Showing posts with label B. fragilis. Show all posts
Showing posts with label B. fragilis. Show all posts

Wednesday, 15 April 2015

Boosting “Tregs” in Autism, IBD, MS and even Obesity with Short-Chain Fatty Acids (SCFAs)

 T Rex - for what turned out to be rather a monster post

If the title of this post already makes sense, you probably do not need to read it.

It is about regulatory T cells (Tregs), which are an interesting way to treat what I have termed the over-activated immune system in autism.  The same ideas can be extended to other conditions related to mast cells, and also potentially Multiple Sclerosis (MS), Irritable bowel Disease (IBD) and even obesity.

Take Home Summary

For those more interested in what can be done, rather than why, here is the conclusion from this post:-

There are at least four possible ways to increase the number of regulatory T cells (Tregs), which should reduce pro-inflammatory cytokines (particularly IL-6) and increase anti-inflammatory cytokines (like IL-10).  

It should also reduce obesity, protect against diabetes and protect against organ damage in those already diabetic.

The simplest method is to increase production of small-chain fatty acids, which are the main metabolic products of bacteria fermentation that occurs naturally in the intestines.  You either eat more fibre or eat the specific bacteria, that causes the fermentation.

1.     Increase specific gut microbiota, namely B. fragilis and Clostridia

2.     Increase natural production of small-chain fatty acids (SCFAs) by eating more fibre.  Here using soluble maize fibre.

3.     Add supplemental SCFAs to your diet.  You just eat a source rich in some of the following:- Formic acid, Acetic acid, Propionic acid, Butyric acid (eat butter), Isobutyric acid, Valeric acid, Isovaleric acid

4.     Have a bone marrow transplant (not recommended)

For regular readers you may recall that B. fragilis appeared in an earlier post:-

Why this post?  - Bumetanide has stopped working

I recently received a comment from a lady who has tried Bumetanide in her child with autism.  After the expected two week delay, she noticed lots of positive behavioral changes, but sadly latter on the Bumetanide “stopped working”.

In the past I received comments about “NAC has stopped working”.

Since I also experienced the same effect of “everything stops working” in the summer, I know how these people feel.

In reality, as I eventually discovered, it is not that Bumetanide/NAC has stopped working, but rather something else has started working.  I wrote once about autism being a Dynamic Encephalopathy, which to be fair was Martha Herbert’s idea and not mine.  This is one reason that a new type of doctor will be needed if autism is ever to be treated.  It is a moving target.

In some types of autism it seems that the immune system can switch to an over-activated state and when in this state all my clever autism drugs appear to stop working.

In some people the problem is driven by so-called mast cellsMast cells play a key role in the inflammatory process. When activated they release granules and various hormonal mediators.  Histamine and the pro-inflammatory cytokine IL-6 are produced and this wreaks havoc in the brain, undoing all the good done by Bumetanide, NAC etc.

Regulatory T cells (Tregs)

In earlier posts I think I have exhaustively covered mast cells and to how to stabilize them.  However, I decided to look further back up the chain in the immune system at what may modulate the mast cells. Regulatory T cells caught my attention.

The regulatory T cells (Tregs), formerly known as suppressor T cells, are a subpopulation of T cells which modulate the immune system, maintain tolerance to self-antigens, and abrogate autoimmune disease. These cells generally suppress or downregulate induction and proliferation of effector T cells.
T regulatory cells are a component of the immune system that suppress immune responses of other cells. This is an important "self-check" built into the immune system to prevent excessive reactions.

The immune system must be able to discriminate between self and non-self. When self/non-self discrimination fails, the immune system destroys cells and tissues of the body and as a result causes autoimmune diseases. Regulatory T cells actively suppress activation of the immune system and prevent pathological self-reactivity, i.e. autoimmune disease

The immunosuppressive cytokines TGF-beta and Interleukin 10 (IL-10) have also been implicated in regulatory T cell function.
Recent evidence suggests that mast cells may be important mediators of Treg-dependent peripheral tolerance.

Regulatory T cells come in many forms with the most well-understood being those that express CD4, CD25, and Foxp3 (CD4+CD25+ regulatory T cells).
Foxp3+ Treg cells are known to produce IL-10 in the colon (Round and Mazmanian, 2010).

Mast cell degranulation is a hallmark of allergic reactions, but mast cells can also produce many cytokines that modulate immunity. Recently, CD25(+) regulatory T cells (Tregs) have been shown to inhibit mast cell degranulation and anaphylaxis, but their influence on cytokine production remained unknown. In this study, we show that, rather than inhibit, Tregs actually enhance mast cell production of IL-6. We demonstrate that, whereas inhibition of degranulation was OX40/OX40 ligand dependent, enhancement of IL-6 was due to TGF-β. Interestingly, our data demonstrate that the Treg-derived TGF-β was surface-bound, because the interaction was contact dependent, and no TGF-β was detectable in the supernatant. Soluble TGF-β1 alone was sufficient to enhance mast cell IL-6 production, and these supernatants were sufficient to promote Th17 skewing, but those from Treg-mast cell cultures were not, supporting this being surface-bound TGF-β from the Tregs. Interestingly, the augmentation of IL-6 production occurred basally or in response to innate stimuli (LPS or peptidoglycan), adaptive stimuli (IgE cross-linking by specific Ag), and cytokine activation (IL-33). We demonstrate that TGF-β led to enhanced transcription and de novo synthesis of IL-6 upon activation without affecting IL-6 storage or mRNA stability. In vivo, the adoptive transfer of Tregs inhibited mast cell-dependent anaphylaxis in a model of food allergy but promoted intestinal IL-6 and IL-17 production. Consequently, our findings establish that Tregs can exert divergent influences upon mast cells, inhibiting degranulation via OX40/OX40 ligand interactions while promoting IL-6 via TGF-β.

Treg cells are reduced in people with Autism

The following study showed that 73% of subjects with autism had reduced levels of Tregs and in particular those with allergies of a familial history of autoimmune disease.

Those in the 73% with allergies are the ones who fit my over activated immune system category.


Autoimmunity may have a role in autism, although the origins of autoimmunity in autism are unknown. CD4( +)CD25(high) regulatory T cells play an important role in the establishment of immunological self-tolerance, thereby preventing autoimmunity. The authors are the first to study the frequency of CD4(+)CD25( high) regulatory T cells in the blood of 30 autistic and 30 age- and sex-matched healthy children. Patients with autism had significantly lower frequency of CD4(+)CD25(high) regulatory T cells than healthy children (P < .001). These cells were deficient in 73.3% of children with autism. Autistic patients with allergic manifestations (40%) and those with a family history of autoimmunity (53.3%) had a significantly lower frequency of CD4(+)CD25(high) regulatory T cells than those without (P < .01 and P < .001, respectively). In conclusion, CD4(+)CD25( high) regulatory T cells are deficient in many children with autism. Deficiency of these cells may contribute to autoimmunity in a subgroup of children with autism. Consequently, CD4(+)CD25(high) regulatory T cells could be new potential therapeutic targets in these patients.

This study was about autism, but for some therapeutic insights we need to go over to Wendy Garrett’s lab at Harvard.

Her group are not researching autism, they are researching inflammation, particularly in the colon. 

But inflammation can occur anywhere.

Their recent work and some relating to it is covered in the following excellent article is from the Multiple Sclerosis Discovery Forum.  It is very readable.


Common compounds made by gut microbes that break down dietary fiber appear to boost the number and function of regulatory T cells (Tregs) in the colons of mice, a new study found. The findings expand the known ways that intestinal bacteria can influence Tregs, which can dial down an immune response and may be malfunctioning in autoimmune and inflammatory disorders, including multiple sclerosis (MS) and inflammatory bowel disease (IBD).

The microbial metabolites, known as short-chain fatty acids (SCFAs), restored the depleted Tregs of germ-free mice, the researchers reported. In mice with normal intestinal bacteria, supplemental SCFAs expanded the existing Treg population and activity. In a mouse model of colitis, SCFAs in drinking water reduced intestinal inflammation by enhancing Treg function.

"It's a terrific paper," said Sarkis Mazmanian, Ph.D., a microbiologist at the California Institute of Technology in Pasadena, in an interview with MSDF. Mazmanian first reported that PSA on the surface of B. fragilis converts CD4+ T cells into Foxp3+ Treg cells that produce IL-10 in the colon (Round and Mazmanian, 2010). "We have been working with a specific organism that makes a molecule unique to B. fragilis that induces Tregs and suppresses inflammation, and Wendy has discovered a more general metabolite produced by multiple bacterial groups that does something similar."

The study builds on discoveries (Nagano et al., 2012) showing that Tregs are dependent upon gut microbiota, specifically B. fragilis and Clostridia, Garrett told MSDF in an email. "We all may not have B. fragilis," she wrote. "In addition, human and mice both have many different strains of Clostridia. However, all healthy humans have regulatory T cells. Since SCFA are such abundant microbial metabolites, we hypothesized that SCFA may regulate Tregs in the colon."

"SCFA exert so many different effects on Tregs by altering molecules that affect the structure of DNA, making some areas of the DNA more open and available for transcription," Garrett wrote in an email. "In this way, SCFA can affect several different Treg functions."

For Garrett and others, the findings advance the therapeutic potential of dietary-based interventions using the SCFA mix and perhaps other molecules that boost signaling through GPR43 to improve Treg function in patients with inflammatory bowel disease and other autoimmune diseases. The concept was also advanced in another new study from Kenya Honda, M.D., Ph.D., of the RIKEN Center for Integrative Medical Sciences in Yokohama, Japan, in a recent Nature paper. A mixture of 17 strains of human-derived Clostridia designed to expand and differentiate Tregs relieved symptoms of colitis and allergic diarrhea in mouse models (Atarashi et al., 2013).

The full paper is here:-

So much for the colon, what about the effect of increasing Treg in autism?

We already know that in the MIA (maternal immune activation) mouse model of autism, treating mice pups with B. fragilis reduces their autistic behaviours.
'Friendly' bacteria treat autism-like symptoms in mice 

That is a pretty good start, since we know that B. fragilis causes more SCFAs to be produced in the intestines.

The most effective way to reset an immune system would be a bone marrow transplant.  The following article from SFARI looks about what happens in mice. 

An altered immune system can cause autism-like behaviors, suggests a study published 31 July in the Proceedings of the National Academy of Sciences1. The researchers found that a bone marrow transplant, which restores the animals’ immune system, alleviates some of their symptoms, including anxiety and repetitive behavior.

Such transplants are too dangerous for treating people with autism, but the findings suggest other treatments targeting immune cells, the researchers say.
When confronted with foreign cells — for example, when infected with a virus — the body typically activates immune cells called T cells to release signaling molecules called cytokines. A different set of T cells, called regulatory T cells, then keep that immune response in check by suppressing the activated T cells.
In the study, researchers injected pregnant mice with a mock flu virus that sets off their immune response. The offspring carry overly responsive T cells and have too few regulatory T cells throughout their lifetime, the study found. These two things together point to an immune system that's overly reactive.

Studies on the effect of Small Chain Fatty Acids (SCFAs) on Humans

The good news is that numerous studies show that Wendy Garrett’s findings seem to apply far beyond the colon.

The reason is that SCFAs are able to cross the Intestinal Epithelium (i.e. cross from the gut to the bloodstream)

CONCLUSIONS Data suggest a potential therapeutic value of Tregs to improve insulin resistance and end organ damage in type 2 diabetes by limiting the proinflammatory milieu.

Short-chain fatty acids (SCFAs) are the main products of dietary fiber fermentation and are believed to drive the fiber-related prevention of the metabolic syndrome. Here we show that dietary SCFAs induce a peroxisome proliferator-activated receptor (PPAR) γ-dependent switch from lipid synthesis to utilization. Dietary SCFA supplementation prevented and reversed high-fat diet-induced metabolic abnormalities in mice by decreasing PPARγ expression and activity. This increased the expression of mitochondrial uncoupling protein 2 and raised the AMP/ATP ratio, thereby stimulating oxidative metabolism in liver and adipose tissue via AMP-activated protein kinase. The SCFA-induced reduction in body weight and stimulation of insulin sensitivity were absent in mice with adipose-specific disruption of PPARγ. Similarly, SCFA-induced reduction of hepatic steatosis was absent in mice lacking hepatic PPARγ. These results demonstrate that adipose and hepatic PPARγ are critical mediators of the beneficial effects of SCFA on the metabolic syndrome, with clearly distinct and complementary roles. Our findings indicate that SCFAs may be used therapeutically as cheap and selective PPARγ modulators.
Recall that from earlier posts, I am already on the look out for selective PPARγ modulators (like Tangeretin)

Increased intake of dietary carbohydrate that is fermented in the colon by the microbiota has been reported to decrease body weight, although the mechanism remains unclear. Here we use in vivo11C-acetate and PET-CT scanning to show that colonic acetate crosses the blood–brain barrier and is taken up by the brain. Intraperitoneal acetate results in appetite suppression and hypothalamic neuronal activation patterning. We also show that acetate administration is associated with activation of acetyl-CoA carboxylase and changes in the expression profiles of regulatory neuropeptides that favour appetite suppression.

Tregs and Allergies

Fortunately some researchers have indeed looked at Tregs and allergies, but they did not seem to know about SCFAs.

T regulatory cells: an overview and intervention techniques to modulate allergy outcome.


Dysregulated immune response results in inflammatory symptoms in the respiratory mucosa leading to asthma and allergy in susceptible individuals. The T helper type 2 (Th2) subsets are primarily involved in this disease process. Nevertheless, there is growing evidence in support of T cells with regulatory potential that operates in non-allergic individuals. These regulatory T cells occur naturally are called natural T regulatory cells (nTregs) and express the transcription factor Foxp3. They are selected in the thymus and move to the periphery. The CD4 Th cells in the periphery can be induced to become regulatory T cells and hence called induced or adaptive T regulatory cells. These cells can make IL-10 or TGF-b or both, by which they attain most of their suppressive activity. This review gives an overview of the regulatory T cells, their role in allergic diseases and explores possible interventionist approaches to manipulate Tregs for achieving therapeutic goals.

Regulation of Inflammation by Short Chain Fatty Acids

Here is a very good paper from Brazil, for those who need more convincing.

Short chain fatty acids (SCFAs), which are the major metabolic products of anaerobic bacteria fermentation, have been suggested to be the link between microbiota and host tissues. The concentration of these fatty acids in the GI tract and blood may predispose to or prevents pathological conditions such as IBD, cancer and diabetes. Modifications in the concentrations or the ability of host
tissues to use SCFAs have been described in these conditions.

Mode of action of SCFAs

If anyone is interested in how SCFAs work their tricks, this is what they say in Brazil:

The main mechanism described for these effects is the attenuation of HDAC activity. Among the SCFAs, butyrate is the most potent, whereas acetate is the least potent inhibitor of HDAC.
This enzyme, together with the histone acetyltransferases (HAT), controls the degree of protein acetylation. By inhibiting the HDAC activity, SCFAs increase the acetylation of histone and non histone proteins including NFκB, MyoD, p53 and N-FAT [57] and, consequently, modulate gene

The production of prostaglandin E2 (PGE2) is also modified by SCFAs. These fatty acids stimulated the in vitro production of this eicosanoid by human monocytes [58]. In accordance with this result, induction of PGE2 production was observed three hours after intraplantar injection of SCFAs and LPS in rat paws [34]. PGE2 has been considered an anti-inflammatory prostanoid due to its ability to attenuate the production of IL-1β and TNF-α by macrophages and Th1 differentiation. However, there is now evidence in favor of a pro-inflammatory action of this molecule [59]. PGE2, through activation of its receptor EP4, facilitates Th1 differentiation and Th17 expansion, two subsets of T helper involved in immune inflammation [59,60]. Considering these findings, SCFAs may also affect T cell differentiation.

In addition to the classical eicosanoids, such as PGE2, other lipid mediators are also generated from polyunsaturated fatty acids including lipoxins, resolvins, protectins and maresins [61]. Despite their relevance to the resolution of the inflammatory process [61], at the moment, no study has been conducted in order to investigate the effect of SCFAs on the production of these lipid mediators.

Anti-inflammatory actions of SCFAs have been also observed in neutrophils. Acetate, propionate and butyrate at 30 mM reduce TNF-α production by LPS-stimulated human neutrophils [62].

Propionate and butyrate inhibit the expression of pro-inflammatory mediators (TNF-α, CINC-2αβ and NO) in rat neutrophils, an effect that seems to involve attenuation of NF-κB activation [21].

Microglial cells are resident immune cells of the central nervous system (CNS). Activation of these cells leads to production of several inflammatory mediators (e.g., cytokines and NO) that participate in the defense reaction of the CNS against insults including microorganisms and damaged cells [63].
Chronic or excessive activation of these cells has detrimental effects on the CNS and seems to be involved in the initiation and progression of neurodegenerative diseases including Alzheimer and Parkinson’s disease. In spite of some controversy about the effect of SCFAs on microglial production of inflammatory mediators [52,53], most of the studies indicate that these fatty acids attenuate microglial activation, an effect that seems to involve HDAC inhibition [53,54]. These observations and the data obtained in vivo [64] support the proposition that SCFAs and other inhibitors of HDAC may be useful in preventing inflammation in the CNS. Indeed, Kim et al. [64] have shown that butyrate, valproic acid and trichostatin A (all inhibitors of HDAC activity) present antineuroinflammatory and neuroprotective effects in the ischemic brain of rats.

Effectors Mechanisms of Phagocytes

Once in the inflammatory site, neutrophils and macrophages internalize, kill and digest bacteria and fungi through mechanisms including production of reactive oxygen species (ROS) and release of granule enzymes. SCFAs affect the production of ROS and the phagocytic capacity of phagocytes.

This effect is important in the course of anaerobic bacteria infection. Both inhibition [65,66,68] and stimulation [4,68] of neutrophil phagocytosis by SCFAs have been described. In macrophages, butyrate reduce the phagocytic activity, an effect that probably arises from its inhibitory action on cell differentiation and maturation [69].

The effects of SCFAs on ROS production by neutrophils remain controversial. Some groups have found that SCFAs induce ROS production [4,70,71], whereas others have shown inhibition [65,67,72–74].

The discrepancy in the results obtained may be explained by differences in the protocols used such as the concentrations of SCFAs, measurement of ROS by using different methodologies (e.g., lucigenin-amplified chemiluminescence or reduction of cytochrome c), stimuli (e.g., PMA or fMLP), solution pH, source and state of neutrophil activation (e.g., neutrophils isolated from human blood or elicited rat neutrophils).

3.3. Lymphocyte Activation and Response

Lymphocytes are involved in the adaptive immune response. These cells display membrane receptors that recognize a broad range of non-self antigens and allow them to generate specific responses to  liminate invading pathogens and infected or tumoral cells. SCFAs modify lymphocytes function as follows:

T-cell proliferation: butyrate inhibits lymphocyte proliferation in response to several stimuli including concanavalin-A and immobilized anti-CD3 monoclonal antibody [41,75].
Production of cytokines: incubation of lymphocytes with butyrate reduces the production of interleukin-2; this cytokine stimulates growth, differentiation and survival of antigen-selected
T-lymphocytes, and interferon-γ (IFN-γ) after stimulation with concanavalin-A or anti-CD3 and anti-CD8 [76,77]. This latter cytokine is particularly important in response to viral infection, tumor cells and in auto-immune conditions. On the other hand, butyrate presents an opposite effect on the production of IL-10 by lymphocytes [75].
Production of regulatory T (Treg) cells: this subpopulation of T cells actively suppresses immune function and is considered an attractive target for the treatment of immunological and inflammatory pathologies. HDAC inhibitors enhance the production and suppressive function of regulatory T cells [77]. Considering that SCFAs, as previously described, also suppress the activity of HDAC, we hypothesize that these fatty acids may also exert their effects on inflammation and immune responses through regulation of this subset of T cells.


Within reasonable limits, short chain fatty acids (SCFAs) are good for you.

Particularly if you have an inflammatory condition or need to lose some weight.

You already produce them and some people would benefit from some more.

P.S. for the Diehards

Proprionic Acid (PPA) in Rats

There is also research indicating that injecting large amounts of one particular SCFA, Propionic acid into the brains of rats does them no good at all.  In fact the opposite of all the good things notes by the Brazilians and others.

Having read an awful lot of autism research, I have to point out that sometimes a little of what does you harm, can actually do you some good.  For example the Valproate mouse model of autism is based on feeding Valproic Acid to the female mouse to make her pup be born with autistic features.  Yet the same drug Valproic Acid, in lower doses, is an effective treatment for autism with seizures in humans.
In pregnant humans the risk of Valproate is slightly different.  According to Harvard:-

Valproate. It’s best to avoid taking valproate (Depakote) during pregnancy, especially during the first trimester, as this drug increases the risk of neural tube defects such as spina bifida. Risk increases with dose. In absolute terms, researchers estimate that one to six babies out of every 100 exposed to valproate in the first trimester of fetal development are born with some type of neural tube defect.



Clinical observations suggest that certain gut and dietary factors may transiently worsen symptoms in autism spectrum disorders (ASD), epilepsy and some inheritable metabolic disorders. Propionic acid (PPA) is a short chain fatty acid and an important intermediate of cellular metabolism. PPA is also a by-product of a subpopulation of human gut enterobacteria and is a common food preservative. We examined the behavioural, electrophysiological, neuropathological, and biochemical effects of treatment with PPA and related compounds in adult rats.

Intraventricular infusions of PPA produced reversible repetitive dystonic behaviours, hyperactivity, turning behaviour, retropulsion, caudate spiking,
and the progressive development of limbic kindled seizures, suggesting that this compound has central effects. Biochemical analyses of brain homogenates from PPAtreated rats showed an increase in oxidative stress markers (e.g., lipid peroxidation and protein carbonylation) and glutathione S-transferase activity coupled with a decrease in glutathione and glutathione peroxidase activity. Neurohistological examinations of hippocampus and adjacent white matter (external capsule) of PPA treated rats revealed increased reactive astrogliosis (GFAP immunoreactivity) and activated microglia (CD68 immunoreactivity) suggestive of a neuroinflammatory process. This was coupled with a lack of cytotoxicity (cell counts, cleaved caspase 3_ immunoreactivity), and an increase in phosphorylated CREB immunoreactivity. We propose that some types of autism may be partial forms of genetically inherited or acquired disorders involving altered PPA metabolism. Thus, intraventricular administration of PPA in rats may provide a means to model some aspects of human ASD in rats.

The short chain fatty acids (SCFAs) acetate (C2), propionate (C3) and butyrate (C4) are the main metabolic products of anaerobic bacterial fermentation in the intestine. In addition to their important role as fuel for intestinal epithelial cells, SCFAs modulate different processes in the gastrointestinal (GI) tract such as electrolyte and water absorption. These fatty acids have been recognized as potential mediators of the effects of the gut microbiota on intestinal immune function and gut-brain axis interaction [4]. Recently it was reported that the three types of SCFAs (acetate, propionate, and butyrate) reduce the production of proinflammatory factors, including TNF-α, IL-1β, IL-6, and NO. Additionally, SCFAs enhance the production of the anti-inflammatory cytokine IL-10 in low concentrations (1–1,200 μmol/L) [5].
In spite of the protective effects of SCFAs, propionic acid (PPA) neurotoxicity was recently demonstrated via intraventricular direct infusion into rat brains [6], passage from the gut to the brain in the case of acute PPA orally administered to rat pups [7] or Chronic administration on postnatal days 5–28 [8] and, most recently, subcutaneous injection once a day (500 mg/kg) in pregnant rats on gestation days G12–16 [9].

I am very much minded to go with Wendy, the Brazilians and the Egyptians (who found Trep low in autism). 

I think the Saudis, with their PPA-neurointoxicated rats, are barking up the wrong tree.

In fact, the Saudis say that PPA is low in humans with autism.

Low SCFAs, like PPA, help produce low Trep, which helps produces high IL-6 and low IL-10, just as I expect to find in autism.

Friday, 27 March 2015

Antibiotics and Autism(s) – Pass the Bacteroides Fragilis?

Today’s post allows me to cross off several topics from my to-blog list, since I can link them all together.

N = 1 or N > 1

If you are the parent of one of more children with autism, you will have a very specific view of autism, since your kind is the only kind that affects you.  This is natural and so for most readers it is case of N = 1.

When it comes to everyone else, and what they (should) teach medical students, it is the big picture that matters.  So large clusters of people behaving in a certain way is more significant that any outliers.  If you are the outlier, this is not much consolation.

In the world of autism, rather strangely, it is the very rare types that have an established medical therapy.  This ranges from the types caused by rare metabolic disorders to the more common PANDAS/PANS.

The large cluster that is classic autism remains untreated.

Polypill N = 3

To date I am aware of only a handful of people who have implemented the majority of my suggested Polypill for classic autism.  Three parents found major improvements and one found no impact; but the no impact case was not classic autism, it was very late regressive autism, later diagnosed as mitochondrial disease.

Many parents have implemented 1-2 elements of the Polypill with good results; these usually are elements that are the non-prescription drugs.

Three is not many, but it is more significant than one; and three out of four is a pretty good success rate.

As it stands, the Polypill will be a therapy for some children whose parents happen to be doctors, or own a pharmacy.

What does this have to do with antibiotics?

The other day I wrote a post about a recent 6 month clinical trial of Minocycline, an antibiotic.  The hope was that drug would reduce microglial inflammation and improve autism; but it did not.

Then I received a comment from Seth, a regular reader of this blog, to say that in his son tetracycline antibiotics really do improve autism.

I just read about John, another Dad, who found his child’s autism improved greatly while on antibiotics.  He has started his own charity N of One (N = 1) to raise funds for autism research and published an account of what he noticed.

There are many other accounts of certain antibiotics improving certain people’s autism.

In the case of PANDAS/PANS antibiotics are just the initial part of the therapy, but unless you live in the US you are unlikely to get diagnosed with PANDAS/PANS, let alone treated for it.

I will not be able to solve this puzzle today, but I will make my observations, for what they are worth.

First of all, Seth is talking about tetracycline-class antibiotics, one of which is Minocycline, the subject of that six month autism trial.  Now as we saw in a recent post, that trial was deemed a failure, but that was a trial of 10 children with regressive autism.  

Note that what people mean by "regressive autism" varies widely; most autism has some degree of regression.  In classic autism, the person is born different and then gradually becomes more evidently "autistic" during early childhood. Regressive autism, as defined by Chez, is when things are normal for at least the first 12 months.  Language can be normal or abnormal and then lost.  

I should also highlight that are other reports of Minocycline being beneficial in Schizophrenia and other neurological disorders.


Pharmacological interventions to treat psychiatric illness have previously focused on modifying dysfunctional neurotransmitter systems to improve symptoms. However, imperfect understanding of the aetiology of these heterogeneous syndromes has been associated with poor treatment outcomes for many individuals. Growing evidence suggests that oxidative stress, inflammation, changes in glutamatergic pathways and neurotrophins play important roles in many psychiatric illnesses including mood disorders, schizophrenia and addiction. These novel insights into pathophysiology allow new treatment targets to be explored. Minocycline is an antibiotic that can modulate glutamate-induced excitotoxicity, and has antioxidant, anti-inflammatory and neuroprotective effects. Given that these mechanisms overlap with the newly understood pathophysiological pathways, minocycline has potential as an adjunctive treatment in psychiatry. To date there have been promising clinical indications that minocycline may be a useful treatment in psychiatry, albeit from small trials most of which were not placebo controlled. Case reports of individuals with schizophrenia, psychotic symptoms and bipolar depression have shown serendipitous benefits of minocycline treatment on psychiatric symptoms. Minocycline has been trialed in open-label or small randomized controlled trials in psychiatry. Results vary, with findings supporting use in schizophrenia, but showing less benefit for nicotine dependence and obsessive-compulsive disorder. Given the limited data from rigorous clinical trials, further research is required. However, taken together, the current evidence suggests minocycline may be a promising novel therapy in psychiatry.

Minocycline is not just an antibiotic; it has several other known modes of action.

Minocycline is the most lipid-soluble of the tetracycline-class antibiotics, giving it the greatest penetration into the prostate and brain, but also the greatest amount of central nervous system (CNS)-related side effects, such as vertigo.

In various models of neurodegenerative disease, minocycline has demonstrated neurorestorative as well as neuroprotective properties
Minocycline is also known to indirectly inhibit inducible nitric oxide synthase (NOS).

As an anti-inflammatory, minocycline inhibits apoptosis (cell death) via attenuation of TNF-alpha, downregulating pro-inflammatory cytokine output.

Early research has found a tentative benefit from minocycline in schizophrenia


The antibiotic that John (from N=1) found to have magical properties was Amoxicillin, a very common type of penicillin.  Amoxicillin is a standard therapy for a strep throat.

Streptococcal infections are the initial trigger for PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections)

Amoxicillin seems to be have just one mode of action, that of an antibiotic.  This means it is a type of antimicrobial used specifically against bacteria, and usually used in medical treatment of bacterial infections. Antibiotics may either kill or inhibit the growth of bacteria.

          From the US National Institute of mental Health  (NIMH):-

Can penicillin be used to treat PANDAS or prevent future PANDAS symptom exacerbations?

Penicillin and other antibiotics kill streptococcus and other types of bacteria. The antibiotics treat the sore throat or pharyngitis caused by the strep by getting rid of the bacteria. However, in PANDAS, it appears that antibodies produced by the body in response to the strep infection are the cause of the problem, not the bacteria themselves. Therefore one could not expect antibiotics such as penicillin to treat the symptoms of PANDAS. Researchers at the NIMH have been investigating the use of antibiotics as a form of prophylaxis or prevention of future problems. At this time, however, there isn't enough evidence to recommend the long-term use of antibiotics.

However, a quick “google” will show more n=1 cases, of people claiming their child’s autism/PANDAS improving on Penicillin and then regressing again afterwards.


The other antibiotic that has been researched in autism is Vancomycin.  This drug is not absorbed from the intestine, so for systemic therapy it has to be taken by injection.  

When given orally it is used for things like treating bacterial infections of the intestines that cause colitis.  Orally administered vancomycin is recommended as a treatment for intestinal infection with Clostridium difficile, a common side effect of treatment with broad-spectrum antibiotics.

Vancomycin was first isolated in 1953 at Eli Lilly, from a soil sample collected from the interior jungles of Borneo by a missionary.

In most cases symptoms of autism begin in early infancy. However, a subset of children appears to develop normally until a clear deterioration is observed. Many parents of children with "regressive"-onset autism have noted antecedent antibiotic exposure followed by chronic diarrhea. We speculated that, in a subgroup of children, disruption of indigenous gut flora might promote colonization by one or more neurotoxin-producing bacteria, contributing, at least in part, to their autistic symptomatology. To help test this hypothesis, 11 children with regressive-onset autism were recruited for an intervention trial using a minimally absorbed oral antibiotic. Entry criteria included antecedent broad-spectrum antimicrobial exposure followed by chronic persistent diarrhea, deterioration of previously acquired skills, and then autistic features. Short-term improvement was noted using multiple pre- and post-therapy evaluations. These included coded, paired videotapes scored by a clinical psychologist blinded to treatment status; these noted improvement in 8 of 10 children studied. Unfortunately, these gains had largely waned at follow-up. Although the protocol used is not suggested as useful therapy, these results indicate that a possible gut flora-brain connection warrants further investigation, as it might lead to greater pathophysiologic insight and meaningful prevention or treatment in a subset of children with autism

What is going on?

The truth is that nobody knows for sure what is going on.  That also applies to PANDAS & PANS, which is why most of the world does not recognize them as genuine diagnosable conditions.

It would seem to me that various different processes are likely involved.  It would not be so hard to do some detective work, on a case by case basis.

For example, both Seth and John were using broad spectrum antibiotics.  If they gave Vancomycin a quick trial, they would find out if the problem was in the intestines, since that is the only place oral Vancomycin can have an effect.

John has written in his paper all about possible changes to the gut microbiome and how repeated antibiotic use early in life could set the stage for the development of autism in some children.  It is very easy to test this hypothesis, just try some Vancomycin.

We know that ulcerative colitis is comorbid with autism.  We know that this will lead to a permeable gut and the flow of unwanted substances to other parts of the body.  We see that Vancomycin is used for treating bacterial infections of the intestines that cause colitis.

So it is no surprise that in some people with autism, Vancomycin will improve behaviors.  You just need to identify which people.

Once apparent that Vancomycin is indeed effective, at least you know where the problem is.  Then it is a question of finding long term solutions to manage the problem.

We already know much about the so-called “leaky-gut” and the many GI problems in autism.  This is very well covered on the SFARI site and blog, so here are some highlights from there.

The new study is the first to show that maternal infection alters the microbiome in the offspring. The finding is significant for autism, as many children with the disorder are plagued by gastrointestinal problems, including diarrhea, vomiting and stomach discomfort. 

Leaky gut is also reported in children with autism and is associated with several other disorders, such as inflammatory bowel disease and Crohn’s disease, and perhaps with Alzheimer’s and Parkinson’s diseases, says Sarkis Mazmanian, professor of biology at the California Institute of Technology.To diagnose leaky gut in the mouse pups, the researchers fed them a carbohydrate molecule attached to a fluorescent molecule. The molecule later turned up in their blood, showing it had escaped through the gut wall. The mice also showed elevated gut levels of an immune molecule called interleukin-6 (IL-6) — a prime suspect in mediating the effects of maternal infection

The researchers then treated the mice with B. fragilis. This strain of bacteria isn’t commercially available, but exists naturally in about 20 percent of the human population. 
Mice treated with B. fragilis at 3 weeks of age don’t have a leaky gut five weeks later, their levels of blood 4EPS and gut IL-6 plummet, and the assortment of bacterial species in the gut reverts to something closer to that of control mice. And the mice do better behaviorally: They stop obsessively burying marbles in their cages, become as vocal as controls and are less anxious.

Sarkis K. Mazmanian, Ph.D.California Institute of Technology
Most research into autism spectrum disorders has focused on genetic, behavioral and neurological aspects of the illness, but people with autism also show striking alterations in immune status.

What’s more, a significant subset of children with autism spectrum disorders show chronic intestinal abnormalities, such as loose stool and altered bacterial microbiota (the collection of beneficial bacteria within the intestine). Antibacterial treatments are reported to provide behavioral improvements in some cases.

In addition, many children with autism have been diagnosed with food allergies and are on special diets. Societal advances (including 'Western' diets and antibacterial products) may have paradoxically compromised human health by reducing our exposure to health-promoting gut bacteria.

The connection between gut bacteria, intestinal disease and autism is a promising area of investigation. Sarkis Mazmanian and his team at the California Institute of Technology used mouse models that show autism-like features to evaluate the efficacy of probiotics.

They found that specific probiotic bacteria ameliorate autism-like behaviors in both environmental models of ‘induced’ disease (by mimicking viral infection of the mother during gestation), as well is in two genetic models of autism spectrum disorder.

These studies are an important step in furthering research that addresses the connection between the gut microbiome and altered behaviors, a link suggested by studies in humans. Finally, Mazmanian’s findings may help validate the use of probiotics as a safe and effective treatment for autism when it is accompanied by gastrointestinal abnormalities.

What it means?

It certainly appears that some people with ASD and GI problems have a something similar going on to my case of “N=1” (ASD + pollen allergy).  An allergic reaction has caused mast cells to degranualate releasing histamine and  IL-6.  That histamine causes further release of IL-6 elsewhere.  IL-6 is a pro-inflammatory cytokine and “public enemy number one” in the case of autism flare-ups.

It does appear that some people with autism + GI problems improve somewhat with supplemental digestive enzymes, like Creon/Kreon.  This does appear to be the basis of CM-AT, the long awaited therapy from Curemark.

However, based on feedback from this blog, it appears that blocking the calcium channel Cav1.2 with Verapamil may be even better.  It will certainly be much cheaper.

The standard treatment for this type of allergy related GI problem, is Cromolyn Sodium, a mast cell stabilizer.  Verapamil is also a mast cell stabilizer, among other properties.
Interestingly, some people “do grow out” of some allergies.  I myself, as a child, was prescribed Intal (Cromolyn Sodium) for GI problems of unknown origin.
You will find countless reports on the internet of children with “autism” who, on various diets, “recovered”.  You will hear plenty of people saying that young children will “grow out of” their autism.  It is generally accepted that most people’s autism does moderate as they become adults, just like many people’s asthma.
There is some sense in all of this.  Allergies can seriously aggravate autism.  So if you have someone with very mild autism, but a severe allergy, when you control the allergy you will see dramatic behavioral improvement.
Some readers of this blog have found that common allergy treatments like Zyrtec (cetirizine), have a profound behavioral improvement on their child, who was supposedly allergy-free.
In “my” subgroup of classic autism one underlying problem appears to be a channelopathy (Cav1.2); this might be genetic, or it might be an “epigenopathy”.  In either case, you could detect it, with existing technology, if you really wanted to.

The clever people at the NIMH think that PANDAS/PANS is a kind of Rheumatic Disease, where an autoimmune disorder (triggered by strep throat infections) causes the body to produce antibodies against the invading bacteria, and the antibodies help eliminate the bacteria from the body. However in a rheumatic disease, the antibodies mistakenly recognize and may attack the heart valves, joints, and certain parts of the brain.  When they attack the joints it is called Rheumatic Arthritis, when they attack the brain it is now called PANDAS.
The NIMH thinks that PANDAS/PANS is distinct from autism.
If you regularly read the research in this blog, you may disagree with the NIMH and see that PANDAS/PANS is just another autism variant.  Likely many things, other than strep infections, can also trigger this over-active immune system.
Many strange things occur in autism, one being that adults apparently cannot have PANDAS.  Of course they can; it just would have to be called ANDAS.
If an adult with autism wants to check for some rare for metabolic disorders leading to “autism” he/she may need to get referred to a children’s hospital, like Arkansas Children’s Hospital.  All the while, some of their diagnoses/treatments continue to be regarded as quackery by many other clinicians.
Some people with Schizophrenia, who improved on Minocycline, should try Vancomycin.  If the benefit is lost (as I suspect, it will be), then we would know that the effect was elsewhere than in the intestines.
Having established that Minocycline had no benefit in children with regressive autism, perhaps Johns Hopkins and NIMH should trial it in early-onset autism (classic autism).  It is Johns Hopkins after all, who believe that regressive autism is primarily mitochondrial disease.  The research indicates that mitochondrial disease is but one feature of classic autism.
Vancomycin is a useful diagnostic tool, rather than a long term therapy, but if Vancomycin improves behaviour, then you have plenty of choices:-
·        Cromolyn Sodium
·        Verapamil
·        Digestive enzymes like Creon/Kreon and, eventually, CM-AT
·        Probiotics & Prebiotics  (one day even Bacteroides Fragilis)
·        Exclusion diets

So if your child improves after taking antibiotics, or anything else, my suggestion is to investigate it yourself, rather than found yet another autism charity.
There is actually plenty of existing research and clever people, like those at the Simons Foundation, are funding further work on a prolific basis.
Other than readers of the SFARI blog and the Questioning Answers blog, is anyone actually reading (nearly) all this research? (let alone applying it)   Evidently not.
The academic researchers just read narrowly around their very focused area of interest.  The majority of clinicians read almost none of the research.

If you want to solve a complex problem, collect all the available data, look for connections and then think about it.
You should not have to do this for yourself, but with autism you do.