Author Archives: lassesen

Unknown's avatar lassesen 12:09 am on November 15, 2016  

uBiome Results #6 The Genus Level

This is the lowest level usually reported by uBiome. At the Family level we had 52 families in the results. At the Genus level we have 128 Genus. Below the Genus level is the Species level. Below the Species level is the Strain level. A Strain level report will likely have over 2000 strains (if it was possible to identify all of the strains).

As with the prior post, I use some thumbnail algorithms to group items into groups. The complete data is available at the bottom for people to do their own analysis.

genus1genus2genus3genus4

Genus being skipped

Criteria: 5 or more (or 50+%) in mid range (60%-160%) OR a middle value inside of this range (60%-160%) with at least 10 results. Some are not on Wikipedia

Major Shift Genus

Criteria: Middle Value below 40% And less than 4 in the middle range with at least 9 results (i.e. < 40%)

The Noisy Genus

The rest of the Genus are difficult to  interpret. As before, I ascribed them as meaningless or connected with specific symptoms (but we do not have enough samples to dig into that).

Analysis

We have 20 Genus of 128 reported with severely low numbers for what appear to be common Genus. What is actually surprising is that there are no consistent pattern of high values for any Genus, just low or normal. 

The treatment issue is how to increase these 20 Genus when most are not available as probiotics.

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Unknown's avatar lassesen 12:16 am on November 14, 2016  

uBiome Results #5 The Family Level

We have now exploded to 53 items to review when we examine the “Family Level” of bacteria in the gut. Our decomposition may reveal that while a higher Order is normal, specific families are not (usually underpopulated).

A few items are close enough to normal by one or another criteria that I will skip them entirely. Definition for normal that I used was 5 or more values in the 60% -166% range with middle value in the same range):

  • Acidaminococcaceae: Middle value 73%
  • Bacteroidaceae: Middle value 104%
  • Clostridiaceae: Middle value 95%
  • Coriobacteriaceae: Middle value 60%
  • Erysipelotrichaceae: Middle value 67%
  • Oscillospiraceae: Middle value 67%
  • Peptostreptococcaceae: Middle value 61%
  • Porphyromonadaceae: Middle value 86%
  • Verrucomicrobiaceae: Middle value 105%

While there may be some significant, the magnitude of this significance is much less than the items below

family1family2

Massive Shifts

Criteria is at least 11 values with 5 or less in the range (60% – 160%) and the middle value is outside of the range

Not Enough Information

If at least three different people have a family of bacteria, I deem it to be noise. It may apply to the person and their symptoms but is not revelant to a general CFS patient.

Possible Symptom Specific Shifts

Must be a clear pattern (i.e. at least 70% very low) and at least 3 results

Analysis

In looking at various families above, I noted a large number of them were first “discovered” in the last 20 years. They were discovered by modern lab methods such as real-time polymerase chain reaction (PCR) that amplifies RNA and DNA.  The downside of this is simple: we can identify the bacteria but we know very little about what is associated or caused with each. We know even less about how to correct shifts. Modern medicine knows how to treat overpopulation of bacteria (antibiotics) but really nothing beyond “eat yogurt”  for dealing with underpopulation — what is clearly seen above.

For four of the massive shift items, we have probiotics available in the world. The problem is that many species do not play well with other species. In terms of correction (in sequence), my best suggestions (which does evolve):

  1. High dosages of different Bifidobacteriaceae, rotating thru as many species as possible. We saw with results C that it does work to shift bacteria. The problem is their failing to take up residence.
  2.  Enterobacteriaceae probiotics — that is E.Coli probiotics from Germany (Mutaflor, Symbioflor-2) – the latter is known to take up residence.
    1. Should be taken with Enterococcaceae probiotic since they appear to support each other. E. faecium SF68, etc
  3. D-Lactic acid free and H2O2 producing Lactobacillaceae probiotics
  4. Streptococcaceae probiotics, for example Streptococcus salivarius K12

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Unknown's avatar lassesen 12:01 am on November 13, 2016  

uBiome Results #4 The Order Level

The Phylum levels had 12 items reported. The Class level had 19 items. The next level down, the Order level has 24 items. Some of the Class will be divided into several parts. For other, we have just one part of the class reported.

order

Common Items

I will not go thru every item, just the high points. For many of the items we have very limited knowledge on what they do. For “normal”, we would expect both an average and middle value between 90% (.9) and 110% (1.1). Using a wider range of 70% (.7) and 140% (1.4) could be describe as “slightly off”.  If the numbers are further off, then something is happening.

The 1998 report on the microbiome shift seen with CFS appears to be confirmed. Low Bifidobacteriales, Lactobacillales, Enterobacteriales (which includes Escherichia, i.e. E.Coli). All of the patients have at least 2 of the three being very low.

Some details

Result C

Result C illustrates that the microbiome can be changed. I suspect that prior to the second test, C2, there was significant intake of Bifidobacteria Probiotics, increasing lactobacillus and reducing verrucimicrobiales and what appears to a pathogenic enterobacteriales overgrowth.

changes

A high level of verrucimicrobiales is reported after antibiotics:

  • “Dramatic colonisation of the human gut microbiota by the Verrucomicrobia phylum following a broad-spectrum antibiotic regimen occurred without significant gastrointestinal manifestations, suggesting that influenced by external factors such as antibiotics, the gut repertoire remains partially unknown.” [2012]
  • ” Proteobacteria (including Escherichia coli), and Verrucomicrobia (including Akkermansia mucinophila) are typically present in smaller numbers in the healthy gut microbiota, but these organisms have considerable potential to influence health outcomes.” [2015]

Result L:

“at the time I took the test I had not taken any probiotics as pills for over a year, but was eating lacto fermented vegetables, yoghurts cultured from whatever was in the commercial greek and natural yoghurts that I had purchased as starter cultures and pseudonatto. I guess the yoghurts could have contained bifidobacteria but I had intentionally bought the old fashioned brands that do not boast any particular probiotic species. The ubiome test did pick up  87 l. delbruekii and  14 s. thermophilus  so I guess I have some idea of what was in the yoghurt.”

  • This is the highest level of Lactobacillales and second highest Bifidobacteriales seen in all of the tests. Unfortunately Enterobacteriales was still very low.
    • One model is that d-lactic acidosis is involved (heavily produced by Lactobacillales) and only a little by Enterobacteriales is the cause of ongoing symptoms. The Enterobacteriales are needed to get the amount lowered.
  • High levels of Erysipelotrichaceae
    • “The importance of Erysipelotrichaceae in inflammation-related disorders of the gastrointestinal tract is highlighted by the fact that they have been found to be enriched in colorectal cancer.” [2015]
      • Decrease (Toxoplasma gondii or Giardia muris infections) or increases (TNF Driven Crohn’s Disease) – see link for more details
      • Impacts obesity

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Excel: order

Unknown's avatar lassesen 12:49 am on November 12, 2016  

uBiome Results #3 The Class Level

The Phylum levels had 12 items reported. The Class level is the next layer down. Class level has 19 items reported for these people. The links are to Wikipedia articles with their [Phylum] after the name. Quotes are from the Wikipedia articles.

class

First starting with items that were seen by 75% or more of the results

The Rare Items

As I suggested in the prior post, these may be bad bacteria, so having none is good. Alternatively, some may be from having fermented foods regularly in the diet (although these bacteria will not persist, they may show up in the sample).

Having low levels may result in some symptoms.

  • Alphaproteobacteria  [Proteobacteria] – includes Rickettsidae.  25% have high values. may be a subset.
  • Anaerolineae [Chloroflexi] – likely just “noise” only in one patient, disappeared on the next test.
  • Epsilonproteobacteria [Proteobacteria] “Autotrophic Epsilonproteobacteria use the reverse Krebs cycle to fix carbon dioxide into biomass” likely just “noise”
  • Fibrobacteria [Fibrobacteres] likely just “noise”
  • Lentisphaeria [Lentisphaerae]  likely just “noise”
  • Mollicutes [Firmicutes]: “Mollicutes are parasites of various animals and plants, living on or in the host’s cells. Many cause diseases in humans, attaching to cells in the respiratory or urogenital tracts” – may be a tag along to other bacteria. 25% have low levels.
  • Synergistia [Synergistetes]: may be a tag along to other bacteria. 33% have low levels.

Bottom Line

I was actually surprised about the number of Classes that had distinct  shifts! Two classes appear to be “either/or”, that is people go high or people go low. I suspect we may find specific symptoms associated with the direction.

For the rare items, there is too much speculation to be comfortable. I would love to know the percentage of healthy individual that have these rare classes.

A comment from Result L who results were not typical (one of two people that are high when most people are low):

” I was eating about 1+/- 0.5 cup a day of pseudo-natto  at the time (ie natto made with legumes other than soy). Of course I was also eating yoghurt and other lacto fermented foods”

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Excel: class

Unknown's avatar lassesen 2:32 am on November 11, 2016  

uBiome Results #2 The Phylum Level

Overview

This is the second of six posts drilling down into uBiome results gracefully shared by my readers. Diagnosis and symptoms vary greatly, but all of them believe they are in the CFS/IBS spectrum. In preparing this series of posts, I was faced with several presentation challenges – brain fogged vs clear head, different education levels, different conditions etc.  My formal training include adult education and medical statistics. My solution is this:

  • Have the raw data available as both a PDF file and an Excel file (so readers may load it into Excel easily) – people can do their own thing
  • Give a simple high level summary of what I have concluded
  • Give a more detail explanation of how I came to my conclusion.

I will try to be conservative in conclusions — wanting to find something can result in selective picking of data.

Example:

  • By uBiome definition of microbiome diversity, these results do not show a lack of diversity (contrary to some studies conclusions),
  • I applied a simple test, what percentage of results fall between the 25%ile and the 75%ile. For controls, you would expect 50%. We had close to 50% of the results in this range, there was no statistical significant shift.

About the Readers Results

Results A

  • ME/CFS for 20 years, 90-100% functional for years 2-8, 60 – 80% functional for years 9-16, 10% – 70% functional for years 16-20 Currently about 50%-60% again. Main symptoms, fatigue, lack of energy, feeling crappy (flu-like), get sick easily and stay sick for months (I have 2 kids 8 – 10 now so they kept bring home infections) no brain fog now, but currently issues with a tired brain, IBS or dysbiosis, Urinary Issues
    • A1 – 9/18/2015
    • A2 3/17/2016

Results B

  • Sure, I got sick with ME after an infection I probably picked up on the airplane back from Asia. Probably lived in mold a few years prior to that that probably took my immune system down too, before the final straw with the infection. Major symptoms: fatigue, unable to do much physically, brainfog, get tired of concentrating too much and being social, my head “shuts down”, joint pain, muscle pain, headaches, swollen lymph nodes, feeling like a flu is coming on very frequently, everything is made worse by too much exertion I do not think I did much probiotics before the sample was done actually…
    • 4/12/2014

Results C:

  • Diagnosis: ME/CFS, POTS, MCAS, IBS-C, mold illness. No probiotics before test. I changed environments and had some health improvement between tests.
    • C1 10/1/2013
    • C2 9/13/2015
    • C3 6/23/2016

Results D:

  • IBS. No CFS
    • D2 1/16/2015
    • D1  3/26/2015

Results E:

  • My symptoms are ibs and exercise intolerance, joint pain, headaches (cfs). I’ve been taking a lot of the “goodbelly” brand of probiotic drinks. And the jarrow brand “ideal bowel support 299v” probiotic pills. These are two brands of the same probiotic. They significantly reduce my ibs symptoms. I came down with ibs 16 years ago, and the cfs started about 5 years after that.
    • 29/04/2016

Results F:

  • Background: 5’7″ 130 lbs, Female 65 yr old, no weight problems, CFS since 1995, omnivore
    • 9/25/2016

Results G:

  • Multi-year flu-like fatigue. Poor sleep onset. Sleep is non-restorative. Near constant brain fog, fatigue, and need for isolation. Proceeded by actual flu (trigger?). Intolerance to exercise despite good athletic conditioning. Unexplained skin rash covering upper arms. Lymph nodes near top of neck swell if antibiotics are discontinued. This is a relapse of episodes that have occurred for ~15 years. A combination of antibiotics and LDN seem to be currently controlling my symptoms. Life is tolerable with the addition of LDN. But I don’t feel like I’m actually healing… more just not getting worse or suffering as much. The antibiotics also cause stomach pain / intestinal upset (which I don’t have otherwise). Fairly normal blood work. No obvious thyroid issues.
    • 10/12/2015

Results H:

  • Spring 2010 began three years pf almost continuous illnesses on top of my flu like feeling.  Endless colds and flu, or at least the body acting like I had these.  9 months the first year, 10 months the 2nd, 10 1/2 the 3rd year.  Beneath these the constant flu like feeling throughout my body. Discomfort from wheat or gluten.
    • 4/16/2014

Results J:

  • This is a relapse of episodes that have occurred for ~15 years.No diagnosis Key symptoms: Severe 24/7 specific point pain in umbilical area Malaise and feeling unwell Some nausea Other key biomarkers Enlarged mesenteric lymph nodes on CT scan Elevated WCC (specifically neutrophils) Very high SIgA levels My own view is a chronic infection – see biomarkers above No probiotics when the change happened
    • J1 9/29/2015
    • J2 10/23/2015
    • J3 12/4/2015

Results K:

  • Lyme diagnosis, chronic fatigue, inability to exercise, and pain. My biggest complaints are neurological. My brain fog is so intense most days
    • K 3/29/2016

Results L:

  • on Canadian consensus criteria

    1) post-exertion fatigue and malaise I meet all criteria (A B and C)
    2) both unrefreshing sleep and a new pattern (trouble getting to sleep and staying asleep and some nights without sleep
    3) yes muscular aches and pains in legs and arms face neck and head, and headaches, forehead back of head and sides + of course the migraine
    4) A, B C (issues with noise and sound, re perhaps also anxiety I find it very hard to watch tv and often have to skip anxiety inducing bits or things that are too emotional.) D if vertigo and tinnitus count (but I had these before and associate them with migraines) . E  lots of brain fog type confusion.
    5)A: 2(POTS) 3 (Vertigo) 5 (IBS the alternate type but mostly D) 6 (palpitations), , 8 respiratory irregularities, I seem to overbreathe a lot and often find I am overinflated.
    B:I think 1 and 5, I have had low auxiliary basal body temperature clustering around 35C; and I do not handle stress at all.
    C:1 2 3 and 4
    6) yes 13 yrs

Results M:

  • I have diagnosis of ME/CFS, MCS and Eosinophilic Esophagitis. Symptoms: OI but not POTS, malabsorption (underweight), total food sensitivity (tube fed via PEG tube), severe brain hyperactivity, sensitive to light and sound, dystonia, persistent coat-hanger pain, persist sinus and mouth burning/pain, paralysed colon, housebound, severe muscle weakness most of the time.

The Phylum Results

The Phylum is a very high level overview with little likely to be revealed.

phylum2

The average for each of the phylums that had results across all reports was effectively 100% except for Actinobacteria at 66%. For the following phylums there were effectively none in any results – which may be good. One is associated with disease, the others have just recently been identified.

“Actinobacteria, are recognized as the producers of many bioactive metabolites that are useful to humans in medicine, such as antibacterials,[7] antifungals,[8] antivirals, antithrombotics,..” Wikipedia. In other words, our police force to keep bad bacteria in control is understaffed at 66%.

A,F,G,H have some synergistetes. Those that gave a summary have digested issues. In particular A had an significant increase between the two uBiome tests.

 

Downloads:

PDF: phylum

Excel: phylum