in the abundance of Firmicutes, Fusobacteria, Pseudomonaceae, Prevotellaceae, Fusobacteriaceae, Pseudomonas, Catenibacterium, Prevotella, Veillonella and Fusobacterium compared to the morbidly obese low insulin resistant group. ” [2016]
  • “two genera were depleted among those with high versus low cardiovascular disease risk profile” [2016]
  • “Brachybacterium, Catenibacterium, Enterobacteriaceae, Halomonadaceae, Moraxellaceae, Nesterenkonia, Polyangiaceae, Pseudomonadaceae, and Thiothrix families were markedly increased in patients with end-stage renal disease.” [2013]
  • “in subjects with a history of  C. difficile associated diarrhea , the dominant species were either Catenibacterium (33.0%) or Ruminococcus (65.6%).” [2011]

Diet

Prebiotics

Probiotics

  • “Ruminococcus, Catenibacterium, Tanneralla, Allstipes, etc.  appeared only in the Enterococcus faecium treatment group,” [2016]
  • “We also observed a significant decreased in Catenibacterium communities with Saccharomyces boulardi” [2017]
  • “30 days after the start of probiotics (BIO-THREE®), the peak of Enterococcus was not seen any more, and Clostridium, Ruminococcus, Eubacterium, Catenibacterium and Bacteroides began to be detected,” [2012]

Antibiotics

  • “There was a reduction in the abundance of Blautia, Catenibacterium, Lactobacillus, and Faecalibacterium species and an increase in Butyrivibrio, Oscillospira and Ruminococcus after (a cocktail of) bacteriophage administration. ” [2017]

BottomLine

Avoid

Take