Dr. Logan on H2S, Fiber and the Gut

July 2, 2009

Posted by Cort Johnson

Dr. Logan is a board certified naturopathic physician who graduated magna cum laude from the State University of New York.  An invited faculty member at the Harvard School of  Continuing Medical Education and published researcher he is the author of “The Brain Diet” and the co-author with Dr. Alison Bested of a recently updated book on chronic fatigue syndrome (ME/CFS) – “Hope and Help for Chronic Fatigue Syndrome.”

He was willing to follow up a substantial comment he made to the “H2S Creator Speaks” blog with this full interview.


A good number of chronic fatigue syndrome patients do experience gut pain but gut pain has never been considered the main or even a main symptom of the disease. It’s easy to see how something like there irritable bowel syndrome could emanate from the gut but given the sometimes enormous debility found in this disease shouldn’t we be in a lot more gut pain than we are if this disease is indeed centered in the gut? The gut is after all a very sensitive area is it not – it doesn’t take much to make gut problems very obvious to the person suffering from them.

Indeed gut pain is not chief among the constellation of CFS symptoms. Yet the vast majority of CFS patients do experience some degree of gut related symptoms and indeed there are many other gastrointestinal (GI) signs and symptoms in CFS that are not pain-specific. For example, alternating constipation, diarrhea, bloating and so-called functional dyspepsia (upper GI discomfort soon after meals) may not involve significant pain per se, however they indicate that not all is right in the GI tract.

It is also true that there may be issues with certain gut bacteria that, while producing no overt gut symptoms, they are still capable of provoking a body-wide immune response and intestinal permeability. From animal studies, we know that even a tiny amount of undesirable bacteria in the gut, at levels not even high enough to cause an overt immune response, can activate brain areas involved in emotions and ultimately influence behavior itself. While we are a long way from confirming that CFS is centered in the gut, early suggestions indicate that gut microbes may be the tail wagging the dog.

On another very basic note – if we are all producing enough hydrogen sulfide gas this disease shouldn’t we all be belching and otherwise releasing enormous amounts of rotten egg smelling gas?

No, not necessarily. It would only take miniscule amounts of H2S gaining access through the gut wall to cause fatigue and a host of other brain and body-wide symptoms. Small amounts of H2S can cause cognitive difficulties, and of particular interest to CFS symptoms, problems with tuning out unwanted environmental stimuli…the sort of “tired but wired” symptoms of CFS. Normally we can clear H2S quite efficiently, breaking it down with enzymatic activity and releasing it through the lungs. Yet there are many unknowns about H2S, including the amount of gut H2S the normal person can tolerate. In addition to the emerging work from Dr K DeMeirleir indicating that there are elevated H2S-producing gut flora in CFS, it may also be the case that in CFS there is a deficit in H2S disposal.

A common remedy for bacterial overgrowth in the gastrointestinal system involves antibiotics. Yet antibiotics, paradoxically, are sometimes blamed for setting the stage for bacterial overgrowth in the first place. Many people are not surprisingly skeptical about taking antibiotics because of this. How do you go about ensuring that you’re not just making the problem worse?

Indeed, there have been studies showing that antibiotics have reduced small intestinal bacterial overgrowth (SIBO) and improves a variety of symptoms (including brain-related symptoms) in CFS and fibromyalgia. Yet, these are very small studies of small duration. What happens when the antibiotics are stopped and the patients are followed in the long term? We do not know. Given that antibiotics and overuse of acid-blocking medications set the stage for SIBO, I would be inclined to worry about using antibiotics as a means of clearing SIBO. I would be more inclined to use probiotics and enteric-coated peppermint oil.

There are quite a few different kinds of probiotics on the market that feature different kinds of bacteria. Are there certain kinds of bacteria that may be more helpful for the kinds of gastrointestinal issues that chronic fatigue syndrome (ME/CFS) patients face?

Yes, the benefits appear to be strain-specific. If it is for symptoms that resemble that of irritable bowel syndrome (IBS) then I would suggest 2 strains of bacteria that have been shown to be helpful for gut-related symptoms – Align (Bifidobacteria infantis 35624) and LactoFlamX (Lactobacillus plantarum 299V). In our University of Toronto study, we used a probiotic made by the Japanese company Yakult. The strain, Lactobacillus casei Shirota had been found previously to improve mental outlook in healthy volunteers who had the lowest baseline mood scores. It also lowers propionate production in the gut.

Recently propionate has been the focus of research in autism; once it gains entry to the brain, it can alter behavior. It is too early to tell, however I feel that bifidobacteria strains such as Align will become the probiotic of choice for CFS. Align has been shown to reduce inflammation systemically, beyond the gut. It also does not contribute to the lactate load in the gut. What was not really emphasized in the reporting of Dr K DeMeirleir’s research is that his team also found elevated lactate producing bacteria and certain Lactobacilli are major manufacturers of D and L lactate.

If I understand you correctly its possible that strains of Lactobaccilus bacteria that are frequently found in probiotic preparations could exacerbate lactic acid production. Apparently Lactobaccillus acidophilus turns sugars into lactic acid.

Yes, but not all Lactobacillus strains produce the undesirable D-Lactate (for example, the well-researched Lactobacillus GG does not produce D-Lactate, but most strains of Lactobacillus have not been investigated for D-Lactate production. Its time to map that out properly).

It’s generally true that L.acidophilus does turn sugars into lactic acid, but not all Lactobacillus strains produce the D-Lactate; the L-Lactate can be cleared with a fair amount of ease by most.

Do you recommend staying away from the traditional formulations (L acidophilus)?

Most probiotics marketed under the umbrella term “acidophilus” have not been researched for health outcomes (let alone stability!) and we have no idea of their D-Lactate potential. It is known from studies in short bowel syndrome that unspecified strains of L. acidophilus can be major promoters of D-Lactate.

Kefir has a different bacterial makeup than yogurt. I did read that kefir grains make it deeper into the gut. What about kefir?

Great question! There have been two studies that have looked at D-Lactate production in fermented milk, commercial yogurts and kefir. Interestingly the kefir did not form D-Lactate, yogurt had high concentrations of D-Lactate (over 40%).

When you get to the store shelf there are probiotics that don’t need refrigeration, that do need refrigeration, that have X million or even billion bacteria ‘at the time of bottling’, that are in liquid or capsule form, etc. Dr. De Meirleir some years ago stated he was simply looking for a probiotics that was strong enough to fit ME/CFS patients needs. I noticed that Prohealth recently advertised a product that has over 50 billion bifidobacteria organisms in one capsule (at over a dollar a capsule). Do you have any advice to offer on specific types of probiotics for chronic fatigue syndrome (ME/CFS) patients?

Until the research shows otherwise I would choose Align for the reasons cited above. There are very good clinical studies to support the product in IBS.

If you do take probiotics are there any supplements that can help boost probiotics effects?

In recent years so-called prebiotics have been touted for boosting levels of Lactobacillus and Bifidobacteria in the gut. It is quite clear that prebiotics (inulin, chicory root, fructo-olligosaccharides) can increase both Lactobacillus and Bifidobacteria, however it remains unknown if they are also promoting undesirable bacteria as well. There have been hints that they can.

There are now two causes of concern for CFS patients and prebiotics – i. prebiotics have been shown to promote intestinal permeability, irritate the gut lining (this is a massive problem, especially when considering the new studies from Dr Michael Maes who documnented intestinal permeability in CFS) ii. prebiotics can increase the amount of lactate produced in the gut (now that we know there is already excess lactate production and/or inadequate lactate clearance, this is an obvious caveat).

On a personal level your conjecture that fiber induced fermentation in the gut could be associated with increased anxiety and aggression was intriguing since I’ve always felt that ’edginess’ is a key factor in my version of ME/CFS. But how do fiber induced problems in the gut translate into central nervous system problems? A study by Dr. Shungu has suggested increased lactate production in the brain may be occurring in ME/CFS patients; could this have anything to do with lactate production in the gut?

When too much fermentable fiber shows up in the large intestine there is a massive uptick in the production of D-lactate. Since, in CFS, we now know there is already over-production of D-lactate the blanket statements to eat more fiber may not be well suited to CFS. For example, animal studies show that excessive D-lactate production, due to excess fermentable carbohydrates showing up in the distant portion s of the gut, can increase aggressive an anxious behavior. It completely throws them off.

The same phenomenon has been written up numerous times in cases of short bowel syndrome. These are individuals who have had a portion of the small intestine removed, they are more prone to the over-fermentation of fiber-rich carbohydrates in the large intestine and an excess amount of D-lactate is produced. They can experience brain fog, lowered mood state, hypothamic dysfunction and anxiety when transient elevations in D-lactate occur.

Since we know that CFS patients have both bacterial overgrowth and excess D-lactate production (and/or lack of D-lactate clearance) a similar situation may be occurring. Ultimately, excess prebiotics and even excess Lactobacillus strains may worsen the situation in short bowel syndrome, and perhaps CFS as well.

I was very interested in Dr Shungu’s work as well. It certainly suggests that if excess lactate is making it to the brain (and we already know that systemic lactate can cause anxiety in adults with no history of anxiety) it can have multiple implications. Obviously, we have just begun to scratch the surface of this research, however in moving forward we should be very selective of the stains we use for CFS clinical trials.

Your statement that ‘fiber restricted’ diets can be helpful in this disease is a little jarring to hear given all the emphasis these days on high-fiber diets. You also noted that a fiber restricted diet cut the production of hydrogen and methane gas by more than half in one study. What is a restricted fiber diet look like? Are certain types of fiber worse than others?

Yes, while most adults and children in developed nations may need more fiber, those of us with CFS may actually be adding fuel to the fire. An elemental (liquid food) diet has been shown to help eradicate small intestinal bacterial overgrowth and gut excess H2S production. At this point we need more concrete studies although the soluble fiber in oats, barley, rye and root vegetables will be more likely to fuel fermentation and increase lactate production.

You noted that excessive fermentation in the large intestine can lead to the overproduction of lactic acid yet fermented lactic acid producing vegetable products such as sauerkraut, pickles and miso (as well as yogurt) are also sometimes recommended for gut issues. Do you recommend against using those products?

No, generally these would be good choices if not in excess. There is a difference between foods that have been fermented, and foods that are awaiting fermentation by our own bacteria. Still, excessive dairy sugars arriving in the lower gut may be an issue and dairy has been associated with problems in short bowel syndrome with excess D-lactate production.

If someone goes on a fiber-restricted diet how soon should they know if it is working for them?

Within a few weeks

What tests can patients take to assess the status of their small intestine with regards to bacterial overgrowth, hydrogen sulfide gas production, leaky gut and fiber problems?

In addition to Dr K DeM’s exciting new H2S urine test, there is also a test for small intestinal bacterial overgrowth…it is called the lactulose-hydrogen breath test. Similar tests are available for assessment of intestinal permeability. In North America, Genova Diagnostics does the small intestinal bacterial overgrowth and intestinal permeability tests.

There are blood tests for D-lactate; however, by the time a CFS patient sets up the testing the lactate may return to normal. That test is unique in that it is all about timing. Hopefully we will see some clinical investigations in CFS with patients consuming prebiotics and/or decent portions of fermentable carbohydrates and then evaluating both blood and urine lactate in the hours that follow.

A study by Dr. Burnett several years ago suggested that chronic fatigue syndrome patients often suffer from ‘reduced gastric emptying’ it seems to refer to food products remaining in the gastrointestinal system for longer than normal. Would this contribute to fermentation and bacterial overgrowth problems ?

It would certainly contribute to the upper gut symptoms after a meal. It also hints that there are electrical problems on GI tract in general. If there are any problems along the line, it can lead to stasis. We need more work in this area. What may be happening is similar to the folks with short bowel syndrome (although CFS patients may have a structurally intact small intestine, the SIBO may make it a functionally poor portion of the organ) where food material may be passing through the small intestine and then literally get “dumped” into the large intestine. When this happens with fructose, for those who do not absorb fructose well and it speeds through the upper gut, there is massive fermentation and mood related symptoms!

One of the beneficial aspects of enteric-coated peppermint oil is that it helps regulate peristalsis. This is almost certainly why most of the dozen plus trials of ECPO (alone or combined with caraway seed oil) in IBS and functional dyspepsia have shown good results.

Can one to some extent assess one’s bowel health simply by noting the consistency and quality of one’s bowel movements? That is could you say that someone who has one regular well formed bowel movement a day which was not accompanied by gas probably did not have problems with fermentation/hydrogen sulfide gas production?

A regular, well-formed bowel movement will not exclude a potential problem with gut flora alterations. I would be much more inclined to work with the tests available. While these breath test and intestinal permeability tests are imperfect (and the new H2S test requires outside validation), they would tell us much more than bowel movements when it comes to the internal consequences of undesirable bacteria.

I’ve always noticed that abstaining from food is helpful for me for short periods. On the converse many ME/CFS patients experience a considerable letdown 10 minutes or so after they eat. It seems that food does make a difference but this is occurring long before, one would think, food reaches the gut. Do you have any idea what’s going on here?

A period of fasting may be lessening the load of lactate, propionate and H2S…but is not going to be the Rx here. I am not sure about the quick exacerbation of symptoms. I have heard from a number of patients that symptoms are worsened within an hour, and this may be indicative of the small intestinal bacteria having a feast in the upper gut. The ensuing increased intestinal permeability allows unwanted material to pass through the gut wall and fire up the flames of low-grade inflammation.

For more on this topic I would urge visitors to your blog to further investigate the work of Dr Michael Maes and colleagues who have been doing great work in CFS, gut flora and intestinal permeability.

Are there any books you recommend on irritable bowel syndrome or the gastrointestinal system for ME/CFS patients?

I have yet to find one that is specifically suited to the needs and complexities of CFS. The problem is that CFS patients don’t have IBS per se, and the approaches don’t always apply.

The findings in the CFS-GI connection (Drs K DeM, Maes in Europe, Dr Bested in Canada) are so new that a well-rounded gut-specific resource is still some distance away – hopefully soon, but we really need clinical trials to validate specific avenues of approach. As exciting as these gut findings have been, it is important to underscore that we are still on the bridge between hypotheses and true clinical guidance in CFS.

Thanks Cort for your dedication and hard work to the amazing, resilient community of medical underdogs, the CFS patients.

Dr. Logan’s website contains articles, his books, recommended supplements and ‘power foods’,  links and more.

H2S Theory Creator Speaks

The Big Breakthrough (!)(?)


{ 35 comments… read them below or add one }

Michelle July 2, 2009 at 2:11 pm

Cort, this was FASCINATING! I’ve had “IBS” since I was 12, but once I got ME/CFS (or it got significantly worse), I started having so many problems with fiber and probiotics. The gastroenterologists and NDs all just kept telling me to eat more fiber! Take more probiotics! No matter how much I said it makes feel worse. Dr. Logan’s explanation made so much sense.

Now I gotta find that Align probiotic. And hope it’s not super expensive.


chris July 3, 2009 at 8:36 am

From what this fellow and others say, it seems prudent to have a stool microbial study done at a serious lab, like Redlabs, Belgium. Perhaps other labs run this complete test? Once the bacteria loads are identified, treatment takes place – and it seems that at the moment this is up for grabs. The question is what to do exactly? Dr. deMeirleir gives specific targeted short term antibiotics that limit the damage to the gut, followed by probiotics and other herbs. It will be interesting to see what his therapy yields in terms of measurable improvement. Perhaps others will have different ideas about balancing specific abnormalities detected in gut microbials? To me this is a solid angle of approach in trying to chip away at this illness.



Beady July 3, 2009 at 12:02 pm

Once again, very interesting, Cort 

I checked out Dr. Logan’s site, and I see that the power food list is differ quite a lot from the diet that Dr. De Meirleir and his nutritionist recommends. While Dr. L mention nuts, fruits/berries, I know that Dr. De Meirleir and his nutritionist recommend a diet low on all kinds of sugars (including fructose), and no nuts. Even all kinds of spices are on the list of non-recommended foods. Green tea is also not recommended on the diet from Dr. DM’s nutritionist, as it contains caffeine.

I am no physician, but to my understanding, this is because they want the patient to avoid everything that could over-stimulate the body (fructose, caffeine), anything that could cause or stimulate to an allergic reaction (nuts). And also, to avoid all foods that could cause increased gas production or in any way be hard to digest or give the gut more work than necessary to break down.

It would be interesting to read Dr. Logan’s comments on this diet?


Cort July 3, 2009 at 12:27 pm

Thanks Beady,

Thanks for the info. Dr. DeMeirleir recommends low sugar, low spice, no caffeine (tears up my stomach!), low fruits and nuts – anything else? Dairy, grains, meats? What about raw vs cooked foods? Anything from him on specific probiotics?

I’m thinking Dr. Logan’s powerfoods may be good foods in general – perhaps they’d don’t all apply to ME/CFS patients.


Tony July 3, 2009 at 8:28 pm

Blake Graham reported in 2007 that Dr De Meirleir recommends a probiotic called VSL#3 mostly and sometimes Mutaflor if required. I think he still does. There are quite a few studies on VSL#3 in Pubmed.
Blake’s 2007 report:
“Kenny did a small study using the antibiotic ciprofloxacin and high quality probiotics. Patients reported a 58% improvement and elastase dropped 74%.”

I’ve done the hydrogen breath tests for fructose (positive) and lactose (negative) recently which confirmed my decision to go gluten free 3 years ago. I noticed a difference very quickly back then, within 2 days I’d gained 5% functionality, and have kept it. A 58% improvement seems like a miracle!

Thanks to Cort and Dr Logan for an excellent, informative interview …:)


drew July 4, 2009 at 1:47 am

Cort, I’d like to echo the other comments … this is absolutely fascinating stuff, and it really speaks to the problem I have been dealing with for nearly 25 years! As I’ve written before, my ME/CFS problems are definitely gut-related, and I cannot eat high-fiber foods without major problems, especially if I then go to sleep. And regardless of what I eat, I feel lethargic, achey, and mentally-fogged afterwards. I have felt like a freak of nature for so long, but it sounds like there is hope now for an explanation and maybe even an effective treatment!

I’m especially fascinated by the discussion on lactase … I’ve noticed that yogurt and acidophilus supplements aggravate my ME/CFS, and maybe this is why.

Thank you Cort and thank you Dr. Logan!



drew July 4, 2009 at 1:50 am

P.S. I’d be very curious to hear Dr. Logan’s thoughts on candida/yeast … i.e., is candida responsible for the gut dysfunction, or is it just “along for the ride”?



Beady July 4, 2009 at 4:40 am

Dr. De Meirleir does food stats tests via http://www.usbiotek.com/ He also does lactose and fructose breathing tests on the patients well enough to come to the clinic.

He leaves it up to the nutritionist to talk about foods, so I would prefer referring her instead of Dr. De Meirleir on this.

The diet suggested to the patient depends on the results of these tests. But in general, I think she is careful with grains and milk as well, at least in the beginning. If you have reaction on grains/gluten, they also recommend avoiding milk, and the other way around, since those two can relate to each other.

Meat – no total avoiding, I think. Low on read meat (1-2 times a week ok), and all kind of birds are ok (as long as the tests say that you tolerate them). Varied is more important than what you eat, I think. In general a varied menu is recommended (not eating the same dinner several times a week). It is important that the gut does not get a continuous load from the same kind of food.

Vegetables – In general, the easiest way to think is that all vegetables that could cause gas are not allowed.
Raw vs cooked – I am not sure. But would guess cooked since the diet focus on getting the digestion job as easy as possible.

For some patients, it is necessary to stay on the strictest diet for only 4-6 weeks before start adding back some products, others longer.

Probiotics – depends on the findings on the tests. Mutaflor and VSL3 are only recommended for the patients with Candida/yeasts, I think. For others, one or two probiotic pearls (from Prohealth) a day might be enough. Lately, I have heard of quite a few of his patients using something called Enterol, containing Saccharomyces boulardii.


Cort July 4, 2009 at 5:54 am

In 2009 a small Swedish study (of 15 patients with severe ME/CFS) by Sullivan on the effect of probiotics found that Lactobacillus paracasei ssp. paracasei F19, Lactobacillus acidophilus NCFB 1748 and Bifidobacterium lactis Bb12 found that 6 or 15 improved. Improvements were seen in neurocognitive function but not in physical activity or fatigue. Interestingly no major changes occurred in the microflora of the patients – suggesting perhaps that simply feeding these patients probiotics was not enough to do that. I only have the abstract – don’t know how much they were getting.



Tony July 5, 2009 at 2:14 am

If you test positive for fructose like me, the diet is a low fructose/fructan diet. This excludes wheat, green and yellow beans, apples, pears and too much of other foods like onions, leeks, dried fruit, fruit juice. Foods with a high fructose to glucose ratio are avoided.
This is a good article but doesn’t mention the beans which my dietitian told me about.


In Blake’s report Dr De Meirleir reckons on 45% of ME/CFS patients having fructose malabsorption and 20% lactose intolerance.

Regarding the VSL#3 and Mutaflor, I think primarily stool testing for the various bacteria gives an indication. The testing I had done (here in Australia) showed no detectable yeast but high strep, low lacto and bifido, just as De M has recently described.


Susan July 5, 2009 at 3:19 pm

While we can change our diets, etc to alleviate symptoms and I’m all for alleviating symptoms, research should continue on the connection between H2S and hibernation. There is some cause for these symptoms, and human hibernation might hold the answer. As we all know, animals go into hibernation but they also come out of it. If CFS is a form of deviant human hibernation, there might be a physiological mechanism to reverse it. Molecular biologist Mark Roth and his colleagues at the Fred Hotchison Cancer Research Center in Seattle are doing such research (Discover Magazine, May 2007) although with no thought of CFS. Interestingly, they have found that oxidative phosphorylation may be at the center of the hibernation mystery. Dr. Cheney and others implicate the same for CFS, I believe. At any rate, the information provided by Dr. Logan was valuable, thanks for more ideas about symptom relief.


Beady July 6, 2009 at 2:18 am

Tony: interesting to see that you are one of the patients on the “Australia project” of Dr. De Meirleir. May I ask if you have got any internet message boards or forums where you (the group of patients from Australia) exchange your experiences?

Naturally, most of Dr. De Meirleirs patients are European, and Europeans are speaking very different languages. So it would be nice to know of any boards or communities with discussions/information in English ;-)


cort July 6, 2009 at 10:47 am

The Australia project – sounds intriguing. If you don’t have a message board/forum I can set you up with one at forums.aboutmecfs.org. We can also set up a special group on the site. Check it out.

This is a powerful forum package that is only going to get better as it undergoes a major update in a month or so. If you have a group that would like a spot on the internet to interact, post attachments/pictures etc. let me know and I can hook you up.


Alan Logan July 6, 2009 at 4:42 am

Hi Cort

I just wanted to follow up on some of the questions and comments in the thread. (Bold Headings added by Cort)

Fructose and Powerfoods – Yes, the powerfoods section listed on my website is directed at brain health for the general population and is definitely not a CFS-oriented list. I would concur that too much fructose can cause problems. Dr Max Ledochowski has authored 4 or 5 studies on what happens when fructose escapes absorption from the small intestine and gets dumped into the colon…depressive symptoms, brain fog and much lower blood tryptophan levels. Correcting this via a low-fructose diet has been shown to improve mood etc. Interestingly, only about 1/2 of those with fructose malabsorption present with the overt gut symptoms.

Diet and Fruits - My only concern with removal of all fruits is that we also take away much needed dietary antioxidants from the deeply colored berries. Blueberry and bilberry actually have anti-microbial properties that may be to the advanatge of CFS patients and cherries have significant anti-inflammatory activity…CFS patients are under increased oxidative stress, have lower levels of antioxidants due to the high demand, and in most studies, dietary antioxidants win vs. those from supplements. Consideration of some very small servings of berries is still warranted in my opinion.

The other concern with nuts, yes, absolutely no doubt they can be a source of sensitivity.

Candida and yeast can’t be ruled out of this emerging equation of gut flora. Over the years the Candida story has been, in my opinion, over-played. Still, there was a study in the journal Family Practice in 2001 which showed that in adults with “unexplained medical conditions” (symptoms typically over-lapped with CFS) Nystatin was helpful. There were significant improvements in anxiety, cognition, depressive symptoms and insomnia. Recently Dr Evengard’s team in Sweden found that Candida levels are much higher in stool during the early stages of CFS and are lower when patients are “in remission”. Since we know that stress and antibiotics can increase Candida in the gut, it possible that once established, it becomes a secondary contributing factor.

Probiotics – The dose used in the Sullivan probiotic study was 10 to the 8th power CFU twice daily…this was not a particularly high dose. The VSL#3 mentioned has a massive 450 billion CFU per sachet…and it is the kitchen sink of a variety of different strains. It may help some, however I know of cases where anxiety increased after taking the product, it may be a D-lactate connection.

Gut Ph and D-Lactate – As Cort knows, we had this interview before the full text of the Dr K D paper on D-Lactate bacteria and CFS was released. Within the paper they note that alkaline therapy might be a future Rx in CFS. It would seem to make sense…we have high levels of acid-producing bacteria so it would appear rational to increase the pH and make it more alkaline.

However, the gut is a complex environment and a study by Jiang in Digestive Diseases and Sciences (1997) showed that raising the gut pH in the alkaline direction increases D-lactate production. In the same study they also showed that if you really want to lower D-Lactate production, add Bifidobacteria to the mix. Bottom line, we have much to learn about gut pH.

It has been shown since the 1920s that oral alkaline solutions can encourage small intestinal bacterial overgrowth and subsequent intestinal permeability (Arnold. Am J Hygiene 1928). Since CFS patients have both SIBO and intestinal permability, it is highly doubtful that alkaline solutions will be the answer.

No financial ties – I should have said that I have no financial ties to Align or any other probiotic company.

Thanks for all the comments and feeback.


drew July 6, 2009 at 8:46 am

“human hibernation might hold the answer”

Every time I eat a meal, I feel like crawling into bed and taking a long nap…



Frankie July 6, 2009 at 3:23 pm

Really value your site. Have made it my main site after co-cure. I was v sick for 12 years – took isoprinosine/immunovir for 3 years 6 pd- 100% recovery after 18 months ,6 pd for another year then recduced to 2pd for 18months . then 4 months ago have had a massive relapse. back on 6/8 immunovir – so far no change, sick extrmemly ill. Also taking whey, probiotics. Watching the H2S and methyl… with interest but completely bamboozled.
thanks for your great informative blog
Frankie from Hamilton ,New Zealand


Tony July 7, 2009 at 1:16 am

Beady: Great idea! Why didn’t I think of it?…:) I don’t know of any forum being set up by us Aussies as yet but I’d like to see it happen.
Thanks for the kind offer Cort, I’ll certainly keep it well in mind. It could be a great place for discussion etc.
If I can get others to ‘get on board’ I’ll let you know. I think many of the patients in this group are pretty low on the energy index, so fingers crossed!


Beady July 7, 2009 at 2:52 am

Thank you to Dr. Logan for interesting thoughts around the diet.

The antioxidants are my main concern on this diet. I have cleared with the nutritionist that it is ok for me to eat a small layer of raspberry/blueberry or half a pear or a slice of Galia melon with my toast twice a day. I am drinking rooibush tea and my local physician does insist on that I should eat some dark chocolate a day (both for indulgence and for the antioxitants). I have decided to give the diet some time, but I have always been a fruit eating person, and I am still not quite relaxed that is enough to get a sufficient amount of antioxidants during the day… I have experienced some more inflammation pain during the months on the diet. But that could also be a die-off reaction (linked to both diet and the medicines), I suppose.


Beady July 7, 2009 at 2:57 am

Thank you for the link to your forums, Cort. I was not aware of this, and I will definitively have a look :-)

Regarding forums for Dr. De Meirleir patients:
I suppose that this would be interesting for more than just the Australian patients. Dr. De Meirleir has similar projects going on in several European countries as well, I think. And since the most of us European do not speak the same language, a forum in English would be great for many of us as well.

I know of aScandinavian forum that has put up an international section (that is yet to be used): http://www.me-behandling.com/forum/viewforum.php?f=19&sid=f568c29f9186adcf97dbb889e8c65b85

But I think that it would be easier/better to start a new forum in a section that is already in English?


Tony July 9, 2009 at 12:27 am

Agree re the English language forum. Mono linguists like me find it much easier!

I’ve not yet consulted with KDM but will see him with my doc here in a couple of weeks. Beady, I’ll join you in a section on Cort’s forum and we can at least create a presence. Build it and they will come…hopefully!


cort July 10, 2009 at 12:13 pm

There are two ways to go: you can create what’s called a ‘social group’ in which you can have discussions, post pictures, test results, attach documents, etc. or create a forum in which you can have discussions. I think the social group is more feasible however if you can get a good number of people together a forum would be more visible.

I’m putting together a sample group on the site right now. You can find it by clicking on the community tab on the menu bar running across the top of the page.

I’ve also started a new service in which you can video chat live with up to six people at a time for free (!) Face to face communication. All you need is a videocam on your notebook.

Forums are are forums.aboutmecfs.org


Beady July 10, 2009 at 3:33 am

Tony: I am now registered in the forum. But I am a bit sensitive to take inn/orient in new sites, so it may take some while before I am able to be an active reader/writer/user in there.


cort July 10, 2009 at 12:20 pm

Excellent: There are two ways to go: you can create what’s called a ‘social group’ in which you can have discussions, post pictures, test results, attach documents, etc. or create a forum in which you can have discussions. I think the social group is more feasible however if you can get a good number of people together a forum would be more visible.

I’m putting together a sample group on the site right now. You can find it by clicking on the community tab on the menu bar running across the top of the page.

I’ve also started a new service in which you can video chat live with up to six people at a time for free (!) Face to face communication. All you need is a videocam on your notebook.

Forums are are forums.aboutmecfs.org


Mark July 17, 2009 at 11:03 am

Thanks Dr. Logan and thanks to you Cort.

This was the first time that I read an article about CFS where I can agree to 100% out of the experiences I made.
People told me to eat fiber, people told me to take all kind of probiotics and people told me to eat prebiotics because they are so good. All they did was making me feel worse.
VSL#3 was kind of balanced it made me feel better on some days and worse if taken on a daily basis. I’m quite sure that this has to do with the lactate production. Salad and raw veggies are just a nightmare to me.

I hope so much that Dr. Logan and Dr. De Meirleir keep on researching. We have to find a cure or at least a treatment for CFS. This illness is destroying so many lives. Reducing intestinal permeability and improving gut function would be the first and maybe most important (?) step.

I’ll try Align and the entericcoated peppermint oil. What does the ppermint oil do by the way? Do we know the advantages of LactoFlamX yet? Could it be worth a try together with Align?

I just was on the Yakult webpage but they only sell a drink here that contains casei shirota but consists of milk and glucose-fructose-syrup.

At least I got some hope now :) And Cort, you were right, when you said that many persons with CFS feel strange or unpleasant after 10 minutes of eating sth.. I made the same experience. It’s crazy because like Dr. Logan said food cannot be absorbed so fast and is not digested so fast. Who knows but I definetly can feel it in my brain, my social interaction skills drop tremendously. It doesn’t happen with all foods.



Stuart July 22, 2009 at 4:15 pm

It may be that those who find increased symptomology after a meal are not suffering immediate problems due to byproducts of digestion, but by the mobilization of blood to the gut.

Recalling the recent research on hypovolemia and hypoperfusion in ME/CFS patients, it seems likely that digestion would reduce volume and flow in other areas including the brain. Additionally that the red blood cells appear altered much like sickle cell disease and may have problems with oxygen transport may have some role in poor digestion.


Els July 27, 2009 at 10:36 pm


I’m a De Meirleir patient from Belgium. Severe gut problems (years of very painful IBS, gutdysbiosis, leaky gut, …) have been part of my life for many years now.
I recently had new tests done by KdM’s lab (Red Labs + other one). Bloodanalysis, stoolanalysis, urine sample, DMPS challange test, fructose breathing test (lactose was negative three years ago). The 4the of August I will know the results and will be able to compare with those done in 2002 till 2005.

What strikes me if I read the postings above, is that many of you have the same type of reactions to food as I do.
I know there is no explanation why the intake of certain foods can have such a powerful effect on the nervous system within one quarter of an hour sometimes.
I wonder myself how this can be possible. But it IS real.
And I don’t think it has anything to do with blood mobilization (allthough a very good idea). If it was because of the blood mobilization for digestion of food, then the CNS reaction (agitated feeling from stomach up accompanied with a kind of “pressure” on my skull) would occur after every meal. But is does not!

The reactions I have are getting increasingly worse btw. I now know that certain foods are to be avoided because of my reaction to them: chinese food, tomatoes, ginger bread, sugar containing foods like wafels (belgian wafels, mmm), chocolate, BBQ, salami, …

I think glutamate/MSG in general plays a big part in it (in my case). Taking Lyrica decreases the symptoms. Which is another clue for me that glutamate plays a part in it. Also E numbers (preservation, colouring, …) are to be avoided. And with tomatoes (which I like to eat so much) I guess histamine has to be considered.

I don’t know what the mechanism is behind this very short reaction-time.
I do know that KdM advises to reduce thyramine foods and glutamate/MSG (also aspartame etc).

About the probiotics he’s describing now: it’s more ProBiotic Pearls (Nutrisan) instead of VSL3. Sometimes together with Mutaflor (only available in Germany).
And the antibiotic-regimes depend on the patient’s profile. Sometimes no AB’s, sometimes short periodes (week, 10 days), sometimes for a long time.

If I know more about my results and his advise on how to treat, I’ll let you all know.

And btw: if you decide to start that Australian mailgroup on the KdM treatments over there, I guess you can expect some European patients on it too. Mostly we Flemish (dutch speaking part of Belgium) speak more than two languages (in my case 4). So we can join in if you want to :-)


Mark July 31, 2009 at 1:51 pm


I’m so glad that you wrote that comment! All the foods you mention cause the same problems for me, all of them! I feel kind of better now since I know that I’m not alone. It’s totally crazy how we react to food. Yesterday I had to eat chinese food (glutamate…), catastrophy today. Tomatoes, chocolate, suger, alcohol, some nuts, E numbers…they all caus ehuge problems for me.

I haven’t been eating normal for 5 years now. We have to find a solution, doctos need to check into this.

Did lyrica also help with your food interolances?

Best wishes



jim August 13, 2009 at 2:12 pm

I live in the uk and sadly cannot get ALIGN here, all the other brands I have looked at contain the PREbiotics mentioned that can exacerbate things and cause more lactate etc, I guess the next best thing sounds like kefir might be an option but this grows best in milk and surely this will increase the lactate?!?!?!?! I am so lost!
(p.s if i did grow kefir I would prob do it in goats milk as I prefer this milk to cows milk, but I sooooooo dont know if it will make the lactate issue worse!)
anyone know????? the Doctor interviewed didnt go into much detail on this stuff for us who cant get hold of ALIGN


Mark August 23, 2009 at 9:34 pm

I’m in the US now for 6 weeks to study. I bought Align on the first day and took it for 2 weeks now. It’s crazy, I tolerate more and more foods, my digestion got better, as well as my concentration and mood. I’m gonna buy 150 capsules before I go home. This is the first probiotic that helps and I’m really thankful for this advice.
It’s time that they make it available in Europe, I just can’t understand how the European Union blocks off a probiotic that is prescription free and absolutely harmless.


Beady August 25, 2009 at 3:27 am

Where can Align be bought in the us? Do andy web shops send to Europe?

Why is it not allowed to import Align by post to Europe? I have bought probiotic pearls from Prohealth – no problems importing that by post…


chris August 25, 2009 at 2:20 pm

Any CVS store in USA has Align, plus many other stores. It is readily available.

One problem with Align is that it has sugar in it.

I can’t imagine why this cannot be ordered in UK and Europe.



sandra742 September 9, 2009 at 6:21 am

Hi! I was surfing and found your blog post… nice! I love your blog. :) Cheers! Sandra. R.


Bee October 12, 2012 at 10:42 am

Custom Brand Probiotics is the only brand I know that makes a D-lactate free probiotic.


Would this be a good one for someone with UC and CFS/FMS and dysbiosis to take?


South December 30, 2013 at 12:39 pm

This man makes the same mistake every other article and researcher does in reporting anything for IBS: stating the same ideas for constipation dominant problems as for diarrhea dominant problems. The enteric peppermint he recommend to “regulate peristalsis” (his words) in fact SLOWS DOWN peristalsis!! Those of us with constipation predominant IBS, slow motility, do WORSE with peppermint, yet he fails to even mention this! How much more vague and non-useful can that information be. Researchers need to avoid using phrases like “regulate” – regulate in what sense? Answer, slows down!

Just one of many references (despite the folklore, outside of actual scientific study, that peppermint is good for either type of IBS, it is NOT):
In this study, toward bottom of text on that page, it states peppermint slowed down peristalsis.

Honestly what is with the fuzzy, vague language used in scientific “reports”?


Jujube April 21, 2014 at 8:20 pm

I have sibo/leaky gut with chronic diarrhea and malabsorption/digestion along with cfs and mitochondrial dysfunction. All probiotics which includes yogurt, align, vsl3, kefir, and many others do nothing to help it. It may even make me feel worse. I find the only thing that helps is bone broth or glutamine but it also causes me serious anxiety and headaches .


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