With the long weekend, I bite off some of the nastier refactoring. In the late spring, I did a trial run of quantiles non-parametric statistics with awesome results. I had arbitrarily picked 4. I have now implemented the data infrastructure to support 8 and 16 quantiles. To this, I added the site source so that mouth bacteria analysis will be automatically supported with more data uploaded.
Update of Taxonomy Data
This allows you to see how your numbers compare to others in terms of percentile buckets (3% of the population in each)
Updated My Biome View
The original version used canned images. This uses scaling and appropriate placement.
Site like mouth was been implicated in certain conditions (Chronic Fatigue Syndrome,
Data Size is sufficient that using the large quantiles should produce more meaningful results.
8 – quantile High Outliers are likely <3%ile chance (most medical tests use 5%ile for high threshold
16 – quantile takes it higher but with some caution being needed
For symptom analysis to microbiome, there is some extra magic needed (i.e. I must test with, 4-, 8- and 16- with too few samples forcing the lower quantiles.
That’s it. Been grinding away this weekend and about to do a 2nd revision of the code refactor.
I had an old Pebble Watch with heart rate monitor – unfortunately the battery was approaching end of life (i.e. watch needed to be charged daily). I went searching for an economical replacement and found a 2019 watch whose price was, was sweet. Ordered one to see how well it worked.
After a week, a second one was ordered for the wife.
The BP Pressure is not in most watches, this is a new 2019 model and using newer chips (the endless dropping of cost for features). There is a cheaper one (appears to be identical) for just $16.00.
The associated application shows your pulse thru out the day.
Having the blood pressure monitor is also sweet (you need to calibrate it using an external BP device- unless you are interested only in unexpected changes).
Bottom Line
Having automatic pulse tracking thru the day is sweet. Having BP being available when or after POTS happen is also informative. The cost is so low that arguments about how long will it last, etc… almost become moot.
Lately I have been getting a number of inquiries of parents with children with autism. I am a high function autism spectrum person myself, the degree of focus on the microbiome is likely a tell-tale ;-). I have done a few prior posts, and will keep my citations to studies after these posts.
If you find this informative, please share on groups you belong to.
Can we modify Autism by Microbiome adjustment?
Can we reduce autism-related gastrointestinal and behavior problems by gut microbiota based dietary modulation? A review. [2019] ” Published studies on the relationship of gastrointestinal and behavioral problems with gut microbiota in autism are very limited and contradictory. The fact that the results of the studies are not consistent with each other may be explained by the differences in the age of participants, geographical region, sample size, presence of GI problems in the selected control group, and feces or biopsy samples taken from different regions of GI system. ” – in short, poorly done studies
A Systematic Review of the Role of Prebiotics and Probiotics in Autism Spectrum Disorders.[2019] “Conclusion: Despite promising preclinical findings, prebiotics and probiotics have demonstrated an overall limited efficacy in the management of GI or behavioral symptoms in children with ASD. In addition, there was no standardized probiotics regimen, with multiple different strains and concentrations of probiotics, and variable duration of treatments. “
Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota. [2019] ” Notably, most improvements in GI symptoms were maintained, and autism-related symptoms improved even more after the end of treatment. Important changes in gut microbiota at the end of treatment remained at follow-up, including significant increases in bacterial diversity and relative abundances of Bifidobacteria and Prevotella. “
In short, the answer is yes — but apart from FMT, researchers/clinicians are tossing random diet and probiotics at the issue resulting is very mixed results.
Bacteria Shifts
” This meta-analysis suggests an association between ASD and alteration of microbiota composition and warrants additional prospective cohort studies to evaluate the association of bacterial changes with ASD symptoms, which would provide further evidence for the precise microbiological treatment of ASD. ” [2019]
For a good summary of current research see Table 2 in The Role of Gut Microbiota in Gastrointestinal Symptoms of Children with ASD [2019] or my condition summary page. In both of these you will see disagreement on some results: for example Lactobacillus to high compared to the controls used in one study and Lactobacillus is low compared to the controls used in another study. To me, this means that it is the metabolites being produced is the likely cause. Different groupings of bacteria can present with a similar metabolite profile. Often members in one of these grouping may be hostile to members of a different grouping — looking for a single bacteria or a single pattern of bacteria is a naive understanding of the microbiome.
” Serum levels of TNFα, TGFβ, NT, and SORT-1 increased in ASD patients. Fecal levels of HMGB1 correlated with GI sign severity in ASD children. ‘” [2019]
In terms of the microbiome site, we are up to 12 samples with autism uploaded. 16 is the threshold for it to showup in the symptom explorer (20-30 samples would be really nice!)
Attempts to date
Nowadays, there is lack of strong evidence about the effect of dietary interventions on these problems, particularly prebiotics. Therefore, we assessed the impact of exclusion diets and a 6-week Bimuno® galactooligosaccharide (B-GOS®) prebiotic intervention in 30 autistic children…. Following B-GOS® intervention, we observed improvements in anti-social behaviour, significant increase of Lachnospiraceae family, and significant changes in faecal and urine metabolites.
” The results showed that PS128 ameliorated opposition/defiance behaviors, and that the total score of SNAP-IV for younger children (aged 712) improved significantly compared with the placebo group. Additionally, several elements were also notably improved in the PS128 group after 28-day consumption of PS128. “
Consistent with previous studies, the microbiota of children with ASD contained a higher number of Clostridium spp. and a lower number of bifidobacteria compared with non-autistic children. B-GOS administration significantly increased bifidobacterial populations in each compartment of the models, both with autistic and non-autistic-derived samples, and lactobacilli in the final vessel of non-autistic models. In addition, changes in other bacterial population have been seen in particular for Clostridium, Rosburia, Bacteroides, Atopobium, Faecalibacterium prausnitzii, Sutterella spp. and Veillonellaceae. Furthermore, the addition of B-GOS to the models significantly altered short-chain fatty acid production in both groups, and increased ethanol and lactate in autistic children. “
It is clear that microbiome shifts impacts the severity and symptoms of ASD. Two studies showed improvements by trying to alter the microbiome, in one case by a probiotic and in the other case a prebiotic. IMHO, any drug that helps ASD, probably helps it by the microbiome shift it induces.
It is unlikely that the natures of the shifts are identical — we are dealing with different shifts for different patients. If you are the parent of an ASD child you have several paths before you:
Use the results of the two studies above, seeking out the specific strain and prebiotic used. Watching for further studies over the next decade
Suggestions included probiotics that are theoretically more likely to help than hurt.
The suggestions can be further refined by including symptoms (which highlights certain patterns in the midst of the noise).
Go with random suggestions from support groups. Often improvements reported are placebo effects or ‘hopeful glasses’ reports (you see what you need to see, not what is there).
As a FYI — my last post linked to an a priori suggestions for Autism (suggestion based on the shifts reported in the literature). The first probiotic on that list was Lactobacillus Plantarum. Also at the top of the lists were arabinoxylan oligosaccharides (prebiotic), fructo-oligosaccharides (prebiotic) . In other words, we have convergence of predicted to reported from studies.
A reader wrote me about problems with chronic congestion. While in theory, altering gut bacteria may be able to influence this is a roundabout way (alter metabolites circulating in the body), this does not seem the most direct and best route.
As a result of this post, I did some ‘biohack’ experiments that had surprising good results. I used two probiotics available as hard tablets (not capsules) under the tongue at bed time. Chronic low grade congestion disappeared in a few days. A little further digging over the weekend end up revealing that it may also help with periodontal issues! (I have seen some improvement there also)
” We conclude that 2 weeks’ nasal administration of a honeybee LAB microbiome to patients diagnosed with CRSsNP is well tolerated, but neither affects symptom severity nor the microbiological flora/local inflammatory activity. “
” This better clinical efficiency of the test preparation was particularly observed during the treatment period, with 12 vs. 27 relapses (p = 0.013), but less during the follow-up observation period, with 27 vs. 39 relapses (p = 0.127). In addition, the time span until occurrence of the first relapse was clearly longer under verum (699 days) than under placebo (334 days) and after the end of the observation period 91% of patients under verum experienced only one relapse compared to 62% in the placebo group (p = 0.01).
Is the Oral Microbiome Associated with Blood Pressure in Older Women? [2019] ” Sixty-five bacterial species demonstrated significant differences in relative abundance in women with elevated BP or using hypertension medication as compared to those with normal BP. After correction for multiple testing, two species, Prevotella oral (species 317) and Streptococcus oralis, “
So far, I have had 4-6 mouth and nose samples uploaded. Not sufficient to do any analysis on 😦
There is practically no literature on modifying the oral microbiome.
Modifying the gut microbiome addresses systemic issues, the impact on the sinus, mouth and eye would be very indirect.
What is known (and explaining my results)
Symbioflor-1 is studied with positive results, it is a human source Enterococcus faecalis. Biofermin S is also Enterococcus faecalis, so the positive effects seen are not a surprise.
For Miyarisan (Clostridium butyricum MIYAIRI 588) we have no direct studies but there is plausible explanation based on studies. First I need to introduce you to LL-37
We now add in butyrate – what is produced by Miyarisan
Recent studies demonstrated that butyrate induces LL-37 mRNA in colonic epithelial cells, however the underlying molecular mechanisms have not been elucidated…. Our results clearly demonstrate that butyrate-mediated up-regulation of LL-37 is influenced by several signalling pathways and receptors including MAPKs as well as VDR and TGF-beta1, but not by PPARgamma.
Role of nuclear hormone receptors in butyrate-mediated up-regulation of the antimicrobial peptide cathelicidin in epithelial colorectal cells.[2007]
So the chain is this: Miyarisan increases butyrate in the oral cavity, this then pushes up the output of LL-37 and periodontitis is reduced. In theory, using sodium butyrate under the tongue may have similar effects. The advantage of Miyarisan is that it will likely contribute longer and have other antimicrobial actions.
Bottom Line
This post is closer to bio-hacking speculation than my usual “Just the studies, ma’am. Just the studies”.
Dragnet: Sgt Joe Friday (TV Show)
If the critical issue is in these areas, the suggestions for the entire body from http://microbiomeprescription.com/ may be a poor fit. The studies on enterococcus faecalis and LL-37 suggests that the above may be able to effect sinus, periodontitis and perhaps dry-eye issues. They are in the same sphere and far removed from the gut.
If I get at least 16 samples for each of these non-gut areas, I will spin out some of the charts for them. A suggestion engines needs facts from studies — and that we do not have. What I have is on this page.
CFS Remission 