A reader that have been following the model with great improvement shared their latest uBiome results. It has some interesting data points which I wish to review.

The patient is not 100% Recovered

My working definition of recovered using uBiome is having a ratio of firmcutes to bacteroides between 2.2:1 and 1.9:1. This patient is at 1.4:1 in April 2017, in January 2017 they were at 1.1:1; they are moving in the right direction but have some distance to go still.

• Akkermansia (usually low in CFS):   Jan – 1.42% (71%), April 5.68% (287%)

Can you alter your microbiome? Looking at the Order changes shown below over 3 months, the answer is a clear yes!

Bifidobacterium and Lactobacillus at or above normal levels

What is very interesting is that after January, 2017 — there was considerable (major) stress on the person in this period — this may not be the cause of the decline, but personally, I consider it a contributor. Learning to deal with stress, flight or short fight or indifference are essential skills.

Looking at the split between Bifidobacterium and Lactobacillus,

• Bifidobacterium: 176% in January, dropping to 0% in April
• Lactobacillus: 3% in January, dropping to 2% in April
• Diversity dropped from 97%ile to 89%ile.

Diet specific comparisons

uBiome provides comparison with average person and heavy consumers of certain things.

In corresponding with this person, they saw that they were low on the Kefir bacteria chart compared to those  who eat Kefir regularly and (thanks to residue brain fog that is progressively clearing) concluded that they need to eat more Kefir.  They were at the average level of non Kefir people. There is no need to add Kefir (or anything else) when you are at the average level for that.

A surprise on raw milk bacteria

This person does not consume raw milk, but the bacteria associated with raw milk have been increasing. This is a good thing. More diversity.

Interesting factoid on consuming raw honey

Some patients have reported improvement from raw honey. The uBiome cites Clostridium butyricum as being in it; this is available as a probiotic (on my recommended list) Miyarisan.  For this patient, they appear to be low… a little raw honey  or Miyarisan would be suggested.  Honey brings lactobacillus kunkeei which is not available as a probiotic.

Increase of Rare Bacteria also occurred with stress

It seems that a higher number of rare bacteria is an indicator for severity of CFS. This would be expected by the model. In January (pre-stress), these bacteria were seen in 1 of 10 healthy controls. Come April, we had the rare Caldicoprobacter, Gallicola, Mobiluncus suddenly appearing, and a few more common one appearing too: Gelria, Thermoanaerobacteraceae, Atopobium. One disappeared, Acidaminococcus — this bacteria uses amino acids as an energy source and its disappearance may imply the amino acids available in the gut has shifted (either not being produced enough OR some other bacteria hogging them).

Jan 2017	April 2017

Bottom Line

Heading into January, this patient was shifting nicely — correcting the typical CFS shifts. While no significant supplements changed, the appearance of heavy duty stress impacted the microbiome greatly …. the major change was that of Bifidobacterium disappearing!!! A secondary impact was the appearance of several rare bacteria.

Suggestions for the patient:

• The stress is a hiccup. It has ended and time to get back to the model with a little preparation for the next stress event.
• Invest in stress-coping techniques — may be prayer, may be yoga, may be self-help books, may be classes.
  • Whenever stress appears — write down plans for how to deal with it
    • Fight – Mark on a calendar when the fight will stop
    • Flight – May be disassociate with people, having excuses to miss meetings, etc
    • Ignore aka let-go of the stress. resignation (What will be will be – Que Sera,Sera!)
      https://www.youtube.com/watch?v=azxoVRTwlNg
• Resume with heavy dosages of Bifidobacterium
  • Consider adding some Lactobacillus (see this post)
  • Take Ashwagandha regularly for at least 2 months.

As a personal note — I am very aggressive in seeking a low stress workplace. If there are dysfunctional managers or co-worker, I start looking for a new job with the simple rule:

• If I cannot get the work stress resolved in 2 months (including doing a HR request under ADA if my physician is willing to write a letter), and
• I am offered a job at a financially tolerable salary which appears to have less stress
• Then I will take the job and give the minimum required legal notice to my employer.

As a recovered CFS patient, you must protect your health (and uBiome results).

Back around 1999-2002, the use of whey, colostrum and goat milk for CFS was popular. A friend was positive for EBV and after 2 months of an EBV specific colostrum, became negative. This was a pre-antibiotic treatment: You infect a pregnant cow with infection X and once the cow calved, you collect the milk which will high in antibodies programming against infection X.  This method was far more expensive than antibiotics and did not scale well…. hence it was forgotten once antibiotics came along. Unfortunately, this EBV specific form of colostrum is no longer available.

“Colostrum and milk are rich in proteins and peptides which play a crucial role in innate immunity when transferred to the offspring and may accelerate maturation of the immune system in neonates.” [2005]

A reader asked about these, so a fresh look at the literature is done below.

Human versus Cow Milk

The chart below illustrate well the difference [source]. They are VERY different.

Colostrum

“Colostrum (known colloquially as beestings,^[1] bisnings^[2] or first milk) is a form of milk produced by the mammary glands of mammals (including humans) during pregnancy. Most species will generate colostrum just prior to giving birth. Colostrum contains antibodies to protect the newborn against disease. In general, protein concentration in colostrum is substantially higher than in milk.” [Wikipedia]

It is heavily promoted in some alternative health circles [Example by a provider with citations to studies]

• Bovine antibodies targeting primary and recurrent Clostridium difficile disease are a potent antibiotic alternative.[2017]
• Milk-derived proteins and peptides in clinical trials.[2013]
• Molecular and biotechnological advances in milk proteins in relation to human health[2009].
  • “Taken together, milk-derived proteins and peptides are bio-available and safe for the prevention and treatment of various disorders in humans and may play a complementary [natural agents] rather than a substitutional role to the toxic synthetic pharmacological drugs.”
• [Therapeutic properties of proteins and peptides from colostrum and milk]. [2005]
  • “chewable tablets (Colostrinin) was recently found to improve or stabilize the health status of Alzheimer’s disease patients….In conclusion, preparations derived from milk and colostrum are effective, easily bioaccessible, and safe, finding wide application in prevention and therapy for newborns and adults.
• Treatment of multiple sclerosis with anti-measles cow colostrum. [1984] “
  • “As a result, of 7 high NT titre (512-5120) anti-measles colostrum recipients 5 patients improved and 2 remained unchanged. Among 8 low NT titre (8-32) anti-measles colostrum recipients 5 patients improved and 3 remained unchanged. However, of 5 negative NT titre (less than 8) colostrum recipients 2 patients remained unchanged and 3 worsened. No side-effects were observed in colostrum recipients. These findings suggest the efficacy of orally administered anti-measles colostrum in improving the condition of MS patients (P less than 0.05).”

Whey

Whey protein is a mixture of globular proteins isolated from whey, the liquid material created as a by-product of cheese production. [Wikipedia]. As you can see from the figure above, why content varies according to source.

Back in 2000, “Non-denatured Whey” was a hot topic. “Undenatured whey protein isn’t heat-treated, so the fragile bonded cysteines that later form glutathione aren’t broken down in pasteurization.”[source] — so no pasturization (or homogenization) so the chemical structures of the whey are not damaged. At a philosophical level, this appears logical.

• “These findings indicate that the effect of heat treatment on whey proteins should carefully be investigated further.” [2017]
• Biochemical and clinical effects of Whey protein supplementation in Parkinson’s disease: A pilot study [2016].
  • “This study is the first to report that Whey protein supplementation significantly increases plasma reduced glutathione, the reduced to oxidized glutathione ratio, BCAAs and EAAs in patients with PD, together with a concomitant significant reduction of plasma Hcy.”
• Limiting prolonged inflammation during proliferation and remodeling phases of wound healing in streptozotocin-induced diabetic rats supplemented with camel  undenatured whey protein [2013].
  • Camel whey protein enhances diabetic wound healing in a streptozotocin-induced diabetic mouse model: the critical role of β-Defensin-1, -2 and -3.[2013]
  • Supplementation with undenatured whey protein during diabetes mellitus improves the healing and closure of diabetic wounds through the rescue of functional long-lived wound macrophages[2012].
• A whey-based glutathione-enhancing diet decreases allergen-induced airway contraction in a guinea-pig model of asthma.[2011]
• The biological activity of undenatured dietary whey proteins: role of glutathione [1991].
  • “The presence in the serum albumin fraction of glutamylcysteine groups (rare in food protein) and the specific intramolecular bond as related to the undenatured conformation of the molecule are considered to be key factors in the glutathione-promoting activity of the protein mixture.”

Other Non-Cow Milks

Looking at other milks, we find that Goat’s milk has less β-lactoglobulin (closer to human milk in a weak sense).

“Because an increase in the plasma Trp-LNAA ratio is considered to be an indirect indication of increased brain serotonin function, the results suggest that dietary protein rich in alpha-lactalbumin improves cognitive performance in stress-vulnerable subjects via increased brain tryptophan and serotonin activities.” [2002]

” The main components of whey proteins in camel milk and colostrum were similar to that in bovine, except for the lack in β-lactoglobulin.” [2007]

• Undenatured Goat Whey (Available from Swanson’s)

• Certified Organic Undenatured Bioactive Whey Protein (Swanson) – cheaper than ImmunoPro which was very popular in 2000.
• High alpha-lactalbumin whey Isolate is available (Davisco) [Product]

Bottom Line

There are no PubMed studies on whey and CFS/FM/IBS. There was one study for FM and one for IBS, one for CFS (by a questionable author – conflict of interests)

• “The objective of this clinical pilot study was to examine the induction of apoptosis in mononuclear cells on treatment of patients with chronic pain syndrome with oral immunoglobulin produced from bovine colostrum (BCC)….These results were accompanied by a relief of the pain symptoms [in 3 out of 4 patients]” [2009]
• “After 4 weeks (i.e. immediately after treatment), the endotoxin levels of [IBS] patients in the colostrum group showed a decrease in 44.4% (4/9) patients, no interval change in 11.1% (1/9) patients, and an increase in 44.4% (4/9) patients.” [2014] – helps some, makes other worst!
• Inconclusive (but positive) study for Gastrointestinal Infections[2008]

I would recommend trying them, especially the high alpha-lactalbumin whey Isolate because of it’s impact on cognitive function and also improvement of sleep.  Please be aware that results are mixed — it’s a for better or for worst supplement.

I wish the infection specific colostrum were still available, and would love to see one specific for staphylococcus aureus [post].

“”

I have done summary of different DNA variations associated with CFS/IBS/FM before:

• DNA: Irritable Bowel Syndrome’s SNPs
• Fibromyalgia DNA SNP’s
• A Serotonin SNP in CFS
• Methylation Testing via 23andMe
• Case Study on Using DNA: Multiple Chemical Sensitivity
• Is CFS in your DNA?

My model has DNA + microbiome shifts –> Symptoms. The DNA reduces tolerances for swings of metabolites produced the microbiome and with a dysfunctional microbiome, some people are pushed over a threshold and develop symptoms. Fixing the microbiome is possible today, fixing DNA is likely a few decades off.

I happened to stumble across some PubMed studies involving hyperacusis, phonophobia and DNA Snps. This post looks at what I found for other conditions with hyperacusis or phonophobia.

Phonophobia (light sensitivity)

• “Dopamin Beta Hydroxylase gene +1603C>T polymorphism” [2016]

Hyperacusis (noise sensitivity)

The recognized associated conditions [2003] are

• ” The most informative marker (69%) was D7S1870, followed by Hei (55%) and ELN 17/exon 18 (44%). The microdeletion was present in 56% and absent in 22% of patients….Two of the syndrome characteristics (an overfriendly personality and hyperacusis) were more frequent in the microdeletion group and these differences were statistically significant (p = 0.006 and p = 0.02, respectively).” [2010]
• ” OCRL gene deletion revealed involvement of several flanking repeat elements… hyperosmia and/or hyperacusis were reported recurrently.” [2015]
• “hemizygosity for a chromosomal deletion at 7q11.23…  hyperacusis [1999]

A reader asked me to look at the results they just got back. I was pleasantly surprise to see some significant improvements in their report

Lactobacillus and Bifidobacterium is now reported

This is a classic CFS profile!

Akkermansia is cleanly reported

Again, a classic CFS result. See this post on Increasing Akkermansia I did earlier.

Rare Bacteria are listed simply

Checking a few other uBiome results that I could access, we did find a strong pattern for three. And an over representation (25% of the CFS samples versus 13% of general samples)

• Thermonaerobacterales 2/8
• Gelria:  2/8
• Synergistaceae: 2/7
• Low Akkermansia 6/8
• Low Lactobacillus 8/8
• Low Bifidobaceria 7/8

One reader was very rich in rare results:

Bottom Line

Three groups appear to be very common as low to non-existent

• Akkermansia  75%
• Lactobacillus 100%
• Bifidobaceria 87%

There is work going on in getting an Akkemansia probiotic approved for sale. Remember to avoid most lactobacillus because it will push out bifidobacteria… instead, focus on only bifidobacteria probiotics.

Metabolism Reports

Another new set of reports have been added, as shown below. This is done using data derived from the KEGG Pathway Database,

Each of these can expand, for example:

We see two items of interest, ALA (alpha-linolenic acid metabolism) is low and Arachidonic acid metabolism is high. See ALA article and Arachidonic acid metabolism: role in inflammation (1991)

• So, taking ALA supplements would be strongly suggested

Spot checking other ubiome results, I saw one reader had

• D-arginine and D-ornithine metabolism being a very low 0.09x
• Flavonoid biosynthesis a low 0.27x

Again, this hits at specific supplements in lieu of gut bacteria doing their jobs.

Bottom Line 2

The ubiome results give much more friendly data and at a low cost. If you are unsure that you have CFS/IBS/FM, then comparing your results to the above may answer the question. Of greater interest is the additional tables of what part of the KEGG pathway may suggest supplementation.

• “I have APS.  Positive on Lupus Anticoagulant. …and now some clogged veins (ischemia disease) and perivascular tunnels. Having POTS also doesn’t help…Latest to tack on is Sojogrins to all the others… Dad had three strokes”

A Lab that appears to offer a reasonable set of tests

• THROMBOPHILIA GENETIC PANEL (this is a ONE TIME test — it tests DNA)
• HYPERCOAGULABILITY PANEL

Allergy of what may be occurring

Your body is like a family. Job and expenses are balanced, in fact, the family may be able to do some savings. A sickness comes along and the body/family deals with loss of income for a few weeks and higher medical expenses. The savings are gone and the family borrows. The family gets over the sickness and get back to work. Unfortunately, the family debt keeps growing and growing. Similarly, the body’s coagulation system is working as it was before. The sickness triggers coagulation (expenses) and the available income is not enough to clear it. The sickness is gone, but the side effect persists. Some families may be able to get rid of the debt over time (spontaneous remission), others gets deeper into debt, going down here.