A reader ask me about methylation. In 2013, I did a post “methylation cycle gut bacteria and chronic fatigue syndrome” which found that E.Coli and Bacillus subtilis are both involved in methylation. CFS patients are very low in both, additionally, I posted in 2015 about Methylation Testing via 23andMe.com

Methylation has been a hot topic for a number of years in the CFS community and other medical areas. For example, Dr. Myrna Hill has written a page about it for CFS patients and cite “Rich van Konynenburg has identified a package of micronutrients specifically to support the methylation cycle”. Rich was very active in this area until he passed away in Sept 2012. There is a lot of his material on line. He was inspired by the work of Dr Amy Yasko.

In the month before he died, we had started discussing the role of the microbiome in methylation. I will attempt touch a few items only (there are over 88000 studies on pubmed)

DNA is a factor, but..

• “methylation is regulated by a family of DNMTs: DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L.^{7–11 [2011}}
• PITX2 and PANCR DNA methylation predicts overall survival in patients with head and neck squamous cell carcinoma [2016].
• Hypomethylation of HLA-DRB1 and its clinical significance in psoriasis [2016].

Epigenetics is also another factor

Epigenetics is modification of DNA’s behavior due to environmental events and stress.  You may have DNA that disposes you towards methylation issues — but it takes the right set of events to cause methylation issues. Sometimes this activation can persist for generations. Note that environmental includes shifts of the microbiome.

• Pregnant women’s cognitive appraisal of a natural disaster affects their children’s BMI and central adiposity via DNA methylation: [2016].
• Epigenome-wide DNA methylation analysis in siblings and monozygotic twins discordant for sporadic Parkinson’s disease revealed different epigenetic patterns in peripheral blood mononuclear cells [2016].
• Changes in methylation of genomic DNA from chicken immune organs in response to H5N1 influenza virus infection [2016]. – an infection can alter methylation!

What about CFS and related conditions?

• Epigenome-wide DNA methylation patterns associated with fatigue in primary Sjögren’ssyndrome [2016].
  • “A total of 251 differentially methylated CpG sites were associated with fatigue. The CpG site with the most pronounced hypomethylation in pSS high fatigue annotated to the SBF2-antisense RNA1 gene.”
• Chronic Fatigue Syndrome and DNA Hypomethylation of the Glucocorticoid Receptor Gene Promoter 1F Region: Associations With HPA Axis Hypofunction and Childhood Trauma [2015].
  • “Overall NR3C1-1F DNA methylation was lower in patients with CFS than in controls.”
  • “We found evidence of NR3C1 promoter hypomethylation (low methylation)  in female patients with CFS and the functional relevance of these differences was consistent with the hypothalamic-pituitary-adrenalaxis hypofunction hypothesis (GR hypersuppression). However, we found no evidence of an additional effect of childhood trauma on CFS via alterations in NR3C1 methylation.”
• DNA methylation modifications associated with chronic fatigue syndrome [2014].
  • “We found an increased abundance of differentially methylated genes related to the immune response, cellular metabolism, and kinase activity. Genes associated with immune cell regulation, the largest coordinated enrichment of differentially methylated pathways, showed hypomethylation within promoters and other gene regulatory elements in CFS. These data are consistent with evidence of multisystem dysregulation in CFS and implicate the involvement of DNA modifications in CFS pathology.”
• Acute psychosocial stress-mediated changes in the expression and methylation of perforin inchronic fatigue syndrome[2013].
  • “These findings suggest methylation could be an important epigenetic determinant of inter-individual differences in PRF1 expression and that the differences in PRF1 expression and methylation between CFS and non-fatigued (NF) controls in the acute stress response (to Trier Social Stress Test) require further investigation.”
• Epigenetic alterations and an increased frequency of micronuclei in women with fibromyalgia [2013].
  • “The majority of differentially methylated (DM) sites (91%) were attributable to increased values in the women with FM. The DM sites included significant biological clusters involved in neuron differentiation/nervous system development, skeletal/organ system development, and chromatin compaction. Genes associated with DM sites whose function has particular relevance to FM included BDNF, NAT15, HDAC4, PRKCA, RTN1, and PRKG1. Results support the need for future research to further examine the potential role of epigenetic and acquired chromosomal alterations as a possible biological mechanism underlying FM.”

And… the microbiome?

• The relationship between early-life environment, the epigenome and the microbiota [2015].
  • ” Epigenetics can change gene expression to modify disease risk; unfortunately, how epigenetics are changed by the environment is unclear. It is known that the environment modifies the microbiota, and recent data indicate that the microbiota and the epigenome interact and respond to each other. Specifically, the microbiome may alter the epigenome through the production of metabolites. Investigating the relationship between the microbiome and the epigenome may provide novel understanding of the impact of early-life environment on long-term health.”
• Epigenetic imprinting by commensal probiotics inhibits the IL-23/IL-17 axis in an in vitro model of the intestinal mucosal immune system [2012].
  • “ Bifidobacterium breve (DSMZ 20213)  and Lactobacillus rhamnosus GG (ATCC 53103) may exert their anti-inflammatory effects in the gut by down-regulating the expression of the IBD-causing factors (IL-23/IL-17/CD40) associated with epigenetic processes involving the inhibition of histone acetylation and the optimal enhancement of DNA methylation, reflected in the limited access of NF-κB to gene promoters and reduced NF-κB-mediated transcriptional activation. …
  • We describe a new regulatory mechanism in which commensal probiotics inhibit the NF-κB-mediated transcriptional activation of IBD-causing factors (IL-23/IL-17/CD40), thereby simultaneously reducing histone acetylation and enhancing DNA methylation.

Bottom Line

Methylation is a very complex area. One path is that of supplements intending to help — think of this as taking B12, except you are taking methylated-B12. 1000 mcg/ 1 mg seems to be the effective ongoing dosage for B12, see this post. The other path is altering the microbiome to enhance methylation — the equivalent of taking Lactobacillus Reuteri to produce your own B12. Of course, you can do both at the same time. The first path will provide temporary symptom relief, the second path raise the prospect of a permanent correction of methylation issues.

There are four probiotic species that are indicated as good candidates:

• E.Coli (Symbioflor-2 or Mutaflor)
• Bifidobacterium breve (DSMZ 20213)
• Lactobacillus rhamnosus GG (ATCC 53103) – aka Culturelle
• Bacillus subtilis

• “. At 3-months the abundance of the genus,  Lachnospira  (L), was decreased (p = 0.008), while the abundance of the species,  Clostridium neonatale  (C), was increased (p = 0.07) in asthmatics. Quartile analysis revealed a negative association between the ratio of these two bacteria (L/C) and asthma risk at 3-months (quartile 1: Odds ratio (OR) = 15, p = 0.02, CI = 1.8 – 124.7; quartile 2: OR = 1.0, ns; quartile 3: OR = 0.37, ns). We conclude that opposing shifts in the relative abundances of  Lachnospira  and  C. neonatale  in the first 3 months of life are associated with preschool age asthma, and that the L/C ratio may serve as a potential early life biomarker to predict asthmadevelopment.” [2016]
• ” One study demonstrated a strong association between high abundance of Faecalibacterium prausnitzii and decreased levels of butyrate and propionate, and established eczema. Lower relative abundance of Ruminococcaceae appears to be implicated in food sensitization and to precede the development of atopic eczema. Decreased relative abundance of Lachnospira, Veillonella, Faecalibacterium, and Rothia in early infancy was reported to be associated with increased asthma risk. Inoculation of germ-free mice with these genera decreased airway inflammation in their offspring thereby proposing a causal role of bacteria in preventing allergic airways disease.” [2016]
• “Low total diversity of the gut microbiota during the first month of life was associated with asthma but not allergic rhino conjunctivitis ( in children at 7 years of age. Measures affecting microbial colonization of the infant during the first month of life may impact asthmadevelopment in childhood.” [2014]
• “Low intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema.” [2012]
• “These results support the general hypothesis that an imbalance in the intestinal microbiome is influencing the development of lifestyle-related disorders, such as allergic disease.” [2011]
• “Presence of older siblings is associated with increased gut microbial diversity and richness during early childhood, which could contribute to the substantiation of the hygiene hypothesis.” [2015]

Actionable Items

Studies have found that generic probiotics and antibiotics do not have any statistically significant effect in human studies. This is not surprising because the same hold true for other conditions associated with a microbiome shift – generic products have no effect. Very specific probiotics and antibiotics do have impact with those conditions. Which ones are effective for Asthma and Eczema is still unknown and to be studied.

There is one exception — Vitamin D, which is known to alter the microbiome

• :”Other known or potential risk factors for severe asthma exacerbations include …vitamin D insufficiency, … In spite of progress in our understanding of the pathophysiology of asthma, we lack reliable instruments or biomarkers to predict severe asthma exacerbations.[2016]
• We find a relationship exists between airway obstruction and 25OHD [Vitamin D] levels in asthmatic adults, and the effect is not explained by the presence of potential confounders such as obesity, allergy and systemic inflammation. [2016]
• “Our results suggest that vitamin D insufficiency is relatively frequent in an equatorial population of children with asthma. In these children, lower vitamin D levels are associated with increased markers of allergy and asthma severity.” [2009]
• ” studies that focused on vitamin D and severity of asthma which suggest a positive association of vitamin D levels with better asthma control, reduced use of asthma medication, fewer asthma exacerbations and lower utilisation of health care facilities for urgent treatment.” [2015]
• “These results suggest that vitamin D supplementation may be effective for the prevention of asthma exacerbations, but the findings need to be confirmed by clinical trials.” [2015]

Vitamin D and the Gut

I thought it would be good to review some of the hundreds of studies published on PubMed in 2016 to see if anything especially interesting has been published.

• “During life, the numbers of bifidobacteria decrease from up to 90% of the total colon microbiota in vaginally delivered breast-fed infants to <5% in the colon of adults and they decrease even more in that of elderly as well as in patients with certain disorders such as antibiotic-associated diarrhea, inflammatory bowel disease, irritable bowel syndrome, obesity, allergies, and regressive autism.” [2016]
  • ” Butyrate is an essential metabolite in the human colon, as it is the preferred energy source for the colon epithelial cells, contributes to the maintenance of the gut barrier functions, and has immunomodulatory and anti-inflammatory properties. It has been shown that the butyrogenic effects of ITF and AXOS are the result of cross-feeding interactions between bifidobacteria and butyrate-producing colon bacteria, such as Faecalibacterium prausnitzii (clostridial cluster IV) and Anaerostipes, Eubacterium, and Roseburia species (clostridial cluster XIVa). These kinds of interactions possibly favor the co-existence of bifidobacterial strains with other bifidobacteria and with butyrate-producing colon bacteria in the human colon.” – hence Clostridium butyricum (Miyarisan) probiotics may be a very significant factor.
  • AXOS => arabinoxylan-oligosaccharides
  • 
• “Low-FODMAP rye bread helps IBS patients to control their symptoms and reduces gastrointestinal gas accumulation.” [2016] I have been a long time advocate of 100% rye bread (with zero wheat flour in it) – 100% rye bread  encourage biodiversity, [2012].
• “a newly emerging condition termed non-celiac gluten (or wheat) sensitivity[NCGS/NCWS] is now well established in the clinical practice. Notably, patients with NCGS/NCWS have symptoms that mimic those present in irritable bowel syndrome.” [2016] – IBS does not mean wheat (or gluten) sensitivity. Many “gluten sensitive” individuals are actually wheat sensitive only.
• “Using strict criteria as recommended for IBS studies, about one third of patients with IBS-D or IBS-M are wheat sensitive, with a similar proportion in both IBS types. ” [2016]
• “Of 1074 patients (44.1%) who responded to open-label rifaximin, 382 (35.6%) did not relapse, whereas 692 (64.4%) did; of these, 636 were randomly assigned to receive repeat treatment with rifaximin (n=328) or placebo (n=308). The percentage of responders was significantly greater with rifaximin than placebo (38.1% vs 31.5%, P=.03). The percentage of responders for abdominal pain (50.6% vs 42.2%, P=.018) was significantly greater with rifaximin than placebo, but not stool consistency (51.8% vs 50.0%, P=.42).” [2016] So Rifaximin helps about 1/3 of IBS patients – but this amounts to actually just 7%  (38% improved with Rifaximin, and 31% improved with a placebo — 38% – 31% = 7%) … so real odds is closer to 1/14.
• “More than every tenth Dane have irritable bowel syndrome. The condition is diagnosed by a positive strategy including fulfilment of the Rome III criteria, absence of alarm symptoms, and if needed a few paraclinical tests. Currently, there is no cure of the disorder. Treatment is recommended on a symptom-based approach targeting the dominating symptom/symptoms. If symptoms are reduced, the quality of life is considerably improved.” [2016]
• “Multispecies probiotic supplementations are effective in IBS-C subjects and induce a different assessment in the composition of intestinal microbiota” [2016]
  • “it is known that the level of bifidobacteria and lactobacilli species is lower in IBS patients compared to healthy persons [28, 29] and several studies show that the supplementation of them, or mixtures including species of these genera, is effective in alleviating symptoms of IBS. Moreover, the selected strains were already known for their effect on intestinal cell lines as previously reported [19].”
  • Mixture F_1: 5 × 10⁹ CFU L. acidophilus , 5 × 10⁹ CFU L. reuteri (30 mg as lyophilized), – 10 Billion CFU
  • Mixture F_2:  5 × 10⁹ CFU L. plantarum, 5 × 10⁹ CFU L. rhamnosus , 5 × 10⁹ CFU B. animalis subsp. lactis – 15 Billion CFU  BEST – see posts on L.Rhamnosus 
  • Mixture F_3:  390 mg inulin (almost a Placebo)
• 
• “self-reported anxiety and depression provide a twofold risk for IBS onset.” [2016]
• “Species richness, but not community diversity, differentiated all IBS patients from Healthy Controls.” [2016]

My last post on lactobacillus rhamnosus was back in 2012, I recently found some new interesting articles on PubMed, so time for an update. Over the weekend, I had a run to Canada to pick up a supply of Mutaflor for my wife (Crohn’s Disease) and spotted Jamieson probiotic for traveler’s diarrhea. They were 10 billion CFU of Lactobacillus Rhamnosus GG per capsule. Culturelle is the same strain and dosage — except for one thing, the wife did not react to Culturelle like she did to Jamieson’s!!! Jamieson’s had a much stronger effect and was 40% cheaper per capsules.  I suspect that the Jamieson’s was a lot fresher (i.e. less time since manufacture) than Culturelle.

I have always found that probiotic intended to treat traveller’s diarrhea tend to be good candidate probiotic (if there is research backing it).

Latest Articles on Lactobacillus Rhamnosus

• Probiotic Lactobacillus rhamnosus reduces organophosphate pesticide absorption and toxicity to Drosophila melanogaster[ 2016]. This hints that it may reduce MCS. My wife is trying an experiment with doing far infrared sauna followed by probiotics. It seems to be reducing her MCS sensitivity.
• Probiotic lactobacilli: a potential prophylactic treatment for reducing pesticide absorption in humans and wildlife [2015]. “Probiotic Lactobacillus rhamnosus GR-1-supplemented yoghurt reduced the bioaccumulation of mercury and arsenic in pregnant women and children.” High mercury levels is associated with MCS
• “The children and pregnant women in the study were found to have elevated blood levels of lead and mercury compared to age- and sex-matched Canadians. Consumption of probiotic yogurt containing 10(10) CFU Lactobacillus rhamnosus GR-1  had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.” [2014]
• Lectin-Like Molecules of Lactobacillus rhamnosus GG Inhibit Pathogenic Escherichia coli and Salmonella Biofilm Formation [2016].
• “We present 4 cases of clinically diagnosed Food protein-induced allergic proctocolitis (AP) whose symptoms quickly and completely resolved with probiotic Lactobacillus rhamnosus GG (LGG) monotherapy. All 4 infants avoided any dietary restrictions. The range of time from probiotic initiation to symptom resolution was 7-28 days.” [2016]
• Lactobacillus rhamnosus induced epithelial cell apoptosis, ameliorates inflammation and prevents colon cancer development in an animal model[2016].
• “clinical and immunologic effect of probiotic and vitamin D supplementation … showed better clinical and immunologic response in children with allergic rhinitis.”[2016]
• Lactobacillus rhamnosus GG Intake Modifies Preschool Children’s Intestinal Microbiota, Alleviates Penicillin-Associated Changes, and Reduces Antibiotic Use [2016].
• “we demonstrated that twice-weekly treatment of sex steroid-deficient mice with the probiotics Lactobacillus rhamnosus GG (LGG) o…reduces gut permeability, dampens intestinal and BM inflammation, and completely protects against bone loss.” [2016]
• “Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants.” [2016] – low butyrate was found in MCS individuals.
• Lactobacillus rhamnosus GG inhibits the toxic effects of Staphylococcus aureus on epidermal keratinocytes [2014].

A reader forwarder to me their results from DOCTOR’S DATA STOOL TEST, and this is my comment  on things to consider (and, of course, consult with your knowledgeable medical professional before taking any action). Tests change every few years and I like to see the latest report. They have been active on herbs and probiotic for a year, with just minor improvement.

As expected:

E.Coli is better than is typically seen, I suspect Mutaflor or Symbioflor-2 supplementation. Symbioflor-2 is my first choice for two reasons:

• Studies found that it does take up residency
• Can be ordered for shipment to the US via Amazon.de (i.e. availability)

Mutaflor would be a secondary choice (much harder to order from the US)

The NG for Enterococcus spp, suggests that a enterococcus probiotic should be used (the more species, the better).

The E.Coli-Enterococcus Marriage

A reader on my enterococcus probiotics post commented:

“E.coli and enterococcus appear to have a symbiotic relationship too! This makes sense.”

So, as is my habit, I decided to determine if this is true, false, or unknown.

The chart below showed that they appear to support each other [2008] and thus may be, and should be, taken together for best effect.

• “E. coli was correlated with enterococci in southern Lake Michigan beaches[2003]
• “This study demonstrated that there was a synergistic effect on virulence when an association of enterococci and E. coli”[2008]

Don’t forget me! Biofilm breakers

You may wish to take the above with herbs and supplements that isted in my biofilm breaker post and the post on biofilm breaker probiotics. Why is this important? It expose the residue infections to the two probiotics so they can be dislodged.

 Bacteria in Imbalance

These are bacteria with larger than normal volumes. They have no explicit issue linked to them, however they could help to support bad bacteria, or needed to sustain them.

For example, gamma hemolytic strep is associated with “pediatric autoimmune neuropsychiatric disorder associated with streptococcus (PANDAS).” [2015], which hints at it being involved with neurological symptoms of CFS.

• “Serotonin Activates Bacterial Quorum Sensing and Enhances the Virulence of Pseudomonas aeruginosa in the Host.[2016]”
• “Volatile Compounds Emitted by Pseudomonas aeruginosa Stimulate Growth of the Fungal Pathogen Aspergillus fumigatus [2016].“

The rest of his lab reports were marked normal on the report. You may wish to look at another readers report from 2014 here which contains further suggestions.

• A mushroom extract that may help, see this post.
• Tulsi may also help, see this post
• Zingerone (related to ginger but not in raw ginger) “The results of the present study revealed the anti-quorum sensing activity of zingerone targeting ligand-receptor interaction, hence proposing zingerone as a suitable anti-virulent drug candidate against P. aeruginosa infections” [2015]
• P. Aeruginosa is associated with IBS, this post, as well as higher histamine levels, in this post.

Bottom Line

First try E.Coli+ enterococcus probiotics + biofilm breakers, then rotate to Tulsi and Zingerone (only product that I could locate is this one on Amazon).