Wednesday, March 12, 2014

More gut bacteria: uBiome and ME/CFS

I just received my alpha microbiome report from uBiome and the results are fascinating. I need to dive into the data more, but so far my results reflect the findings of researchers on Chronic Fatigue Syndrome, especially research from de Meirlier. Here are my phylum level results; note how low my Bacteroidetes are compared to the average sample and the lack of overall bacterial diversity compared to the average.
Gut Bacteria Phylum results compared to average
I still think ME/CFS may be triggered by the same forces that trigger autism. The recent research published in Nature is very interesting and relevant:

Ken Lassesen's blog at is the best one I have seen for information on what is often wrong in patients' microbiomes and ideas on how to shift the microbiome back to a healthy one.
Here are my order level results; note that I have 79 times less bifidobacteriales than the average participant in ubiome thus far.  And my cyanobacteria is 159.69 times lower than the average; according to uBiome "Cyanobacteria residing in our gut appear to help generate B and K vitamins that we depend upon for nutrition." Uh oh.....
Gut bacteria Order Results Part 1

Gut bacteria Order Results Part 2

I will add genus-level information soon. My Streptococcus levels were 2.63% vs .75% for controls and my bifidobacterium levels were 67x lower than the controls (<.01% vs. .13%.) I can see the species-level percentages for different sub-groups ("Paleo", "Healthy Omnivores", "Vegans", "Heavy Drinkers", etc.) but don't appear to be able to see my own sample's percentages yet. Of course, it's probably a reasonable guess that my bifidobacteria species such as b. breve and b. bifidum will all be less than <.01%.

 Unfortunately I don't seem to be able to see data for any of the species in the Enterobacteriaceae family. That includes e-coli and Klebsiella, both of which are of interest in ME/CFS. I don't know if that is due to a limitation of the current alpha reports or whether uBiome is unable to provide results for these species.

Friday, January 3, 2014

Quick links: Gut Bacteria, B vitamins, and epigenetics

A few links-- -- Do those of us with ME/CFS need extra B (and other) vitamins because our gut bacteria aren't producing enough? -- There is usually much more focus on mothers' nutrition vs fathers'. But it appears that our fathers' nutrition and health can have a big impact.

Monday, August 26, 2013

Gut Bacteria and Mast Cells: My current model for my illness

Current model of my specific illness: mold + bacterial infection in India=> dysfunctional gut microbiome=> mast cell activation, immune dysregulation, food intolerances, major inflammatory symptoms

As is often the case I have been meaning to write a comprehensive blog post for awhile but for now will write some notes.

I am always looking for a model that covers all of my symptoms/test results and can also explain the differing symptoms that other people have.  I think gut bacteria-gone-wild is the best model.

From my perspective, Ken Lassesen has the best theory (see:

A stable dysfunction of gut bacteria can explain every symptom that I have.  It can explain chronic yeast and viral infections as well.

As I've mentioned in previous posts, Align probiotics work much better for me than any other probiotic.  Guess what probiotic was found in a recent study to lower TNF-a and IL-6 in CFS patients?  If you guessed Align (B. infantis 35624) you win!

To get even more technical, check out for a discussion of how gut bacteria can affect mast cells which, as I've discussed before, release many of the inflammatory mediators that have been found to be high in CFS.

More to come once I finish a project I foolishly said yes to before going into remission like Ken.

Friday, June 28, 2013

Histamine Intolerance--contributor to symptom spectrum?

I have a ton of drafts for my blog that I keep planning to complete.  I am going to publish some incomplete posts that hopefully still have some relevant info since I am unlikely to do the editing I would like to before posting.

Since I got sick I have had some allergic-like reactions that don't seem to be true allergic IgE reactions.  They usually consist of burning eyes, a swollen tingly face, some dizziness, and a stuffy nose.  Sometimes my lips and tongue are swollen but I never feel like I can't breathe at all (at least, not more than I do normally.)  It took me a long time to figure out the pattern as it seemed random.

I appear to be having problems with high histamine foods.  I finally figured it out after I had another reaction to smoked salmon, one of my favorite foods even though I can't enjoy it on a bagel with cream cheese any more.  I react worse to smoked fish than I do to mold.  I also react some to dark chocolate and tomatoes.  Histamine levels are the one thing I see that tie the foods together and it fits well with the mast cell reactivity theory but I am always open to other explanations.  I don't feel well when I drink wine but there are multiple potential causes for that.

Soooo... I am trying a low histamine diet.  It's tough for me to combine with  paleo (no more avocado or smoked fish!) but it's nice to have a clear nose and a less swelled face.  Eventually I will try out some of the potentially high histamine foods so that I am not restricting foods needlessly.  Lots o' links below and there may be a more-organized post in the future.

Da man Chris Kresser talks about histamine intolerance:

research article on histamine intolerance:

That paleo guy talks about histamine being a problem for some paleo peeps:

Story on an individual with histamine intolerance:

Histamine food list:
Note: Avocados and spinach are somewhat high and smoked meats are very high.  Fish and meats have to be very fresh.

I like this summary of a low-histamine diet from an individual with CFS and MCAD:

Overview of a restricted diet for Mastocytosis /

Good overview articleL

Testing sensitivities to other chemicals:

Thursday, June 20, 2013

A Mold History

I was just giving my history to a new doctor who has really impressed me thus far.  He even sent me the WHO document on indoor air quality.  Going over my history and reading the WHO document inspired me to write a mold history.

My history of known Mold Exposure/ significant water leaks along with health issues that arose at the same time (coincidental or not):
Age 2-4 Every time it rained the basement (where I spent much of my time playing) flooded.  Family moved due to flooding issue. Health: No known issues
Age 4-6 More flooding in the next house
Age 8-12 Several major water leaks in townhouse due to faulty roof. Water poured down walls.  Family had to replace bedroom furniture due to room flooding.   Health: Started having severe dust allergies diagnosed by doctor.
Age 23-24 When we first moved in the carpets were wet and covered in plastic.  Slept on floor for the first week.  The upstairs bathtub constantly leaked.  At one point part of the 2nd floor roof fell into the 1st floor due to water damage. Health: Gained ~20 pounds in first few months living there despite not changing eating or exercise habits. Started feeling constantly dehydrated despite drinking a lot. I had frequent colds and flus, although that started in college.
Age 28-31 Lived in Florida. House had some mold issues that increased after 3 hurricanes.  Actual mushroom grew out of the closet ceiling where there was a constant leak.  Visited grandmother several times a week.  She didn't use A/C.  Her house had visible mildew on the walls, especially in the living room and kitchen.  Health: When I visited my grandmother's house I would suddenly feel incredibly tired and frequently napped for 4-5 hours despite having slept a full night the night before.  I started to feel tired all the time and felt like I never could fully concentrate.  Had to drink coffee every day despite sleeping well.
Age 31-33 Started a job that involved working from home in San Francisco. House was very well-insulated and often had condensation on the windows.  Unbeknownst to me there was mold in the walls.  Health: I couldn't sit up to work any more and was working from bed.  My concentration got worse.  When I needed to get something done I would drink a Red Bull and could temporarily feel like my old self.  Leaving the house started to be very difficult.  My digestive system got slower and slower. I developed GERD.  My legs started feeling like it was being pricked by electric needles. Eventually caffeine stopped having an effect, my head was permanently cloudy, and I had CFS.

Wednesday, May 29, 2013

Quick link: Gut Bacteria and brain function

Interesting study-
My gut symptoms started before my neurological ones; I find it frustrating that most doctors still appear to think that "IBS" is caused by anxiety when the causality is probably the opposite.

Friday, March 15, 2013

Potential drug for autism

Since I think CFS could also be characterized as post-infancy-onset autism I try to keep up on autism research. The research on the purinergic system discussed at is fascinating.  It is still early days, but Suriman sounds really promising, albeit not without risk. And I like the idea that a drug for African sleeping sickness (a disease that kills people if untreated) could help people with Chronic Fatigue Syndrome.
There is a detailed discussion of purinergic signaling and how it could connect to Chronic Fatigue Syndrome on a 2010 Bulletin for IACFS/ME, so this isn't a novel hypothesis.