A reader wrote:
“I know your research is confined to CFS. I have EBV with associated Hashimoto’s thyroiditis. How can I find out what species I have or am low in, so that I can find out what probiotics are best to take? Thanks in advance.”

In this post, I will document the process that I would go thru with PubMed. Sometimes you are lucky that appropriate studies have been done. After this I will go thru ‘self-service’ options – that is what tests are available and what information they may bring to bear.

EBV and the Microbiome

• Step 1: Search for the condition:
  • and microbiome – 14 hits for EBV Microbiome
  • and probiotics – 2 hits for EBV probiotic

What I found that may be relevant was:

• “A similar effect was found for plasma EBV antibody titres in EBV seropositive participants (p < 0.01) with antibody titre falling in the Lactobacillus casei Shirota group but increasing in the placebo group over time.” [2016] See this post (Yakult)
• “The fatigued athletes had clinical characteristics consistent with re-activation of EBV infection …After one month of daily capsules containing 2 x 10(10) colony forming units of L acidophilus LAFTI®L10 (DSM Food Specialties, Moorebank, NSW, Australia) , secretion of IFNgamma from T cells had increased significantly (p = 0.01) to levels found in healthy control athletes.” [2006]

Step 2 Repeat for the next condition

• and microbiome – 17 hits for Hashimoto Microbiome  all but one has a Hashimoto as the author (not the condition!)
• and probiotics – 6 hits for Hashimoto probiotic – all of them has a Hashimoto as the author (not the condition!)

What I found that may be relevant was: [2012]

• “. In experimental autoimmune thyroiditis (EAT), a murine model of Hashimoto’s thyroiditis, probiotic strains Lactobacillus rhamnosus HN001 andBifidobacterium lactis HN019, which had been shown to enhance splenocyte IFNγ production in mice (Gill et al., 2000), exhibited neither stimulatory nor inhibitory effect on the disease development (Zhou and Gill, 2005). Taken collectively, the presence and the role of intestinal dysbiosis and the effect of alteration in the gut microbial composition remain to be investigated in Hashimoto’s thyroiditis.”
• “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.”

Looking at likely candidates for microbiome – autoimmune issues, i.e. Vitamin D levels

• 25 Hydroxyvitamin D Deficiency and Its Relationship to Autoimmune Thyroid Disease in the Elderly. “The prevalence of autoimmune thyroiditis was significantly higher in subjects with vitamin D deficiency (25(OH) vitamin D < 20 ng/mL) when compared with subjects with normal 25(OH) vitamin D (25(OH) vitamin D ≥ 20 ng/mL) levels (28% vs. 8%, respectively, p = 0.002).”
• This is echoed for EBV in The beneficial effects of vitamin D3 on reducing antibody titers against Epstein-Barr virus in multiple sclerosis patients[2015]. and other studies

Bottom Line from the Literature

• For EBV
  • Vitamin D (in very significant quantities)
  • Yakult (Lactobacillus casei Shirota)
  • L acidophilus LAFTI®L10

Self Serve

With physicians being cooperative, I would suggest getting

• DOCTOR’S DATA STOOL TEST (see this post for an example) – it’s a 10,000 meter view of your microbiome
  • A university research lab analysis
  • https://www.gdx.net/product/gi-effects-comprehensive-stool-test
  • http://www.secondgenome.com/solutions
• Or go the ‘citizen scientist’ approach with a detail analysis (hundreds of strains reported) from one of:
  • http://ubiome.com/  $89
  • http://americangut.org/ $99

These later analysis should not be taken as “gospel” there can be disagreements from the same sample:

• ScienceNews Article by Tina Saey
• Blog Post by Tim Steele
• Blog by PostDoc at MIT

I would advocate doing both of the citizen science tests — we do not know which one is more accurate.

The wrong way is to take lactobacillus probiotics!! Why? Lactobacillus probiotics in general kill off E.Coli which CFS patients are very low in (if they have any), and most lactobacillus are also D-Lactic acid producers (which most CFS patients are very high in! see this post).

The amount of information on interactions is actually quite thin, and often come from veterinary studies.

• “All tested Lactobacillus strains presented inhibitory activity against Staphylococcus aureus, Salmonella Typhimurium, Salmonella Enteritidis, Listeria monocytogenes and Escherichia coli,” [2016]
• “Associants (E. coli and Enterococcus faecium) were “friend” species, in which bifidobacteria exometabolites did not change growth properties and stimulated anti-lysozyme activity(by 17,5–32%) and formation of biofilms (by 25 – 39%).” [2011]
• ” After the introduction of probiotic enterococci, the quantity of lactobacilli and bifidobacteria in the intestines of rats increased, and the content of Klebsiella spp. and Escherichia coli decreased in comparison with the control group 1 and the group fed lactobacilli.” [2013]
• “Enterococcus faecium L5 led to the rapid disappearance of dysbiosis symptoms, normalisation of the microbiota, increase in expression of IL-10 and decrease in IL-8 expression.” [2010]
• “probiotic E. faecium on enterococci was strain specific and the growth of certain Lactobacillus spp. was enhanced by the probiotic,” [2015]
• “E. faecium had lower (P < 0.05) concentrations of E. coli on d 14 and 28, less (P < 0.05) Clostridium perfringens on d 28, greater Lactobacillus counts on d 14 and 21, and greater (P < 0.05) Bifidobacterium in their cecal contents on d 21″ [2013]
• “In general, probiotic bacteria proved to be more inhibitory towards lactic acid bacteria than vice versa since the latter did not exert any effect on the growth of the former, with some exceptions” [2001]
• “using a synbiotic comprising Bifidobacterium bifidum BB-02 and Bifidobacterium lactis BL-01 (probiotics) …. Counting of viable organisms showed significantly higher total numbers of fecal bifidobacteria, total numbers of lactobacilli, and numbers of B. bifidum during synbiotic feeding.”[2005]

Bottom Line

I read that the following three “play well with each other” and will raise lactobacillus in a balance style. Taking lactobacillus probiotics will destroy the balance and lactobacillus will dominate, resulting in the low populations staying low (or non-existent) of the families that CFS patients are abnormally low in.

• Enterococcus faecium – Symbioflor-1 and others
• E. Coli (mutaflor, Symbioflor-2)
• Bifidobacteria

A reader (with Crohn’s Disease, not CFS) asked me about this probiotic — especially as it is just $20 at Costco. The probiotic lists all of the strains (finer identification than species) – which is a very good thing. You know better what you are getting (in terms of expected health impacts).

This is NOT recommended for CFS because it will reduce E.Coli (which are very low to non-existent with CFS). With Crohn’s disease there is an overgrowth of E.Coli.

So what to expect?

Lactobacillus plantarum 299v (DSM 9843)

• Clinical trial: Lactobacillus plantarum 299v (DSM 9843) improves symptoms of irritable bowel syndrome [2012] [2001] Not repeated in [2002] [2014] unfavorable in [2010]
• Probiotic strain Lactobacillus plantarum 299v increases iron absorption from an iron-supplemented fruit drink: a double-isotope cross-over single-blind study in women of reproductive age[ 2015 ].
• Lactobacillus paracasei and Lactobacillus plantarum strains downregulate proinflammatory genes in an ex vivo system of cultured human colonic mucosa[2013].
• Lactobacillus plantarum 299v reduces colonisation of Clostridium difficile in critically ill patients treated with antibiotics [2008].
• Lactobacillus plantarum 299v inhibits Escherichia coli-induced intestinal permeability [2002].

Lactobacillus paracasei DSM 13434 (8700:2)

• “In conclusion, intake of the probiotic strains Lactobacillus plantarum HEAL 9 (DSM 15312) and Lactobacillus paracasei 8700:2 (DSM 13434) reduces the risk of acquiring common cold infections.”[2011]
• “Our findings indicate a therapeutic potential of oral administration of a combination of probiotics and provide a more complete understanding of the host-commensal interactions that contribute to beneficial effects in autoimmune diseases.” [2010]
• Lactobacillus paracasei 8700:2 (DSM 13434)

Lactobacillus plantarum DSM 15312 (HEAL9)

• “In conclusion, intake of the probiotic strains Lactobacillus plantarum HEAL 9 (DSM 15312) and Lactobacillus paracasei 8700:2 (DSM 13434) reduces the risk of acquiring common cold infections.”[2011]
• “Our findings indicate a therapeutic potential of oral administration of a combination of probiotics and provide a more complete understanding of the host-commensal interactions that contribute to beneficial effects in autoimmune diseases.” [2010]
• Academic Paper [2015]

Lactobacillus bulgaricus lb-87

• “In his study, both Salmonella sp. and E. Coli are inhibited when mixed with GLB44 invegetable juice.^[9] ” Wikipedia
• No PubMed studies

Lactobacillus brevis LBR-35

• Supplier monogram
• No information

Lactobacillus salivarius LS-33

• “Ratios of Bacteroides-Prevotella-Porphyromonas group to Firmicutes belonging bacteria, including Clostridium cluster XIV, Blautia coccoides_Eubacteria rectale group and Roseburia intestinalis, were significantly increased (p ≤ 0.05) after administration of Ls-33. The cell numbers of fecal bacteria, including the groups above as well as Clostridium cluster I, Clostridium cluster IV, Faecalibacterium prausnitzii, Enterobacteriaceae, Enterococcus, the Lactobacillus group and Bifidobacterium were not significantly altered by intervention.” [2013]
• “Lactobacillus salivarius Ls-33 and Bifidobacterium infantis 35624 preferentially induced IL-10.” [2011]

Lactobacillus paracasei LPC-37

• “L. paracasei Lpc-37 and B. lactis 420 are able to colonize the intestine transiently.” [2008] i.e. does not stay
• “The use of probiotic cultures significantly increased the availability of calcium (~2.5%), phosphorus (~6%), and magnesium (~18%).” [2014]

Lactobacillus acidophilus LA-14

• “Trends toward significant changes in immunoglobulin serum concentrations compared with controls (P<0.1) were found for six out of the seven probiotic strains.” [2008]
• “Consumption of L. acidophilus La-14, L. rhamnosus HN001 in combination with bovine lactoferrin leads to vaginal detection; even 1 week after consumption was stopped.” [2015]
• “L. acidophilus La-14 produces bacteriocin active against Listeria. monocytogenes ScottA… L. acidophilus La-14 shows a good resistance to several drugs and may be applied in combination for therapeutic use.” [2011]

Bifidobacterium lactis BL-04 (ATCC SD5219)

• Monograph from supplier
• “Trends toward significant changes in immunoglobulin serum concentrations compared with controls (P<0.1) were found for six out of the seven probiotic strains.” [2008]
• “The pollen season induced a reduction in Bifidobacterium, Clostridium and Bacteroides which could not be prevented by the probiotic intervention… Fecal IgA was increased in the placebo group during the pollen season; this increase was prevented by the probiotics ” [2009]
• “The risk of an upper respiratory illness episode was significantly lower in the Bl-04 group ” [2014]

Lactobacillus casei Lc-11 (ATCC SD5213)

• Excellent inhibition of E.Coli,  Good inhibition of Salmonella typimurium, Straphylococcus aureus, Listeria monocytogeners
• Produces only L(+) Lactic acid (no D-Lactic) [2008]
• No pub med studies

Bottom Line – Not for CFS Patients

Why? The answer is simple — many of the above strains inhibits or kill E.Coli. E.Coli is very low or non-existent with CFS patients.  This probiotic may make a bad situation worst.

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