I had done an analysis of his original before doing deep-dives in this Aug, 2017 post and a followup post later that month.

Reminder: This is all based on a model, a hypothesis that appears to match the known studies. The model purpose is to increase the odds of getting improvements. There are many factors that may influence what works and does not work – DNA, specific strains of some bacteria. We do not have enough knowledge to know what will work for any individual — we can make suggestions that appear to be far more probable to work.

Reader Notes

First, Thank you for all the work you do that so benefits this community.

Standard Items:

• Lactobacillus: 0.04x ( 0.04 Prior)
• Bifidobacterium: < 0.01 (< 0.01 Prior)
• Akkermansia:  1.98x (7.36x prior)
• Diversity:  68%ile (95%ile prior)
• Firmicutes to Bacteroidetes:  1.0:1 (Normal 2.1:1)
  • 1.1:1 prior
  • Bacteroidetes 1.25 –> 1.5
  • Firmicutes  0.64 –> 0.7

Historic Trends

We can see there are significant shifts of some phylums

Uncommon Bacteria

High Bacteria

Following have dropped below 1.5x

Akkermansia (was 5.26x –> down to 1.42): , Intestinibacter (was 5.0x –> down to 0.24x): 

References

• Oscillospira: https://cfsremission.wordpress.com/2017/10/15/decreasing-oscillospira-genus/
• Alistipes: https://cfsremission.wordpress.com/2017/10/09/decreasing-alistipes-genus/
• Parasutterella: https://cfsremission.wordpress.com/2017/10/19/decreasing-parasutterella-genus/
• Coprobacter: https://cfsremission.wordpress.com/2017/11/06/decreasing-coprobacter-genus/
• Intestinimonas: https://cfsremission.wordpress.com/2017/11/05/reducing-intestinimonas-genus/
• Butyricimas: https://cfsremission.wordpress.com/2017/10/14/decreasing-butyricimonas-genus/
• Thalassospira: https://cfsremission.wordpress.com/2017/10/22/reducing-thalassospira-genus/
• Flavonifractor: https://cfsremission.wordpress.com/2017/11/05/reducing-flavonifractor-genus/
• Pseudobutyrivibrio: https://cfsremission.wordpress.com/2017/10/15/decreasing-pseudobutyrivibrio-genus/

Bottom Line Suggestions For New Ones

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

• Barley and oat
• Bifidobacterium animalis subsp.  lactis  B-12®
• Bifidobacterium catenulatum
• Bifidobacterium pseudocatenulatum
• Black Tea
• Clostridium butyricum (i.e. Miyarisan) probiotics
• Generic Bacillus probiotics
• Lactobacillus fermentum
• Lysine supplements and foods
• Metformin
• Saccharomyces boulardii
• Vitamin K2
• Walnuts

Take

• Alchohol
• Bacillus subtilis natto
• Bifidobacterum Bifidum
• Bifidobacterum Infantis
• Cranberry bean flour (or fresh cranberries)
• E.Coli Probioitics
• Enzymatically modified resistant starch
• Faecalibacterium prausnitzii
• Flaxseed
• Gallate – Green Tea
• Inulin
• Lactobacillus Casei
• Lactobacillus kefiri LKF01
• Lactobacillus paracasei
• Lactobacillus salivarius
• L-glutamine
• Polymannuronic acid
• Resistant starch (type II & IV)
• Tannin and Gallate   — green tea see this web page.

Personal Comments

It is interesting that Black Tea is a to avoid, while Green tea is a to take.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

For updated information see Microbiome Prescription

DataPunk.Net

Nothing

PubMed Data

There are 3400+ studies on PubMed, many dealing with fish.

Disease

Diet

Prebiotic

Probiotics

Antibiotics

BottomLine

Avoid

Take

A reader starting taking this and their two earlier uBiomes had zero lactobacillus and zero bifidobacterium.  Both of these bacteria genus appear at low level afterwards (an improvement of both microbiome and general state).

“Pyrroloquinoline quinone (PQQ), an aromatic tricyclic o-quinone, was identified initially as a redox cofactor for bacterial dehydrogenases. Although PQQ is not biosynthesized in mammals, trace amounts of PQQ have been found in human and rat tissues because of its wide distribution in dietary sources. Importantly, nutritional studies in rodents have revealed that PQQ deficiency exhibits diverse systemic responses, including growth impairment, immune dysfunction, and abnormal reproductive performance. Although PQQ is not currently classified as a vitamin, PQQ has been implicated as an important nutrient in mammals. In recent years, PQQ has been receiving much attention owing to its physiological importance and pharmacological effects.” [2015]

” PQQ supplementation resulted in significant decreases in the levels of plasma C-reactive protein, IL-6 and urinary methylated amines such as trimethylamine N-oxide, and changes in urinary metabolites consistent with enhanced mitochondria-related functions. ” [2013]

PubMed Literature

• Pyrroloquinoline Quinone, a Redox-active o-Quinone, Stimulates Mitochondrial Biogenesis by Activating SIRT1/PGC-1α Signaling Pathway. [2017]
• The Effect of Pyrroloquinoline Quinone on Apoptosis and Autophagy in Traumatic Brain Injury.[2017]
  • “. Electroencephalogram indicated that pyrroloquinoline quinone improved brain electrophysiological function after traumatic brain injury. The results of CCK-8 test showed that pyrroloquinoline quinone could increase the viability of primary astrocyte treated with Glutamate. Lactate dehydrogenase (LDH) assay demonstrated that pyrroloquinoline quinone decreased LDH content in primary astrocyte exposed to Glutamate.”
• Modulation of glycine sites enhances social memory in rats using PQQ combined with d-serine[2016].
• Neuroprotective effects of pyrroloquinoline quinone against rotenone injury in primary cultured midbrain neurons and in a rat model of Parkinson’s disease.[2016]
• Effect of the Antioxidant Supplement Pyrroloquinoline Quinone Disodium Salt (BioPQQ™) on Cognitive Functions [2016].
  •  “Subjects were orally given 20 mg of BioPQQ™ per day or placebo, for 12 weeks. “
  • “The preliminary experiment using near-infrared spectrometry (NIRS) suggests that cerebral blood flow in the prefrontal cortex was increased by the administration of PQQ. The results suggest that PQQ can prevent reduction of brain function in aged persons, especially in attention and working memory.”
• Pyrroloquinoline Quinone Decelerates Rheumatoid Arthritis Progression by Inhibiting Inflammatory Responses and Joint Destruction via Modulating NF-κB and MAPK Pathways. [2016]
• Effects of Pyrroloquinoline Quinone Disodium Salt Intake on the Serum Cholesterol Levels of Healthy Japanese Adults. [2015]
  • ” Our study findings suggest that PQQ suppressed the LDL-chol level, which is an important finding, because a high level of this lipid is a risk factor for various lifestyle-related disease”
• “When provided PQQ, E. coli utilizes it as an enzymatic cofactor in enzymes important to glucose and alcohol metabolism. Although it seems likely that PQQ supplements may alter metabolic features of E. coli, whether PQQ influences lactobacillus and other organisms that are utilized as probiotics remains to be examined.   Making the link between PQQ and probiotic use nevertheless has potential in describing certain effects of PQQ.” [src]

Informal Comments

One discussion group:

1. THUMBS UP: “DID yield decent enough beneficial therapeutic effects; and DID NOT EXPERIENCE intolerable side effects; and IS WORTH the cost” (71 votes [61.74%] – View)
2. THUMBS DOWN: “DID NOT yield decent enough beneficial therapeutic effects; and/or EXPERIENCED intolerable side effects; and/or IS NOT WORTH the cost” (44 votes [38.26%] – View)

• “I have FMS/CFS and started taking PQQ recently and it has made a huge difference in my mental health as well as fatigue. Nothing has ever made any difference to the crippling fatigue I experience day in day out, so I was so happy to have come across this. I also started taking ubiquinol (Coq10 did nothing for fatigue) which also has the same effect as the PQQ (or maybe it is boosting what the PQQ has regenerated?) but sometimes when I take them together I become really angry and can end up in an uncontrollable rage. B12 also does this to me so maybe it is a methylation issue.” [Src]

• I take it at Klimas’ suggestion. IIRC, she said I should get my CoQ-10 levels up before adding PQQ for the best effect. PQQ supposedly helps us generate more mitochondria, but I guess if you don’t have enough CoQ-10 for the mitochondria you already have to work properly, how smart is it to try to grow new mitochondria that also wouldn’t be able to function properly? [Src]

  This study found that PQQ helped fatigue, tension-anxiety, depression, anger-hostility and confusion, appetite, sleep, obsession and pain, with the full effect appearing after 8 weeks supplementing daily with 20 mg of PQQ. [Src]

Bottom Line

The documented neuroprotective aspects of PQQ makes it an attractive supplement for CFS. There is an absence of studies on the microbiome or studies with CFS/IBS/FM.

There is no supporting evidence that it increases Lactobacillus or Bifidobacterium, nor evidence of adverse effect.

Looking at this uBiome, I noticed that the standard items are far less extreme (today) than most CFS readers. This was not the case a year ago, or 3 years ago. This appears to agree with only 1 uncommon bacteria and just 2 overgrowth bacteria genus (the lowest number that I recall seeing).

Reader Notes

Standard Items:

• Lactobacillus: 0.02x (2014, 2015 – 0x)
• Bifidobacterium: 0.18x (2014, 2015 – 0x)
• Akkermansia:  0.28x (2.66x in 2014, 0x in 2016)
• Diversity:  75%ile
• Firmicutes to Bacteroidetes:  2.0:1 (Normal 2.1:1)
  • 5.1:1 in 2014
  • 1.1:1 in 2016

Historic Trends

Uncommon Bacteria

High Bacteria

Reference

• Subdoligranlum: https://cfsremission.wordpress.com/2017/10/10/decreasing-subdoligranlum/
• Sutterella: https://cfsremission.wordpress.com/2017/10/13/decreasing-sutterella-genus/

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

• Berberine
• Bifidobacterim Breve
• BPA bottles
• Lactobacillus Casei
• Lactobacillus salivarius
• Omega 3
• Saccharomyces boulardii
• Walnuts

Take

• Bifidobacterium Longum probiotics
• High Fat diet
• Inulin
• Lactobacillus plantarum probiotics

Personal Comment

The appearance of Lactobacillus and Bifidobacterium, with Firmicutes to Bacteroidetes approaching normal is a very positive sign. I need to revisit “Feeding of Lactobacillus”.

I will be researching Pyrroloquinoline quinone (PQQ) it is not something that I have come across before.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

The reader whose uBiome I reviewed  here in September, did a followup with his FMT donor and got permissions from the healthy donor to share. This is of great interest because FMT for CFS tend to work well for a while and then the patient relapse. Understanding the factors involve with FMT is an important quest.

Reader Notes

Standard Items:

• Lactobacillus: 0x
• Bifidobacterium: 4.07x
• Akkermansia:  0x
• Diversity:  59%ile
• Firmicutes to Bacteroidetes:  1.8:1 (Normal 2.1:1)

Uncommon Bacteria

High Bacteria

It is interesting to note that every high genus (apart from Bifidobacterium) is on the list of typical overgrowths seen with CFS (see this post)

Bottom Line

In my earlier post, Theortical Protocol for Fecal Transplants for CFS/IBS etc, I suggested “donor should not have any bacteria genus > 1.5x that the recipient has > 1.5x.”  This donor match this criteria, so well it may be helpful (as it was in this case), I would like to suggest raising the threshold to: “No bacteria genus > 1.5x should be on the list of common bacteria genus overgrowths listed at Overview of this Blog and the Microbiome.“

How can the donor be healthy with no Lactobacillus?

There are several possible answers:

• He may be taking adequate supplements to compensate.
• His DNA (remember DNA SNPs are associated with CFS/IBS/FM and symptoms).
• Other bacteria may be compensating
• He may be borderline CFS
• The high Bifidobacterium compensated.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.