Reducing Pseudoflavonifractor Genus

For updated information see Microbiome Prescription

Was reported high in Ian Lipkin study (see this post).

  • “This genus [Pseudoflavonifractor] is one of the most prominent butyrate producers, providing energy to the colonic mucosa and known to regulate gene expression, inflammation, differentiation, and apoptosis in host cells (Luo et al., 2013).”

DataPunk.Net Data

Nothing

PubMed Data

There are 10+ studies on PubMed.

Disease

  • “We also performed species classifications and found Holdemania filiformis and Pseudoflavonifractor capillosus to be increased and decreased in the PPI cohort, respectively.” [2016]

Diet

  • Phosphorus in diet increases [2016]

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

  • Phosphorus containing food

Take

  • Proton pump inhibitor

Reducing Anaerotruncus Genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 32+ studies on PubMed.

Disease

  • “Genus Anaerotruncuswas increased in children of gestational diabetes mellitus  women ” [2017]
  • Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms.. Parkinson’s disease” [2017]
  • “The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with age-related macular degeneration ,” [2017]
  • “Several taxa were found to be significantly enriched in samples belonging to the endometrial cancer cohort: Firmicutes (Anaerostipes, ph2, Dialister, Peptoniphilus, 1-68, Ruminococcus, and Anaerotruncus), Spirochaetes (Treponema), Actinobacteria (Atopobium), Bacteroidetes (Bacteroides and Porphyromonas), and Proteobacteria (Arthrospira). ” [2016]
  • “Notably, the increased bacteria included Bifidobacterium spp. and various representatives of Clostridium clusters IV and XIVa, such as Clostridium leptum, Oscillospira guillermondii, Sporobacter termitidis, Anaerotruncus colihominis, Ruminococcus callidus, R. bromii, Lachnospira pectinoschiza, and C. colinum, which are presumed to be anti-inflammatory.. after a fecal transpant” [2014]
  • “Depression correlated inversely with Lachnospiraceae family (rho =-0.58, FDR_p = 0.018), anxiety with genus Anaerotruncus (rho = 0.65, FDR_p = 0.001), and IBS severity with genera Ruminococcus (rho = 0.62, FDR_p = 0.005) and Coprococcus (rho = 0.59, FDR_p = 0.013). ” [2017]

Diet

  • “Walnuts increased the abundance of Firmicutes and reduced the abundance of Bacteriodetes. Walnuts enriched the microbiota for probiotic-type bacteria including Lactobacillus, Ruminococcaceae, and Roseburia while significantly reducing Bacteroides and Anaerotruncus. ” [2017]

Prebiotics

Probiotics

  • “Lactobacillus salivarius SMXD51 ..Anaerotruncus sp. decrease and Subdoligranulum sp. increase.” [2017]
  • ” In particular, during the recovery phase the [L. rhamnosus A 191, Lactobacillus acidophilus, Bifidobacterium breve, Bifidobacterium longum (CVS Maximum Strength Probiotic)] probiotic caused a suppression of Enterobacteriaceae outgrowth (Shigella and Escherichia) while promoting a blooming of Firmicutes, particularly from the Anaerotruncus genus. ” [2016]

Antibiotics

Bottom Line

Avoid

Take

Reducing Haemophilus Genus

For updated information see Microbiome Prescription

“the metabolism of Staphylococcus produces the necessary blood factor byproducts required for Haemophilus growth.” [wikipedia]

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

ANTIBIOTIC RESISTANCE

  • Cephalosporin
  • Chloramphenicol
  • Lincosamide
  • Macrolide
  • Penicillin
  • Streptogramin b
  • Tetracycline

PubMed Data

There are 28077+ study on PubMed

Disease

  • ” both of Moraxella and Haemophilus colonization are associated with higher risk of lower respiratory infection ” [2015]

Diet

  • “Vitamin D… Haemophilus and Veillonella were less abundant  in the subset with the highest vitamin D intake ” [2017]

Prebiotic

Probiotic

  • “at species level, a higher abundance of Blautia productaBlautia wexlerae and Haemophilus ducrey was observed, together with a reduction of Holdemania filiformisEscherichia vulnerisGemmiger formicilis and Streptococcus sinensis abundance.. from Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 .” [2017]
  • “after the end of Lactobacillus kefiri LKF01 DSM32079 (LKEF) probiotic administration Bacteroides, Barnesiella, Butyricicomonas, Clostridium, Haemophilus, Oscillibacter, Salmonella, Streptococcus, Subdoligranolum, and Veillonella were significantly reduced if compared to baseline samples.” [2017]

Antibiotic

Bottom Line

Avoid

Take

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.

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 OscillibacterFaecalibacteriumButyrivibrio, 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