More On Propionic Acid and Autism (or…I’m sorry, but I Can’t Help Myself…)

I know that everyone (including me) wants answers to the question “how do you fix a broken biome.”  I am always happy when I come across any information that may actually help people, especially since, at this point, there’s precious little known about how to actually make things better.

On Tuesday, I wrote about new papers on the adverse effects of excess levels of the short-chain fatty acid, propionic acid (PPA), on the developing brain.[i]  At one point, in the paper on how PPA affects the amygdala (the emotion center of the brain), I was struck by the following sentence:  “…recently it was established that the patients who are unable to metabolize PPA are more common than previously thought; many of such patients have cognitive impairments, movement disorders, and seizures.”  The reference given was for a paper written by Dr. MacFabe back in 2013.[ii]  I was curious – what did that sentence mean?  So, I went and read that older paper.

Firstly, I have to say that it was a wonderful read – more “user friendly” than ordinary scientific papers.  Dr. MacFabe talks about how he came up with the PPA theory of autism, and this story-like quality that makes it really enjoyable.  To boot, there were some extraordinary bits of information in it that I absolutely need to share with you.  In fact, there are so many that I’ll need to narrow things down to make sure this doesn’t turn into a Biome Buzz version of War and Peace.

1. To start, I learned a new term:  “gap junctions.”  These are defined as, “An organized collections of protein channels in cell membranes that allows ions and small molecules to pass between adjacent cells.”[iii]  In other words, these junctions allow cells to communicate with each other.

2.  Why is this important? Because it turns out that PPA closes gap junctions:  “…closed glial gap junctions may render neuron hyperexcitable…In turn, this decrease in gap junction coupling may lead to inhibited cortical pruning in development, consistent with the larger brain sized found in ASD.  Gap junction communication is involved in neurotransmission in the basal ganglia, prefrontal cortex, nucleus accumbens, and hippocampus: all areas that are implicated in seizure and movement disorders.  Given these findings, it seemed possible that propionic acid-induced alterations to gap junction function and in neural development, as well as systemic effects (ie. GI motility), may play a role in ASD.”  Thus, PPA has the potential to cause the pattern of brain issues seen in the autism population.

3.  Back to the fact that difficulty metabolizing PPA is more common than once thought. There are apparently people with various inherited metabolic disorders, including one called propionic acid academia, who cannot metabolize this SCFA.   There are much higher rates of these disorders than was recognized in the past.  Dr. MacFabe references 2 papers from which he derived this information, one of which was published back in 2002:  a study of 130,000 infants born in Japan found that, there was “…a frequency of patients with propionic academia more than ten times higher than reported.”  There are mild forms of this illness which are much harder to detect.  Why is this significant for the ASD population?  Firstly, the overlap in symptoms between those with ASD and those with this inheritable disorder are remarkable:  “…regressive cognitive impairment, seizure, and movement disorder, often in the context of GI symptoms.”  Secondly, the difficulty of diagnosing PPA toxicity applies to both populations: “Propionic acid’s habit of ‘hiding’ inside cells makes it difficult to detect, even in patients with a metabolic crisis.”  It does make you wonder if PPA toxicity in the autism population (or even in the non-autism population!) is not WAY under-diagnosed.

4.  Back in May 2018, I wrote a post about Desulfovibrio bacteria in autism.  In today’s paper, Dr. MacFabe mentions this and it’s worth bringing up here again to remind everyone that we are talking about a very complex dysbiosis:  “Ongoing work by Dr. Finegold has identified further novel bacterial populations (ie. Desulfovibrio), which in addition to making propionic acid also produce hydrogen sulphide to damage mitochondrial function, thus potentiating propionic acid’s effects.”  Science has barely scraped the surface of how these citizens of the human biome interact and affect each other.

5.  We know that those on the autism spectrum have issues with mitochondria, the powerhouse of the cell.  The cells are consistently “underpowered,” meaning that they work in a suboptimal way.  As you can imagine, this has a major effect on the functioning of the body.  PPA “…puts a ‘wrench’ in mitochondria…” by affecting the metabolism of carnitine, a substance that is critical in energy production in the mitochondria.

6.  On the bright side (if there is a bright side in all this), there are some things that may help. Firstly, since PPA is produced in large part by certain members of the Clostridia family of bacteria, diets that reduce carbohydrate consumption may work as well as they do by reducing substrate for these bacteria.  This may well explain the incredible efficacy of the Specific Carbohydrate Diet in autism.[iv]  Giving carnitine and  vitamin B12 to “…improve fatty acid metabolism or, in the future, eradicating/reducing ASD-associated propionic acid-producing GI-tract bacteria” may make a difference as well. (Don’t forget too, that back in September 2019, during the first Biome Buzz Propionic Acid Week, I described research showing that the old diabetes medication, pioglitazone (Actos), may treat the negative effects of excess PPA.  I’m waiting for follow up studies on that.

I want to conclude with a wonderful sentiment expressed by Dr. MacFabe.  In my personal opinion, the fact that he adheres to this belief is what makes him such an extraordinary researcher:

“The people who have taught me the most are the parents who refuse to believe what they were told –  that their child’s regression and associated symptoms were all in their imagination….I must stress that we absolutely need the scientific rigor of asking the proper questions and designing the proper experiments and controls, but we also need the art of medicine and the ability to actually observe and listen to patients.  The spark for understanding autism and the GI tract could come only from seeing the patients as an individual, not as a collection of symptoms, and seeing some of the assets as well as the disabilities in this condition.  Deducing whether clinical expertise or science is more important in addressing enormous problems like ASD is like asking which half of a pair of scissors are more important.  We need both.”

Truer words have never been spoken.


[i] Lobzhanidze, G, Lordkipanidze, T, Zhvania, M, Japaridze, N, MacFabe, DF, Pochkidze, N, Gasimov, E, Rzaev, F. Effect of propionic acid on the morphology of the amygdala in adolescent male rats and their behavior. Micron. 2019.  doi: 10.1016/j.micron

[ii] MacFabe, D. Autism: Metabolism, Mitochondria, and the Microbiome.  Global Advances in Health and Medicine. 2013;2(6):52-66.



New Research into the Negative Side of Short-Chain Fatty Acids: Too Much of a Good Thing

I have spent a fair bit of virtual ink over the years talking about both the positives and the negatives of short chain fatty acids (SCFAs), mentioning that indeed, you really can have too much of a good thing.  For example, as healthy as it is to stay well hydrated, you can actually kill yourself by drinking too much water.  (This is called water intoxication, and by diluting the blood too much, you can dilute the levels of electrolytes (like sodium), which leads to swelling of cells and disruption of brain function.)  When it comes to health, just-the-right-amount is key.

Gut bacteria produce SCFAs upon their consumption of polysaccharides (fibers) and in turn, SCFAs feed other good bacteria, on top of having many direct positive effects upon the human body.  Science has shown  that some diseases (Parkinson’s, for example), are associated with low levels of SCFAs.

SCFAs are really complicated:  it turns out that not only do you need just the right amount, but you also need just the right amount at just the right time, especially when it comes to brain development. I’ll come back to this in a moment.

As I mentioned above, I have actually talked on this blog about the dangers of excessive levels of SCFAs, especially propionic acid (PPA or propionate), excess levels of which are now generally accepted as one of the likely causes of autism in our current epidemic. (Read about that here. )  I first mentioned this concept several years ago, not long after I started this blog, in a post about Dr. Derrick MacFabe, a Canadian neuroscientist, whom I first saw speak at a conference many years ago – and whose research I believed from that first moment to be among the most critical ever done in the field of autism.    Dr. MacFabe has spent nearly 2 decades now looking at the neurotoxic effects of excess levels of propionic and his findings have been continually ground-breaking.

In that first post, I described a paper he published back in 2012:  “According to Dr. MacFabe, PPA can readily enter the blood stream from the gut.  In his rat models, in the short term, small amounts immediately produce hyperactivity, repetitive behaviors and social impairment.  Repeated administration of PPA over time, increases the severity and effects, which suggests ‘…that PPA can exert permanent effects on brain and behavior.’”[i]

My regular readers may remember that Dr. MacFabe actually contacted me not long after that, and I had a conversation with him just this past week about some of his more recent research.  Over the next few months, I am going to delve in depth into both his work and other research into PPA as it is a topic of major concern for all of us, in regards to our health and the health of our children.

While excess PPA is now implicated in the development of autism (so all you prospective parents, new parents, and parents of children already on the spectrum should pay particular attention to these posts), PPA also looks like a likely suspect in many other chronic illnesses of our modern era, including potentially obesity.  This past September (during what I dubbed the Buzz’s first official Propionic Acid Week), I discussed research out of Harvard which showed that PPA  adversely affects metabolism by raising blood sugar levels.[ii]  From that post:  “The scientists looked at both animal and humans, and the latter were involved in a double-blind trial with 14 healthy volunteers. The researchers discovered that PPA stimulates the liver to produce more glucose by increasing levels of the hormones, glucagon and fatty acid-binding protein 4, which signal the liver to release sugar into the blood…In the humans in the study, this continued release of unneeded blood sugar led to insulin resistance:  their bodies no longer responded optimally to insulin, which lowers blood sugar levels.”

Remember:  PPA is not just produced by gut bacteria but is ubiquitous in foods commonly eaten in industrialized societies, including cheeses, baked goods and artificial flavors. So between those exogenous sources and what is produced in the gut from potentially altered bacterial composition, raised levels of PPA may be becoming one of the big health dangers of modern times. Fetuses, who are exposed to maternally derived PPA through the placenta are especially at risk during this critical period of brain development.  PPA easily passes through the placenta and the blood-brain barrier.

A very recent paper of Dr. MacFabe and colleagues demonstrates that even physiological levels (normal amounts found in humans) of SCFAs, including PPA, may affect brain development.[iii]  In vitro experimentation done on human neural progenitor cells (hNPCs, which are stem cells that develop into either neuron cells or glial cells (support cells for the neurons)) shows that exposure to normal, physiologic doses of SCFAs (acetate, propionate, butyrate), “…increased the growth rate of hNPCs significantly…,” while “…high levels…of SCFAs had toxic effects on hNPCs.”  As the authors write, “The SCFAs present in the human body fluid derive mainly from bacterial carbohydrate fermentation in the gut.  However, they are also present naturally in dairy, fermented foods, maternal milk and are added as antifungal agents in refined carbohydrates and dairy.  The amounts and composition of gut short-chain fatty acids are dependent not only on bacterial species but also on type of substrate (increased propionate with wheat and dairy, increased butyrate with inulin-containing diets).  Their effects are remarkably tissue and dose dependent.”  And timing dependent, too.  If babies are exposed to high levels in utero, brain development is potentially affected.

On the topic of altering the brain: Dr. MacFabe and other scientists published another 2019 study that showed that in rats, “…the data indicate that even low dose of propionic acid produces in adolescent rodents immediate changes in social behavior, and structural/ultrastructural alterations in amygdala.”[iv]  The amygdala is the area of the brain responsible for the perception of emotion (anger, fear, pleasure, etc.) and for controlling aggression.

The take-away message:  in the right amounts at the right times, SCFAs, including propionic acid, are crucially important for good health.  On the other hand, excessive amounts, from altered gut flora and dietary intake (and in fetuses, maternal exposure) appear to have profoundly negative effects on brain development and human health.

In one of those coincidences you all know I love, I happen to notice a market research report just released over this past weekend:  Sodium Propionate Market Will Generate Massive Revenue in Coming  Years.[v]  I’ll end this post then on an extremely disturbing note: “Rising demand for food preservatives in the food industry is the major driving factor for the global sodium propionate market. Sodium propionate prevents the growth of mold and some bacteria, thereby prolonging the shelf life of packaged baked goods. According to the Code of Federal Regulations, sodium propionate is generally recognized as safe when used as a food additive. It is also used to prevent mold growth in packaged and processed cheese products.”

(For more information on Dr. MacFabe’s work, check out his website, The Kilee Patchell-Evans Autism Research Group (KPEARG))


[i] MACFABE, Derrick F.. Short-chain fatty acid fermentation products of the gut microbiome: implications in autism spectrum disorders. Microbial Ecology in Health and Disease, [S.l.], v. 23, aug. 2012. ISSN 1651-2235.

[ii] Tirosh, A, et. al.  The short-chain fatty acid propionate increases glucagon and FABP4 production, impairing insulin action in mice and humans.  Science Translational Medicine. 2019:11(489).  DOI: 10.1126/scitranslmed.aav0120

[iii] Yang, LL, Millischer, V, Rodin, S, MacFabe, D, Villaescusa, JC, Lavebratt, C. Enteric short-chain fatty acids promote proliferation of human neural progenitor cells.  Journal of Neurochemistry. 2019.  doi: 10.1111/jnc.14928

[iv] Lobzhanidze, G, Lordkipanidze, T, Zhvania, M, Japaridze, N, MacFabe, DF, Pochkidze, N, Gasimov, E, Rzaev, F. Effect of propionic acid on the morphology of the amygdala in adolescent male rats and their behavior. Micron. 2019.  doi: 10.1016/j.micron


2019: A Top Post Roundup

As promised, I am writing my annual review of top stories from the previous year but this time, I’m not picking my favorites, I’m picking yours. I thought it would be fun to see which of my posts got the top views for the year.

So, for your enjoyment, here are the top 5:

At number 5:  February 14th:  Your Blood Type and Your Microbiome

This was one of my personal favorite posts of the year as the information in was entirely new to me:  the antigens in your blood that designate it type A, B, AB, or O (which are carbohydrates that evokes an immune response), are also expressed on platelets, immune cells, bodily excretions, tissues, etc.  These antigens, as it turns out, have a major effect on the composition of the gut flora.  One of the studies  I describe in this post  states: “Our novel finding indicates that the ABO blood group is one of the genetically determined host factors modulating he composition of the human intestinal microbiota, thus enabling new applications in the field of personalized nutrition and medicine.”  This may go a long way toward explaining the individual variations in gut flora composition found even among health individuals.

At number 4:   April 18: Evolutionary Mismatch, The Human Biome…and a Bit More on Obesity

This post provides strong support for the biome depletion paradigm (formerly known as the hygiene hypothesis).  It’s about how our  modern lifestyles have led to massive and abrupt changes to our biomes, leading to our current epidemic of inflammatory diseases and obesity.  For example, our western diets – high in unhealthy fats and sugar – have led to a global disturbance of the gut flora.  The main paper I focus on in this post concludes, “Public health efforts to counter negative effects of the Western diet, support breastfeeding, and assure access to high-fiber, low-sugar, and low-fat foods may have an outsized effect on seemingly unrelated widespread diseases such as diabetes, autism, and childhood obesity.”

At number 3:  April 11:  Spondylitis and Microbiome Dysbiosis: Both Bacterial and Fungal

I referred to this old post just this past Tuesday.  I was really surprised at the enormous viewership this April post received.  It describes a small study on 22 people with Spondylitis and the significant differences found between their microbiomes and those of healthy controls.  The biggest surprise to me was that it was the degree of mycobiome (yeast) dysbiosis that correlated to disease severity and the level of inflammation in the body, more than the dysbiotic bacteria.  I’m not sure that finding has yet been replicated, but certainly – as I talked about on Tuesday – the altered bacterial microbiome found in those with the disease now has been.

At number 2:  August 29: The Bacterial Microbiome and Immune Response to Vaccines

If you remember, I was really nervous about writing this one, but it turned out to be a non-issue. Reader response was very balanced and you all seemed to find this as scientifically interesting as me.  As I wrote last August, “When you consider that at least 70% of your immune system is in your gut, and the crucial role we now know the gut flora plays in immunity, it makes perfectly logical sense that there may be a connection, especially considering the variability in immune responses to vaccines. Some people require only 1 to achieve a lifetime of immunity while other people need to be re-inoculated multiple times, while still others never gain immunity at all.  Why that is, no one knows, but scientists are starting to suspect that gut bacterial variability is a key factor.”

You all know how much I love coincidences!  Well, what was crazy about this post was that a week later, big news came out of Stamford University that was all over the press:  “People’s response to flu vaccine influenced by gut microbes:  Decimating levels of intestinal bacteria with antibiotics reduced the immune system’s responsiveness to a seasonal influenza vaccination, a Stanford-led study found.”[i]

I am particularly glad that this is a growing area of research as its importance cannot be overstated.

At number 1, most read post this past year:  June 13:  Zeoring in on an Inflammatory Bowel Disease Culprit

Researchers at Harvard University have narrowed down the bacterial culprits in IBD and one of the prime suspects is a little-known species that ordinarily comprises less than 1% of our flora:  Ruminococcus gnavus. During IBD flare-ups though, this little devil can jump to 50% of the bacteria in the gut and it produces a polysaccharide that causes huge increases in inflammation in the body.  No one yet knows why or how this bacteria suddenly blooms, but as their findings were so significant, research is ongoing.  Hopefully I’ll be able to report more on this story in 2020.



Alterations in the Bacterial Microbiome Associated with Ankylosing Spondylitis: A Larger and Confirming Study

My long time readers know that at this time of year, I typically review my favorite stories from the prior year but I was so darn busy this holiday season, I simply did not have the time this past week.  I will try to do so as a throw-back Thursday present this week.

In the meantime, I know that one of the most read posts of 2019 was the one I wrote on April 11th about a small study that showed that those with Ankylosing spondylitis (AS) have distinct bacterial and fungal microbiome differences from healthy controls:  “The study included 22 patients with  AS and 16 healthy controls (HC).  They found major differences in the bacterial microbiomes between the two groups, including a ‘significant increase’ in diversity in the AS group that included a nearly 3-fold increase in Proteobacteria and a decrease in Bacteroidetes species, including Prevotella.” The researchers also noted that the fungal microbiome was depleted in those with AS, in relation to the bacterial:  that is, the ratio of bacteria to fungi is off.  And the severity of disease completely coincided with the degree of alteration to the bacterial microbiome.

That study though was on only 22 patients.  Obviously, the results needed to be replicated with a larger cohort, and I am happy to announce that a new study has done just that.  Researchers at a Swedish University evaluated the fecal microbiota in 150 patients with AS, and compared them to patients with ulcerative colitis and healthy controls over a 5 year period of time.  Like the earlier, smaller study, they also assessed inflammation levels.[i]

Sure enough, “…the fecal microbiota in AS was characterized by a higher abundance of Proteobacteria, Enterobacteriaceae, Bacilli and Streptococcus species, as well as Actinobacteria, but lower abundance of Bacteroides and Lachnospiraceae.”[ii]  Notice that these results somewhat parallel the earlier smaller study:  a higher level of Proteobacteria, a decrease in Bacteroidetes.

One other interesting finding in this study:  the scientists also measured calprotectin, a marker for intestinal inflammation.  Those individuals with dysbiosis, including lower levels of anti-inflammatory bacteria and higher levels of Streptococcus, had higher levels of calprotectin in their feces.  As 87% of those with AS in the study suffered from dysbiosis, the researchers conclude that intestinal inflammation is common in the disease.

Which leads me to a few points that I never knew about AS.  Yes, I knew that gut issues are commonly found alongside AS, but here are a few facts I did NOT know:

  1. “AS is characterized by microscopic intestinal inflammation, which has been demonstrated in 40–60% of the patients.”
  2. “AS patients also have an increased risk of developing IBD, especially CD.”
  3. “Interleukin (IL) 23 and IL17, which are key cytokines in AS, are produced in the inflamed gut, both in AS and in IBD.”

What to do about it, no one yet knows, just as is the case with all these inflammatory illnesses that seem to originate in the gut.  I did point out, in my first ever post about AS, that in one 2007 study, patients with AS were given Moxifloxacin, an antibiotic and that this “…resulted in a significant and sustained improvement…”  on top of reducing inflammation.  I haven’t found any kind of follow up on that though.

Spondyloartropathies are incredibly common, as I’ve pointed out before – way more common than Parkison’s, MS, and other much better known diseases.  As so many of you seem interested in this topic, I most certainly I will continue to watch out for any new information.


[i] Klingberg, E, et. al. A distinct gut microbiota composition in patients with ankylosing spondylitis is associated with increased fecal calprotectin.  Arthritis Research & Therapy. 2019.  doi:10.1186/s13075-019-2018-4.


Migraines and the Bacterial Microbiome: Are Probiotics a Solution?

For those of you who suffer migraines (or know someone who does): I don’t know about you, but I’ve been waiting for an article relating those damn headaches to the gut biome.  (You knew it had to be coming…)  Considering that migraine is the 3rd most common illness in the world[i], I reckon many of you will be really interested in this. .

In 2016, research was published which showed that migraine sufferers have more bacteria (especially in the mouth) which produced the gas, nitric oxide, a known migraine trigger.  This was an association only – not proof – but it was a great first step in that it potentially explained why some people are more susceptible to the headaches and also, why certain foods (like chocolate and wine) may be problematic.[ii]

It turns out that when bacteria in the GI tract break down nitrates (such as those found in many foods, including some kinds of hotdogs), the nitrates are converted to nitric oxide which dilates blood vessels.  (It is already known that medications which contain nitrates (which are given for angina or heart failure) trigger migraines.)

This most recent study involved examining the bacteria from oral (172) and fecal (1996) samples from migraine sufferers.  In both types of samples, the bacteria that break down nitrates were at slightly higher levels than in the normal controls.  The researchers next step is to look at how foods affect blood levels of nitric oxide.

Some good news:  another 2019 study[iii] was conducted on 100 people with migraines (50 with episodic, 50 with chronic); half received a placebo, half received a probiotic.  The results were incredibly significant, and showed that those with episodic migraine, who received the 14 strain probiotic (which contained Bifidobacterium, Lactobacillus and Bacillus subtilis) for 10 weeks had dramatic improvement:  “After a 10-week intervention, among episodic migraineurs the mean frequency of migraine attacks significantly reduced in the probiotic group compare to the placebo group…A significant reduction was also evident in the migraine severity…Episodic migraineurs who received the probiotic also showed significant reduction in abortive drug usage per…while there was no significant changes within the placebo group.”

Those with chronic migraines, who took the probiotic for 8 weeks, had equally dramatic improvement compared to controls:

“The frequency of attack fell by 45% among those with chronic migraine and by 40% among those with episodic migraine. For a reduction in migraine intensity, the corresponding figures were 31% and 29%.”[ii]

For those interested, the probiotic the experimental group was given was 2 capsules daily of Bio-Kult.

Now that I know a relationship between the gut biome and migraines is likely, I will be sure to watch out for ongoing research to share with you all.




[iii] Jahromi, SR, et al. The effects of a multispecies probiotic supplement on inflammatory markers and episodic and chronic migraine characteristics: A randomized double-blind controlled trial.Cephalalgia 2019;39(7)

High-Fat Meals, the Gut’s Endocrine System and Bacteria

As you know, there are certain topics that are of particular interest to me including autism; Parkinson’s; -omes, other than just the bacterial microbiome; neglected illnesses like chronic fatigue and fibromyalgia; obesity; etc.; and of course, diet and its relationship to the organisms of the biome and health.  A short post today about a research out of Duke University, looking at how a high fat diet affects the gut and its contents.[i]

One thing I haven’t had much opportunity to write about is the endocrine (hormone) system of digestive system, simply because I really haven’t seen much about it and its interaction with the gut bacteria.  The scientists noticed, in zebrafish, that these endocrine cells (in the gut, they are referred to as entereoendocrine cells and they are found in the mucosal lining), which normally send signals to brain and body by releasing hormones, shut down for a number of hours after a high fat meal.  Ordinarily, the hormones they produce tell the body about gut movement, fullness, digestion, nutrient absorption, insulin sensitivity and energy shortage.  However, after encountering high fat food, they shut down for several hours – and no one has a clue why.

There are several possibilities.  A possible negative view: one of the authors states, “Since enteroendocrine cells are key players in digestion, the feeling of being full and subsequent feeding behavior, this silencing may be a mechanism that somehow causes people eating a high-fat diet to eat even more….If this happens every time we eat an unhealthy, high-fat meal, it might cause a change in insulin signaling, which could, in turn contribute to the development of insulin resistance and Type 2 diabetes.”

Inside cells are multiple organelles (their version of organs), including one called the endoplasmic reticulum, in which new proteins (like neurotransmitters and hormones) are synthesized.  This organelle appears to undergo stress when the cells are confronted with a high-fat meal, and become overstimulated and then exhausted.  For a time then, the cells are silenced – they cannot communicate with the rest of the body at all.

What’s even more interesting is that in germ-free fish, this does not happen.  In fact, the researchers were able to narrow down and isolate the specific bacteria that causes this effect:  Acinetobacter.  This is a really rare (les than .1% of the gut bacteria), but after a high-fat meal, they increase 100-fold.

At this point, the scientists don’t even know yet if it’s a good or a bad thing.  It’s possible that it’s a “maladaptive response to high-fat foods” ultimately leading to metabolic disorders.  On the other hand, it is “…also possible that the silencing is a beneficial adaptation to protect the animal from over-stimulation of the gut cells.”

Considering the incredibly dramatic increase in metabolic disorders and obesity in the last 3 decades, figuring out this kind of thing is incredibly important.  I’ll watch for updates.



Using Yeasts to Fight Yeasts

I like it when I can report on -omes other than the bacterial microbiome, especially when the research is about using a natural and benign substance to treat a serious pathogen in fighting disease.  In this case, researchers in the USA and India have found a way of treating the life threatening, often fatal, infection, Candida auris, a yeast which is resistant to treatment by antifungal medications.[i]  C. auris infections, which are rife in hospitals and a major threat to people with weakened immune systems, was recently listed as an urgent threat by the USA’s Center for Disease Control.

A relation of the much more commonly known Candida albicans – which is the leading cause of fungal infections acquired in the hospital – C. auris, is virtually impossible to treat.  It typically affects people who are immune-compromised or who have had implanted medical devices.  Candida yeasts can penetrate the tissue of the gastrointestinal tract and make their way into other internal organs, causing systemic infection, including the deadly blood infections seen with C. auris.  One of the reasons it is so resistant to treatment is that it can form biofilms – complex matrices which protect the species inside.  I’ve written about the threat of biofilms before here and here.  (Think of the film on your teeth before brushing.)

It turns out that two food derived yeasts, Issatchenkia occidentalis, which grows on foods like fruit, and common Baker’s yeast, Saccharomyces cerevisiae, can actually inhibit adhesion of these pathogenic yeasts to epithelial tissue (the lining of the gut) and prevent the formation of biofilms.  When applied to non-biological surfaces, such as you’d find in medically implanted devices, these yeasts were able to reduce C. auris’ ability to adhere to these surfaces by 53% and to form biofilms by 70%. They also inhibited the pathogenic yeasts’ ability to evade the immune system.

More than that, the scientists found that these yeasts were effective against adhesion to human epithelial cells and, when given to C.elegans (the worm I’ve mentioned many times before that is frequently used in experiments to mimic the human intestinal tract – for example, here) infected with C. auris, the worms lived longer.  The pathogenic yeasts were less active when treated with the two beneficial ones.  Interestingly, extracts from the food-derived yeasts also worked, which suggests that it is, at least in part, metabolites of the yeast which have this beneficial effect.

The fact that these probiotic yeasts successfully treat infections with pathogenic ones did not surprise me.  It’s long been known that Sacchromyces boulardii is a probiotic yeast which does so.  It is considered a safe treatment for many ailments, even in children.  According to WebMD:  “Saccharomyces boulardii is most commonly used for treating and preventing diarrhea, including infectious types such as rotaviral diarrhea in children, diarrhea caused by gastrointestinal (GI) take-over (overgrowth) by ‘bad’ bacteria in adults, traveler’s diarrhea, and diarrhea associated with tube feedings. It is also used to prevent and treat diarrhea caused by the use of antibiotics.”[ii]  I myself have used it very successfully for years with both my family and nutrition clients.  The study I am writing about today, however, had results which did shock me:  “The probiotic properties of these novel yeasts are better than or comparable to those of the commercially available probiotic yeast Saccharomyces boulardii, which was used as a reference strain throughout this study. These results indicate that yeasts derived from food sources could serve as an effective alternative to antifungal therapy against emerging pathogenic Candida species.”

I will not be surprised if a commercial supplement with one or both of these species hits the market very soon.  Baker’s yeast is obviously already commercially available, although there’s no standardized amount for treatment as yet.  And of course, we don’t know for sure if it will treat these pathogenic yeast infections in humans.  But without any good alternatives, we can only hope those studies are carried out quickly:  “To meet the growing need for treatment options for biofilm-associated clinical complications, these food-derived yeasts represent a safe and attractive alternative to conventional treatment for Candida infections.”


[i] Kunyeit, L, Kurrey, NK, Anu-Appaiah, KA, Rao, RP. Probiotic yeasts inhibit virulence of non-albicans Candida species. MBio. 2019.  10:e02307-19.


Another Promising Treatment for Leaky Gut?

Researchers at Wake Forest School of Medicine (in North Carolina), have discovered that using inactivated (dead via the application of heat) Lactobacillus paracasei (derived from humans) appears to have a remarkably beneficial effect in an animal model of leaky gut, thereby reducing inflammation.[i]  In doing so, they significantly extended the lives of C. elegans, a roundworm frequently used in laboratory experiments. They then tested the inactivated bacteria on elderly mice, finding that it “…helped prevent the development of metabolic dysfunctions that a high fat diet causes.  It also improved gut permeability, making leakages less likely, reducing inflammation, and boosting cognitive function…”[ii]

If you a regular reader of this blog, you will remember that leaky gut is a major factor in inflammatory diseases.  For those unfamiliar, this is a condition in which inflammation leads to the mucus lining of the intestines becoming permeable, allowing bacteria, toxin metabolites of bacteria and yeast, undigested food, etc. to make their way into the blood stream.  Leaky gut is also a natural result of the aging process: the gut becomes increasingly permeable and while a result of inflammation, it is also a major cause, increasing the risks of developing illnesses like obesity, diabetes, cardiovascular illness, Alzheimer’s and other cognitive problems, and many more.

 The scientists discovered that it is a component of this bacteria’s cell wall (lipoteichoic acid) which led to the health improvements in the animals. This is not the first time an inactivated bacterial strain has been shown to have major health benefits.  Many of you may remember that back in July of this year for one, I wrote about using inactivated Akkermansia to treat the development of fat (i.e. obesity) and insulin resistance. In that case, a 3 month long, double-blind, randomized trial in human showed that heat-killed Akkermansia “…helps to limit the increase of different cardiovascular risk factors in subjects who are overweight and obese.”  Again, the researchers believe that it is a component of the cell wall which has the beneficial effect.

This story gets even more interesting.  The Wake Forest scientists discovered that this inactivated species “…significantly increases mucin production, and proportionately, the abundance of mucin-degrading bacteria Akkermansia muciniphila also increases.”  (Mucin is a component of mucus.  Thus, increasing the food supply leads to an increase on probiotic species that thrive on that substance.) Likely then, the L. paracasei is exerting its beneficial effects both directly (i.e. it’s cell wall) and indirectly, by boosting levels of other beneficial probiotic species.

Considering the importance of finding effective treatments for leaky gut, this is very promising.  This has obviously not as yet been tested in humans but the lead researcher has applied for a patent for the product.  I’ll keep an eye out for any further news.


[i] Wang, et. al. Lipoteichoic acid from the cell wall of a heat killed Lactobacillus paracasei D3-5 ameliorates aging-related leaky gut, inflammation and improves physical and cognitive functions: from C. elegans to mice. GeroScience. 2019.


Helminths and the Microbiome: An Anti-Inflammatory Partnership

It isn’t often that I find new research on helminths and equally rare to find one on the interactions of the various species of resident in the gut, so I was particularly pleased to find an actual human clinical study looking at how the presence of helminths affects the microbiome and the immune response.[i]

The authors point out in their introduction that, “Diseases of modernity, such as allergy, autoinflammatory, and metabolic diseases are increasingly observed in industrialized countries,”…and that the loss of helminths which “may have protective effects against autoinflammatory diseases,” are suspect as a major cause.

One study they point out that I found particularly interesting:  transferring the microbiota from mice infected with a helminth to mice without helminths actually protected the latter group from allergic airway inflammation.  Studies such as this imply that a part of the protection against inflammation afforded by helminths is through their beneficial effect on the bacterial microbiome. Unfortunately, there are no such studies as yet in humans.

This paper though is at least a start.

66 people in Indonesia, where helminth are endemic, took part in this randomized, placebo-controlled study.  At the start the trial, stool was tested to look at both bacterial content and to test for the presence of helminths. 40 of these people had helminths at the start of the trial; 4 species of helminth were found (Ascaria lumbricoides, hookworm (Necator americanus), Ancylostoma duodenale and Trichuris trichuria (whipworm).  Some people had more than one species. The patients also had blood taken.  For 21 months, in a randomized fashion, anti-helminth drugs were given to those in the experimental group (the control did received a placebo) every 3 months, and stool and blood were taken, to look at changes in bacterial makeup and cytokine levels.

I was not at all surprised by the results:  “When subjects were free of helminth infection…increasing proportions of Bacteroidetes was associated with lower levels of IL-10 response to LPS…This association was significantly diminished when subjects were helminth-infected…”

That is, higher levels of Bacteroidetes were found in those without helminths.  This family of bacteria, when proportionally too high, appear to depress regulatory cytokine levels (IL-10 is a major one) so that, when challenged with a bacterial toxin (LPS is lipopolysaccharides, a highly inflammatory toxin produced by certain bacteria), the patients had markedly higher levels of inflammation.

“IL-10 was already marked as a key anti-inflammatory cytokine involved in the induction of immune suppression by helminths.  Our observation that helminths counteract the suppressed IL-10 response to LPS in subjects with higher Bacteroidetes proportions supports the so called “old friends hypothesis”…stating that certain infectious agents such as helminths may have protective effects against immune dysfunction and inflammatory diseases…”

There is a lot more interesting information in this paper but this is the main takeaway:  helminths appear to positively affect the bacterial content of the human digestive system and thus, both directly and indirectly (by boosting levels of regulatory cytokines) keep the inflammatory system in check.

By the way, if this topic is of particular interest to you, I highly recommend spending a few minutes reading at least these other two posts (hereand here) on this site.  (There are many more articles on the subject but I tried to pick two highlights!)  While of course much more research needs to be done, the evidence is pretty damn overwhelming at this point:  the loss of our native macrobiomes is a really bad thing.


[i] Martin, I, et. al. The effect of gut microbiome composition on human immune response: an exploration of interference by helminth infections.  Frontiers in Genetics. 2019;10(1028).

Lactose: Food for Gut Infection/Dysbiosis?

This little article caught my attention.[i]  It’s an animal study so it may not be applicable to humans…but it’s certainly something on which I should keep an eye.  As you all know, I’m especially interested in the connection between food and gut bacteria.

A particular kind of bacteria, Enterococcus, are “particularly risky” for people who are immune compromised – for example, those having bone marrow transplants or those on immune suppressors following an organ transplant.  It can cause a serious infection.  It turns out that (at least in mice), lactose, the kind of sugar found in milk and dairy products, feeds Enterococcus.

In a study of 1,300 people with bone marrow transplants a definitive link was found between Enterococcus and a potentially lethal immune condition called graft-versus-host disease (wherein immune cells attack the newly transplanted organ).

After giving mice bone marrow transplants, their intestines could no longer produce lactase, the enzyme that breaks down lactose for digestion:  “The high levels of undigested lactose in turn led to a total domination of Enterococcus.”  (The theory is that the chemotherapy agents given to those getting a bone marrow transplant damages the cells which line the intestines, the enterocytes. These cells produce the enzymes which break down disaccharide sugars like lactose.)

The researchers were shocked at these results.  What’s even crazier is that when the scientists cultured this bacteria in vitro, and added lactase (in the form of the over-the-counter pill, Lactaid), growth of Enterococcus was blocked.  They, therefore, started to feed it to their lab mice and low-and-behold, the mice were protected from Enterococcus growth.

While not as yet tested in humans, there is existing data that suggests the same connection.  People with the gene that tends to make them more lactose-intolerant are already known to have a harder time clearing Enterococcus from their gut biome.  The researchers are contemplating a trial in humans who are on chemotherapy drugs to test the efficacy of Lactaid and/or the removal of lactose from the diet.

I took a quick look around to see what other illnesses with which Enterococcus might be associated.  According to the Merck Manual, two strains of Enterococcus (Enterococcus faecalis and E. faecium), “…cause a variety of infections, including endocarditis, urinary tract infections, prostatitis, intra-abdominal infection, cellulitis, and wound infection as well as concurrent bacteremia.”[ii]  (Bacteremia means bacteria in the blood…which is a really, really bad thing (like sepsis).)  Perhaps even more interesting:  studies in people with Crohn’s have shown greatly increased levels of Enterococcus as compared to healthy controls.[iii]  According to this paper, this species is associated with intestinal inflammation, at least in animal models.

I don’t yet know what to make of all this.  It struck me, reading all this, that the Specific Carbohydrate Diet – which for so many years has proven unbelievably successful for treating inflammatory bowel diseases – requires the complete removal of disaccharides like lactose from the diet.  Coincidence?

I think  it’s worth following this research in the future, right?




[iii] Yu, L.C. Microbiota dysbiosis and barrier dysfunction in inflammatory bowel disease and colorectal cancers: exploring a common ground hypothesis. J Biomed Sci 25, 79 (2018) doi:10.1186/s12929-018-0483-8