(Ken Lassesen has recovered three times from chronic fatigue syndrome (ME/CFS).  In his gut series on ME/CFS/FM he provides his personal prescription for better health through gut flora manipulation. Please note that Ken is a patient, not a doctor; these blogs are for informational purposes only. Please consult with your physician before making changes to your treatment regimen.)

Before we look at correcting the microbiome, we should understand better what we are striving to do and why.

gut flora

Our fertile (or not so fertile) flora may have impacts far beyond the gut itself

Microbiome is the fancy new name for the gut and other bacterial systems that keeps us alive.  All microbiomes are not the same — in fact, the microbiome you have is connected strongly with your DNA and is actually more unique than your DNA. A recent study of  identical twins found that they can be told apart by their microbiome and not by their DNA.

You have around 100 trillion bacteria according to a recent New York Times article which states:

Our resident microbes also appear to play a critical role in training and modulating our immune system, helping it to accurately distinguish between friend and foe and not go nuts on, well, nuts and all sorts of other potential allergens. Some researchers believe that the alarming increase in autoimmune diseases in the West may owe to a disruption in the ancient relationship between our bodies and their “old friends” — the microbial symbionts with whom we coevolved.

Microbiome Under Attack?

stricken figure

Modern times with our poor diets, low use of fermented foods and high antibiotic use have not been good for our gut flora

Modern times have not been good for our gut flora. Our modern high carbohydrate and fat diets have been shown to negatively effect the gut microbiome but for increasing numbers of us the negative impact to our gut flora began long before junior had his first french fries.  Research indicates mothers actually pass important parts of their microbiome to their children as they move through the birth canal. Some researchers believe the higher rates of C-sections in the modern era maybe inadvertently contributing to the higher rates of allergy, asthma and autoimmune problems present.

Frequent antibiotic use may have snuffed out some good gut flora in many of us. Nor do we eat the array of probiotic saturated fermented foods our ancestors did.  Given all that it’s no surprise that the diversity of our gut flora compares poorly with those living in more traditional societies with their healthier, more varied diets and reduced C-section and  antibiotic use rates.

Shifts Confirmed in a June, 2013 Study

Marc Frémont, Danny Coomans, Sebastien Massart, Kenny De Meirleir just published a study (full text free) which found

“A highly significant separation could be achieved between Norwegian controls and Norwegian patients: patients presented increased proportions of Lactonifactor and Alistipes, as well as a decrease in several Firmicutes populations.”


“129 Different bacterial genera could be identified from the 79 samples included in the study. A majority of these however were present only in a few samples (sometimes just one or two subjects, in a very small proportion).”

Micro in Name Only: Little Bugs With Big Impact

There is already abundant evidence that microflora can have system-wide effects and influence immune responses, brain  development and behavior. Williams, Hornig and Lipkin et. al.

Researchers are still figuring out how important gut flora is our health but studies suggest the state of our gut can impact many areas, some of which are listed below.

  • inflammatory gastrointestinal disease – reduced levels of a helpful bacteria appear to set the stage for Crohn’s disease
  • cognition – specific bacterial families are associated with poor cognition and inflammation
  • obesity – certain bacteria that metabolize food more completely may increase the risk of obesity/weight)
  • B12 levels (Lactobacillus Reuteri produces most of it)
  • autism – people with autism appear to have a unique gastrointestinal flora that has less variety than healthy individuals.

Autism provides an intriguing example of a dysfunctional gut  (increased intestinal permeability, aberrant immune profiles, etc.)  possibly contributing to severe cognitive and emotional dysfunction. Hornig and Lipkin’s Center for Infection and Immunity recently published a study suggesting reduced levels of carbohydrate digesting enzymes may lead to high carbohydrate levels  that foster the growth of unhealthy bacteria.  Indeed, RNA sequencing indicated an abnormal gut flora was present (decreased levels of Bacteroidetes, increased Firmicute/Bacteroidete ratio,  Firmicutes and Proteobacteria, and increased Betaproteobacteria.)

A CFIDS Association of America pilot study recently found greatly increased ratios of Firmicute/Bacteriodetes bacteria before and after exercise in ME/CFS. People with ME/CFS also may have deficits in the bacteria that produce B-vitamins in our guts.)

These researchers believe changes like these could effect immune functioning, brain development and behavior.

The Infection Connection

ill woman

Could an infection have altered the gut flora permanently for some people with ME/CFS?

It turns out that most infections do temporarily change the microbiome which usually reverts to normal after the infection has passed. In approximately 4-8% of  cases, though, this fails to happen and the microbiome remains in a new stable state.

That percentage is pretty close to the percentage of  people who come down with a CFS-like state after flu-like infections. Researchers have examined  immune, autonomic, endocrine functioning in people with ME/CFS at the start of infection and afterwards with marginal success. Thus far, immune up regulation and increased symptoms during the  early course of an infection and autonomic variables later on are the only unique factors found in people with infections who come down with ME/CFS.

No one yet,however, has examined the most immune-rich substrate of all – the gut. I propose that an infection induced change of gut microflora – which do not revert to normal – plays a key role in chronic fatigue syndrome.

A Historical Analogy

Think of your gut (an ecosystem or biome, if there ever was one) as a land; in fact, think of  your original gut (hopefully fully  populated with your mothers microbiome)  as Newfoundland in Canada prior to the entrance of the Vikings.  The Native Americans living there, the Beothuk, flourished until an invading species (an infection) arrived  called Lief Eriksen and the Vikings. The Vikings lived there for a few seasons but the native species eventually pushed them out,  just as your body does to an infection. The next time around, the Boethuks met a more difficult match in English settlers and the settlers eventually pushed the Beothuk out.

Has our original microbiome been altered by unwanted invaders?  I believe it has.

Your Microbiome is Unique to you — and So May Be Your ME/CFS/FM

If my hypothesis on the cause of ME/CFS/FM is correct (a stable dysfunction of your microbiome) then every patient will have a different variations of their unique microbiome! This means that your symptoms will be slightly different because your dysfunctional bacteria are slightly different. This actually goes one step further, the signaling chemicals from these bacteria interact uniquely with your DNA.

Getting a good idea of your gut composition, however, is difficult. Unfortunately currently available medical tests only characterize a small percentage of the species in our gut. Tests done at  academic centers (not available at commercial labs) using PCR and DNA fragments are more accurate. Furthermore, many species(~ 80%) cannot be kept alive outside of the body which makes study very difficult.

A good review is at Aging of the human metaorganism: the microbial counterpart from which the diagram below comes from.

Commercial labs test for less than 2% of the bacterial strains present in our gut.

Altering Gut Flora: More Art Than Science

That means there’s more art to changing the gut flora than science.

On the plus side, it appears very possible – by effectively declaring war against the offending bacteria – and then aggressively repopulating it with good ones, to alter the gut flora. The disruption is not easy — before the arrival of antibiotics- a reset of the gut flora often began by inducing a gut infection (often cholera) to clear the slate, so to speak. Asking a MD to infect you  with cholera to treat CFS today , of course, would be met with complete disbelief ; at one time, it was conventional medical practice and was reportedly successful. (Then again who would have thought we’d be talking about fecal transplants or using worms to alter gut flora….)

light bulb

Ken Lassesen has a plan…

In following posts, I will share my current understanding and experience in being an anarchist against this dysfunctional microbiome. To me, any change is better than resignation to the current state of health in CFS.

The key items are:

  • Killing off bad species (may have collateral damage on the good species) – antibiotics, herbs, spices
  • Feeding the good species (so they start to dominate) – prebiotics, often FOS, but there are other things
  • Disruption of the new stability (so the old ones have a fighting chance)
  • Importing good species (a.k.a. probiotics of the appropriate type, fermented foods, raw milk and fecal transplants)
  • Starving the bad species (so there are less of them) – no gluten and no sugar diets are likely doing this

I believe the following approaches have the right general approach but may lack the fine-tuning needed for ME/CFS and other disorders. Early reports suggest that ME/CFS patients, for instance, may have a major drop in all E.Coli species but in Crohn’s Disease over 95% of the invasive species are E.Coli. With one, you want to encourage (healthy) E.Coli; with the other, you want to kill off (unhealthy) E.Coli — one treatment plan does not suit all conditions.

These approaches below are correct, I believe, that we should attempt to enhance our gut flora — but they have not evolved enough to address specific gut dysfunctions.

If you are doing any of the above,  I suggest that you keep doing them  but consider adding a few modifications that I will be suggesting in my following posts that are specific to the microbiome shift that may be occurring in CFS (which is likely similar to that seen with IBS). I have yet to see any reports of the above consistently resulting in remission of CFS  but I have seen reports of symptoms reduction. I believe they are likely part of the solution but are insufficient in themselves.


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