This uBiome was different than others — age may be a factor dealing with microbiome shifts in CFS.

Short History of Key Points

1. Original Onset appear to have been triggered by an amalgam being removed in grade 12
2. Subsequent was sinus infection etc with likely an inappropriate antibiotics for this person
3. Repeat when the amalgam was replaced again a year later
4. At university, the dorm he was in appear to have had significant mold issue
   1. fresh fruit would go moldy in 1-2 days constantly
   2. room mate with autoimmune issues was having constant flares
5. Today, he is back at university in a different dorm (does not appear to have mold issues)
   1. Has been doing variety of herbs etc that been suggested on this blog over this year
   2. Greatly improved compared to the last few years
   3. No stomach or digestive issues at present
   4. This uBiome was done in the last few weeks (his current state)

“Interestingly enough, I’ve also had a higher precedence of cavities since college started and they only got worse when my symptoms of fatigue began as well”

Current Status

Unlike most CFS patients, the ratio of Firmicutes to Bacteroidetes was close to normal.

• Bifidobacterium was 61% of normal
• Lactobacillus was < 1% of normal
• Akkermansia – none reported.

At the Genus level, there were several abnormal high:

• Collinsella: 263% of normal (high seen in 25%)
• Enterorhabdus: 326% of normal (only rarely seen)
• Intestinibacter: 241% of normal (high seen in ~50%)
• Roseburia: 247% of normal (high seen in 30%)

What do we find:

• Collinsella and Enterorhabdus are reduced with smokers with Crohn’s Disease [2016]
• “A lower abundance of Roseburia has been observed in patients suffering from inflammatory bowel disease.” [ubiome]
• Higher level seen with diets with whole grain [2013]
•  Metformin will “increases Escherichia and lowers Intestinibacter abundance” [2015]
  • “elevated levels of Roseburia may be associated with weight loss and reduced glucose intolerance.” [ubiome]

Pre-diabetic?

Looking at some articles, there is a possibility that being pre-diabetic may be a factor (hint: testing should be considered).  A pre-diabetic diet should be consider – see this WebMD page. Diabetes does run in his family.

Analysis

This reader abnormalities do not have any association with IBD etc. His values were high when a low value was associated. The uBiome agrees with his symptoms.

I was at my dentist recently and she gave me a list of supplements that help with dental gum health (will do a post on this) which almost looks like it was written for CFS patients — the same items occur constantly. One of my own crowns is a concern to her because the x-rays are unclear if I have grown a colony of bacteria under the crown (a location very hard to treat with antibiotics, but also a location which could re-infect the body). She was recommending removing the crown and send samples for analysis.

For amalgams, the traditional view has been the mercury has created health issues. There is an alternative explanation, the area under the amalgam may be an ideal colony site for some types of bacteria; bacteria that could be release slowly or in quantity when dental works occurs. This reader appear to have suffered multiple insults: Amalgam-bacteria onset, antibiotics that further shifted his microbiome, prolonged mold exposure adding more shifting of his microbiome.  He is getting his mouth into better shape, he found brushing with Alpha-Lipotic Acid helped his mouth(I love readers sharing successful experiments!) . His mouth appears to be a key source for his CFS.

Fortunately, he appears by symptoms and ubiome to be on his way to recovery.

Bottom Line

My usual criteria for probable CFS using uBiome is having two of the following three very low:

• Bifidobacterium
• Lactobacillus
• Akkermansia

This uBiome made that criteria but not in the usual way. He appears to be on the way to recovery (but need to be wary of factors that could cause flares or worst)

• The glucose/diabetes related issues hints that Lactobacillus Fermentum ME-3 should be tried. [2014][2016]
  • Consider breaking a capsule apart and leave the contents in your mouth for a while after brushing your teeth
  • You may wish to try this with other probiotics.
• The chewing of various natural gums (myrrh, mastic, boswellia) should also be considered because of the dental issues (and the potential of the mouth being a reserve to re-introduce bacteria into the guts).
  • Do a variety of oral probiotics
• Do appropriate herbal teas: Triphala, Neem, etc — we want their contents to hang out in your mouth area.
• Redo uBiome in December to see what shifts has occurred

As always, consult with a knowledgeable medical professional before adding or changing supplements.

This is my 700th post and at the same time, a reader asked

Another uBiome result, as with other patients, low or no bifidobacterium and lactobacillus. Similar to most other patients, biodiversity was very high, 97%ile, with the usual many families at a very low (0.01 or 0.02) (trace) level compared to controls with the same families.

Again, many rare ones show up

Firmicutes to Bacteroidetes ratio was low 1.1: 1 instead of the normal 2.1:1. (about 1/3 have low ratios so far, and 2/3 have high ratios).

• Akkermansia level is high (6.83) -seen in about 25% of the uBiome, the other 75% are low.
  • This subset of high patients also tend to be high in:
    • Alistipes, Bilophila, Intestinibacter,  Oscillospira, Intestinimonas,  Butyricimonas
    • This hints that 7 genus may be mutually beneficial to each other.

Notes on person: hepatitis triggered CFS over 20 years ago. Currently not doing any protocol.

The Low Amount of Abundance Bacteria Genus

I have been recording the relative percentage (compare to controls) of different uBiome that I have reviewed. I took the numbers at the Genus (lowest) level, counted and plotted them.

The expectation for a normal group of patients would be a bell/Normal-curve with the top of the bell being at 100. With CFS patients we find a large number of genus with a very low level compare to control.  In other words we have high biodiversity but it is very fragmented and made up of nominal populations. If the tests being applied to the microbiome was less sensitive than uBiomes, then a result of low biodiversity could be reported on the same sample because all of the trace, 10%, 20% may not be recorded.

Bottom Line

My best suggestion (especially since information on reducing Alistipes, Bilophila, Intestinibacter,  Oscillospira, Intestinimonas,  Butyricimonas is almost non-existent) is to discuss with their medical professionals the items on my “Cookbook Summary for the Brain Fogged“. The items are linked (eventually) back to the PubMed studies that provided dosage information.

Another reader shared their uBiome results with bioscreen results (done the old fashion was of culturing bacteria). First thing is the classic “where’s the bifo and lacto!!” result seen with CFS/

Looking at: Firmicute to Bacteriodetes ratio: 3.8 (double the typical ratio of 2.1), the volume of Bacteriodetes was the cause of the shift (50% of typical).

Over on Bioscreen, we see the rest of the normal story for CFS patients: Zero E.Coli and overgrowth (remember this is cultured, so only a few results will be shown — most gut bacteria cannot be cultured).

Going back to the uBiome results — we again see a fair number of rare bacteria appearing. There is no clear pattern beyond “a lot of rare ones appear”. For example, this is the first sample showing any of the Spirochaetia Phylum (The TOP level of bacteria tree). This family includes Borrelia burgdorferi, B. garinii, and B. afzelii, which cause Lyme disease.

Drill Down

Phylum Level

• Lentisphaerae was 19.21x the average where as most CFS patients have zero
• Tenericutes was 4.31x the average where as most CFS patients have zero

Class Level

• Mollicutes (under Tenericutes) was 4.30x the average where as most CFS patients have zero. The best-known genus in the Mollicutes is Mycoplasma.

Order

• Rhodospirillales (Under Proteobacteria) was 5.94x the average where as most CFS patients have near zero (Except “B”)

Family

• Victivallaceae (under Lentisphaerae) was 20.17x the average where as most CFS patients have zero

Genus

• Victivallis (under Lentisphaerae) was 20.32x the average where as most CFS patients have none

Bottom Line

There was two major surprises in this uBiome — beyond seeing the usual CFS pattern:

• Overgrowth of the class that contains mycoplasma – Mollicutes 
• Overgrowth of the phylum that contains lyme bacteria – Spirochaetia

I do not know if one or the other have been tested for. The prescription antibiotics for both of these classes also overlap the generic CFS antibiotics and would likely reduce the overgrowth. My own preference (for myself), would be [with regular rotation]:

• Tetracyclines: for example:
  • Doxycycline
  • Chlortetracycline.
  • Clomocycline.
  • Demeclocycline.
  • Lymecycline.
  • Meclocycline.
  • Metacycline.
  • Minocycline.
• Macrolides:
  • azithromycin (brand name Zithromax),
  • clarithromycin (brand names Klacid and Klacid LA),
  • erythromycin (brand names Erymax, Erythrocin, Erythroped and Erythroped A),
  • spiramycin (no brand), and.
  • telithromycin (brand name Ketek).

Normally, lyme and mycoplasma are done by blood tests. If their “first cousins” and thriving in your gut, then the metabolites that they produce may be similar to those produce by lyme and mycoplasma — producing similar symptoms.

The lab results concluded “mild neutropenia” – WebMD cites for this condition

• “Antibiotics for bacterial infections, if the underlying cause is an infection”
  • There appears evidence from the uBiome that there are atypical gut infections.

Again, this is not medical advise — just inferences from the data and the model that I am using. These inferences should be discussed with your knowledgeable medical professionals.

I will add to my backlog posts looking for herbs/spices etc that have been demonstrated effective for these two abnormalities.

A reader was very kind to share with me their uBiome results. Ross River Virus is an infection (one of many) associated with the subsequent development of CFS. In March 2017, the reader was positive for Ross River Virus (6 months after symptoms started). We have someone in possible early CFS (less than 1 year from onset).

Does the ubiome fit the CFS Pattern?

• Low Bifidobacterium – Check
• Low Lactobacillus – Check
• Akkermansia is very high: 8.27x.
  • This is the bacteria that reduces inflammation. This may be a response to this being a recent infection/onset (the very low level seen later in most CFS patients, could be a result of ‘exhaustion’, i.e. the metabolites that this bacteria needs were badly depleted).
  • One earlier result had higher values
• Firmicutes/Bacteroidetes ratio: 0.45 (both high and low ratios are seen)
  • Bacteroidetes: 1.33x
  • Firmicutes: 0.6x

Looking at some prior uBiomes from prior posts:  B and F uBiomes are vary similar with shared spikes in the same groups (not seen with other CFS uBiome results):

• High Genus: Odoribacter, Parabacteroides, Sarcina, Intestinibacter, Allermansia
• High Family: Peptostreptococcaceae, Porphyromonadaceae, Clostridiaceae 

New (not seen in others)

• Class: Opitutae, Order: Puniceicoccalea, Genus: Butyricicoccus,

From Lab Reports

• “Most essential and other elements are very low, suspected malabsorption issue. About half are below 16th percentile: calcium, magnesium, sodium, copper, manganese, lithium, phosphorus, strontium, cobalt, iron, zirconium.”
• “Main symptom is fatigue. I can work on my computer from home 4 hours a day, … can walk comfortably in total in and around home about 1-1.5km in steps a day, 2km feels like a marathon. Wish I could sleep more, feel terrible in the mornings. Lately I’ve been feeling nauseous on and off. I need to rest regularly throughout the day. No pain thankfully, occasional headaches.”

Items to Discuss with Your Professional(s)

The nausea(and IBS) aspect is where I would start, and in that direction, I would suggest taking herbs and probiotics documented to work in this area. The goal is to adjust the gut while the dysbiosis is still fresh (and less stable). My short list would be:

• Probiotics:
  • Prescript Assist
  • Mutaflor
  • Symbioflor-2
  • Bifidobacteria Probiotics:
    • See this post for ones that are documented from studies 
    • this is a newer one (after above post): Kijimea IBS Probiotic
  • You indicate that you make water kefir, and found the bacteria typically in it on this page.  I tend to advocate avoidance of lactobacillus (not a single lactobacillus strain was been found effective for IBS) because it tend to suppress/kill off many of the bacteria that are low; possibly  making a bad situation worst.
• Herbs and Spices
  • Ginger
  • Haritaki (or Triphala which is 1/3 Haritaki)
• Magnesium Malate
• Consider Folinic Acid (the bioactive form of Folate), it may be more effective in the face of mal-absorption.

Bottom Line

You appear to match the uBiome of a subset of CFS patients. I recall from studies that lab tests for CFS start changing about 2 years after onset (the likely cause is cumulative mal-absorption). Given that it appears to be less than a year since you developed symptoms, there is a reasonable chance (likely 20-40%) that you may go into spontaneous remission over the next year. I believe that the above items will increase your odds.

If you can get Vitamin 1,25D measured, it will likely be very high (and should drop as you move towards remission). This is from my own personal experience and just 1 or 2 studies hinting at this.