A reader asked me about this element today. I know that the abundance or absence of some minerals/elements have health impact. A simple introduction is here. A quick summary of interesting studies is shown below

• Comparative psychopharmacology of autism and psychotic-affective disorders suggests new targets for treatment [2019] ME/CFS have neurological issues often and this discusses some possible pathways.
  • Psychotropic treatment of chronic fatigue syndrome and related disorders [1993]
• Lithium’s antiviral effects: a potential drug for CoViD-19 disease? [2020] ME/CFS often have virus re-activation as a contributing factor, sometimes reinforcing ME/CFS.
• The mood-stabilizing drug lithium eases repetitive behaviors seen in mice missing SHANK3, an autism gene, according to a new study. [2020]
• Emotionality is a common problem with ME/CFS. Fortunately, the people are too exhausted to become violent. But this paper raise some speculation: Is violence in part a lithium deficiency state?[2016]
• It is known to lower suicide rates [2020]
• “Trace lithium in water is negatively linked with changes in AD mortality, as well as obesity and type 2 diabetes, which are important risk factors for AD. “[2018] Translation: more lithium means less AD, obesity and diabetes.
• “Long-term increased lithium exposure in drinking water may be associated with a lower incidence of dementia” [2017]

Problems

Lithium increases hypothyroidism [2020] [2020], unfortunately hypothyroidism is common with ME/CFS [2019]. This makes it a high risk experiment if thyroid levels are low. Zinc supplements may reduce the risk [2017]

It’s known impact on the microbiome is below (and has been added to the analysis site)

” Lithium, valproate and aripiprazole administration significantly increased microbial species richness and diversity, while the other treatments were not significantly different from controls. At the genus level, several species belonging to Clostridium, Peptoclostridium, Intestinibacter and Christenellaceae were increased following treatment with lithium, valproate and aripiprazole when compared to the control group. “

Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function [2018]

“Bacterial richness was increased in both treatments compared to vehicle-treated animals; moreover, at the genus level, lithium increased the relative abundance of Ruminococcaceae and decreased Bacteroides“

Psychotropics and the Microbiome: a Chamber of Secrets… [2019]

Bottom Line

It appears that Lithium was tried on ME/CFS patients a few decades ago [See the old egroup CFSFMExperimental posts on the wayback machine). We can infer that the results were not significant on the patient population as a whole. On the flip side, it does appear to have positive neurological impact for select conditions, with some risk. For Autism where it is known that the SHANK3 defect is present, we need a well constructed study to determine the benefits to risk factors.

FMTs have been tried for Chronic Fatigue Syndrome/ME with mixed success. The why of failures has been an ongoing interest of mine. We may now have a significant factor that has been ignored in these attempts.

 Fecal microbiota transplantation (FMT) as a special organ transplant therapy, which can rebuild the intestinal flora, has raised the clinical concerns. It has been used in the refractory Clostridium difficile, inflammatory bowel disease, irritable bowel syndrome, chronic fatigue syndrome, and some non-intestinal diseases related to the metabolic disorders. But this method of treatment has not become a normal treatment, and many clinicians and patients can not accept it. 

[Research progress of fecal microbiota transplantation] 2015

This week’s Economist had an extended essay on Viruses and the like: The aliens among us/The Outsider within, this provides good background.

In addition to this, there was a podcast reporting success with FMT was associated with higher Phage Diversity in the donor. Phages are the police of the microbiome.

In this retrospective analysis, FMTs with increased bacteriophage α-diversity were more likely to successfully treat rCDI. In addition, the relative number of bacteriophage reads was lower in donations leading to a successful FMT. These results suggest that bacteriophage abundance may have some role in determining the relative success of FMT.

The success of fecal microbial transplantation in Clostridium difficile infection correlates with bacteriophage relative abundance in the donor: a retrospective cohort study (2019)

My earlier posts on FMT

• Fecal Microbiota Transplantation (FMT)
• An ideal FMT Donor scenario for ME/CFS
• Fecal Transplants – not for the herx adverse!
• A Healthy FMT Donor Microbiome and response to FMT
• uBiomes before and after a Fecal Microbiota Transplant

Bottom Line

This implies that for a greater chance of success and less risk, than DYI fecal transfer, that a lab that tests for possible infections AND for phage state may yield the best results.

I just pushed a new page. The model is simple: as the microbiome changes, these changes may cause new symptoms to appear. I have personally seen this cascade in people around me. This page uses symptoms sets entered by users to give rough estimates of what may be occurring next. In some cases, seeing the future may encourage pre-emptive actions today.

The process is simple, pick an initial symptom in the drop down.

For the symptoms below, just click the one that you have also. This will build up a list symptoms and a qualified list of predictions.

You can change any selected items… in some cases, it may result in nothing being shown.

You can reset to the top one only, or modify what is shown (more or less)

Digging down to the bacteria pattern

As you build up a collection of symptoms, you can quickly determine if there is a bacteria pattern associated. There is nothing gained from adding a 100% item to it…. it means that everyone is the subset has those symptoms so it is redundant. You want to add items that are less then 100%, ideally a symptom you have with the lowest probability.

This transfers your selection across to the page that does statistical analysis on the associated bacteria, as shown below

Accuracy of Prediction depends on YOUR Symptoms being added!

I know there is a “bias” in the data because we do not have an ideal population of samples and symptoms to work from. This page uses what we have, I believe the prediction is better than what a typical medical professional would suggest.

It can be made better by people adding more microbiomes and associated symptoms to the database. This is Citizen Science.

I have a M.Sc. in Statistics and roll my eyes with the ranges being given by most commercial labs. I know precisely the process that most are rote-following:

To set the normal range, take samples from a group of people with no known issues. Compute their average and standard deviation. Abnormally low is average – 1.95 standard deviations and abnormally high is average plus 1.95 standard deviations.

Other approaches use just 40 people with the values of the 2.5%ile and 97.5%ile being used. Unfortunately, with 40 people that becomes the lowest value and the highest value. At both ends, that is a volatile number 😦

My goal with MicrobiomePrescription is to show the numbers from over a thousand samples and let people determine if the numbers are actually unusual by visual inspection.

What should be seen is illustrated below. The average line should be close to the 50%ile with this large of a sample. Two views are usually best.

Atypical Bacteria

This bacteria is only reported by one lab, Ombre Labs was Thryve Inside. If is actually is a sibling to Bifidobacteria genus, both are children of Bifidobacteriaceae.

For another bacteria, we have the average a long distance from the 50%ile and we see what looks like three patterns — each with their own straight line (and not one like above). To get the true 50%ile (including those with zero count) it’s (50+38.2)/(100+38.32 [for Zeros]) = 63%ile on the chart.

Is it bad to be atypical? If there is not a medical condition or illness associated with it, then likely not. Variety is the spice of life, and the reality of the microbiome.

Some Extreme Examples

Bottom Line

Bacteria have a wide variety of growth patterns. Without inspect of the distributions and related information, you may either assume that there is no problem (because the lab ranges are poor — a false positive), or there is a problem when you may have 40% of people have less or more than you (– a false negative).

Do not expect labs to look at the distributions — they only have time to print the numbers and give a canned interpretation. For the microbiome, a canned interpretation is dangerous because of the impact of diet can have. I have oatmeal for breakfast every day, dark 100% rye sandwich for lunch, indian food with chicken for supper. I am pretty much wheat free… and that absence will shift my microbiome greatly.

You have to look at them yourself. You can look up most bacteria reported by labs at this URL: https://microbiomeprescription.com/Library/Lookup

I am reasonably complete in updating the database. If you know of any substances not shown below that have published peer review studies (a.k.a. PubMed) please email me with links so I may update it.

IBS is often concurrent with ME/CFS and FM.

The drill down page requires you to login. Which means nothing more than going to the login page, enter your email and wait for a login link to arrive in your email. The page is below for those who do not wish to login … my comments continue below it in “Review”

Irritable Bowel Syndrome

This list modifiers reported for specific conditions with links to studies.

Some of the items listed as improving may have inconsistent results from studies. It is recommended that the studies cited be review before considering any change.

Modifier	Impact	Citations
aloe vera	Can cause/Worsen	1
aloe vera	Improves/Treats	1
bacillus coagulans (probiotics)	Improves/Treats	8
bifidobacterium (probiotics)	Improves/Treats	1
Boswellia serrata	Improves/Treats	2
clostridium butyricum (probiotics)	Improves/Treats	4
enterococcus faecium (probiotic)	Improves/Treats	1
Human milk oligosaccharides (prebiotic, Holigos)	Improves/Treats	2
hypericin(St. John’s Wort)	Can cause/Worsen	1
lactobacillus plantarum (probiotics)	Can cause/Worsen	2
lactobacillus plantarum (probiotics)	Improves/Treats	2
lactobacillus rhamnosus gg (probiotics)	Improves/Treats	4
l-glutamine	Improves/Treats	1
low fodmap diet	Improves/Treats	13
mutaflor escherichia coli nissle 1917 (probiotics)	Improves/Treats	1
peppermint (spice, oil)	Improves/Treats	5
Prescript Assist (Original Formula)	Improves/Treats	2
rifaximin antibiotics	Improves/Treats	2
Serum-derived bovine immunoglobulin/protein isolate	Improves/Treats	4
symbioflor 2 e.coli probiotics	Improves/Treats	1
vitamin d	Improves/Treats	3
vsl#3 (probiotics)	Improves/Treats	5

Quantities from PubMed Studies on Irritable Bowel Syndrome

Show 30100200All entriesSearch:

Direction	Substance	Notes	Source
Improves	vitamin d	supplemented weekly with 50,000 IU Vitamin D improve the severity of symptoms and QOL in patients with IBS	Source
Improves	vitamin d	oral vitamin D3 2000IU/day for 6 months can be effective in treating adolescents with IBS and vitamin D deficiency	Source
Improves	vitamin d	50 000 IU vitamin D3 The IBSSS and the IBS-QoL scores in the vitamin D group significantly improved compared	Source

Showing 1 to 3 of 3 entriesPrevious1Next

Bacteria shifts from Pub Studies

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Show 30100200All entriesSearch:

Observed	Bacteria Name	Rank	Documentation
High Levels	Actinobacteria	phylum	Citation
High Levels	Akkermansia muciniphila	species	Citation
High Levels	Bacillus aeruginosus	species	Citation
High Levels	Bacteroidaceae	family	Citation
High Levels	Bacteroides	genus	Citation
High Levels	Bacteroides	genus	Citation
High Levels	Bacteroides thetaiotaomicron	species	Citation
High Levels	Christensenellaceae	family	Citation
High Levels	Clostridia	class	Citation
High Levels	Clostridiales	order	Citation
High Levels	Desulfovibrio	genus	Citation
High Levels	Desulfovibrionaceae	family	Citation
High Levels	Dialister invisus	species	Citation
High Levels	Enterobacter	genus	Citation
High Levels	Enterobacteriaceae	family	Citation
High Levels	Enterobacteriaceae	family	Citation
High Levels	Enterococcus	genus	Citation
High Levels	Erysipelotrichaceae	family	Citation
High Levels	Escherichia coli	species	Citation
High Levels	Escherichia coli	species	Citation
High Levels	Faecalitalea	genus	Citation
High Levels	Lachnospiraceae	family	Citation
High Levels	Methanobrevibacter smithii	species	Citation
High Levels	Mycoplasma hominis	species	Citation
High Levels	Oscillospiraceae	family	Citation
High Levels	Prevotella	genus	Citation
High Levels	Prevotella	genus	Citation
High Levels	Prevotella	genus	Citation
High Levels	Prevotella	genus	Citation
High Levels	Prevotella	genus	Citation

Showing 1 to 30 of 74 entriesPrevious123Next

Bacteria shifts from Citizen Science

This is based on the machine learning implemented on this site. Unpublished results.

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Observed	Bacteria Name	Rank	Relative Strength
High Levels	Eubacteriaceae	family	62
High Levels	Eubacterium	genus	48
Low Levels	Akkermansia	genus	105
Low Levels	Bifidobacterium	genus	100
Low Levels	Pseudobutyrivibrio	genus	77
Low Levels	Subdoligranulum	genus	76
Low Levels	Lactobacillus	genus	72
Low Levels	Anaerotruncus	genus	61
Low Levels	Blautia	genus	60
Low Levels	Coriobacteriia	class	58
Low Levels	Roseburia	genus	55
Low Levels	Roseburia faecis	species	55
Low Levels	Acidaminococcales	order	53
Low Levels	Erysipelatoclostridium	genus	52
Low Levels	Bacteroides thetaiotaomicron	species	51
Low Levels	Faecalibacterium	genus	51
Low Levels	Peptostreptococcaceae	family	45
Low Levels	Verrucomicrobiaceae	family	45
Low Levels	Lachnospiraceae	family	44
Low Levels	Dorea formicigenerans	species	44

Review

For citizen science looking at probiotics, we actually have a short list and a longer one from PubMed. Lactobacillus GG showed up on both, and on the actual studies list. Clostridium butyricum (probiotics) also has a match from PubMed bacteria to Actual Studies. Different oligosaccharides were on the take and avoid list. Unfortunately, most studies on IBS did not test differences (i.e. tested the forest and not the tree species).

On the avoid list was inulin and it’s associated jerusalem artichoke. Recommending that is a “pro-forma” suggestions from many physicians. So what gives? For that one I did find a study. The study results suggested that you should avoid it — a nice agreement.

 However, flatulence severity was improved by prebiotics at doses ≤6 g/d (SMD: -0.35; 95% CI: -0.71, 0.00; P = 0.05) and by non-inulin-type fructan prebiotics (SMD: -0.34; 95% CI: -0.66, -0.01; P = 0.04), while inulin-type fructans worsened flatulence (SMD: 0.85; 95% CI: 0.23, 1.47; P = 0.007).

Prebiotics in irritable bowel syndrome and other functional bowel disorders in adults: a systematic review and meta-analysis of randomized controlled trials 2019