The Gut Microbiome is the Next Target for Autism Therapies

autism microbiome

An increasingly detailed and interconnected body of scientific literature is establishing the connection between the pathology of autism spectrum disorder (ASD) and the gut microbiome, leading some to wonder whether manipulation of the gut microbiome can alleviate ASD symptoms. In recent years, a number of studies have clarified the mechanisms behind the gut microbiome’s role in ASD presentation and spurred researchers to investigate possible treatment options specifically targeting the gut microbiome. This growing body of research is now opening up the door to more effective therapies, potentially allowing people with ASD to find relief from symptoms that conventional treatments have not resolved.

Connecting Autism to Aberrant Gut Microbiomes

Between 2015 and 2016, Drs. Richard Frye, John Slattery, and Derrick MacFabe of the Arkansas Children’s’ Hospital Autism Research Program published a trio of studies that sought to clarify the relationship between ASD and the gut microbiome. A number of researchers had examined this relationship prior to Frye, Slattery, and MacFabe’s experiments, producing promising data indicating that the proportions of bacterial populations within the GI tract of ASD patients could impact ASD symptoms. However, the underlying mechanism of this phenomenon remained unclear. As such, Frye, Slattery, and MacFabe aimed to further elucidate the links between bacterial population proportions, mitochondria, and ASD symptoms and examine potential treatment avenues based on their findings.

In 2015, the group examined the mitochondria within the GI tracts children with and without ASD to determine whether there were observable differences in mitochondrial function between them. This study successfully established several specific metabolic mechanisms by which gut microbiota might cause mitochondrial changes and, thus, cause physiological changes. Not only were the associations between mitochondrial dysfunction, ASD, and GI pathologies confirmed, but the researchers found that these associations were due an overrepresentation of the Clostridia genus of bacteria in ASD patients’ gut microbiomes.

The Clostridia genus of bacteria produces the fatty acid propanoic acid (PPA) as a result of fermentation, one of the processes by which bacteria metabolize nutrients. GI-tract mitochondria are negatively influenced by high concentrations of PPA, explaining some of the GI issues commonly experienced by patients with ASD. This is because PPA acts as a regulator for a wide variety of mitochondrial genes, meaning that exposure to PPA causes mitochondria to function at lower efficiencies, causing adverse physiological changes in the GI tract. By connecting Clostridia over-representation and mitochondrial dysfunction, the study proves that the microbiome’s proportion of Clostridia was an important clinical factor for ASD symptoms.

With these findings confirmed in the clinical trial cohort of children with ASD, the researchers then shifted their attention to experiments using animal models of ASD to further investigate the relationship between PPA and ASD symptomatology. Prior to initiation of their investigations, Frye, Slattery, and MacFabe had worked for over 15 years to develop and validate these animal models so that they could follow up on the results of experiments performed using human subjects more invasively. Through their animal model experiments, the researchers found that:

  • Malfunctional mitochondria in the GI tract lead to high concentrations of PPA
  • High concentrations of PPA in the GI tract lead to higher concentrations in the brains of animal models
  • High concentrations of PPA in the brain lead to ASD-like symptoms in the animal models of autism
  • Providing Clostridia genus bacteria with an alternative nutrient source lowers concentrations of PPA
  • Lower concentrations of PPA in the GI tract allow for normal mitochondrial function
  • Normal mitochondrial function leads to fewer GI symptoms in ASD animal models

As a result, Frye, Slattery, and MacFabe were able to identify a set of potential PPA producers within the gut microbiota that might be responsible for ASD-related GI issues via their influence on mitochondria.

Following Up on the PPA Hypothesis

As a result of their experiments, the research group was able to add further confirmation to what is known in the ASD research community as “the PPA hypothesis.” The PPA hypothesis is a core theory explaining the relationship between gut microbiota and ASD GI symptoms. As described by Frye, Slattery, and MacFabe in their 2016 paper, “the PPA theory of ASD suggests that ASD may be a result of disturbances in the enteric microbiome resulting in the production of elevated levels of PPA in genetically susceptible individuals during a critical neurodevelopmental period.” Though the PPA hypothesis predated Frye and Slattery’s experiments, their findings filled critical holes in the hypothesis and contributed invaluable evidence in support of it.

To investigate further, Frye, Slattery, and MacFabe used the PPA hypothesis as an investigational framework to review currently used, but not comprehensively understood, treatments that manipulate the microbiome in patients with ASD. These included:

  • Antibiotics
  • Antifungals
  • Probiotics
  • Specialty Diets
  • Digestive Enzymes
  • Vitamins
  • Fecal Microbiota Transplantation (FMT)

PPA concentrations were used as core metrics indicating whether a therapy might be clinically useful. As a result of their investigation, they suggested several treatments that should be examined further. In particular, FMT and probiotics were singled out as the two most promising—but least investigated—avenues for treating ASD-related GI issues by altering the gut microbiome to remove PPA-producing colonies.

Gut Microbiota Can Be Altered to Produce Symptom Relief In ASD

Frye, Slattery, and MacFabe’s piqued the interest of the research community, including a clinical trial group led by Dr. D.W. Kang. In order to further investigate the effects of microbiome manipulation on ASD symptoms, Dr. Kang’s group conducted a study in which the entire gut microbiome of pediatric ASD patients would be removed and then replaced with a probiotic and fecal transplant product. Referred to as Microbiota Transfer Therapy (MTT), the protocol incorporates probiotics into a customized and replicable fecal transplant product with the goal of providing long-lasting relief from ASD symptoms.

Following MTT, ASD patients’ parents reported that their children experienced reduction of abdominal pain and other GI symptoms by as much as 82% over the course of the treatment protocol, with 89% of the study cohort responding positively to the treatment. However, symptom reduction was not confined to GI symptoms; parents also reported improvements in ASD-related behavioral disturbances. Though Dr. Kang’s study wasn’t blinded, controlled, or randomized, it nonetheless suggests that ASD is treatable via GI interventions designed to manipulate the microbiome and that these interventions can effectively alleviate a broad spectrum of symptoms.

While MTT is a promising treatment, it is also an intensive one. There is, however, evidence that suggests that less invasive means of microbiome manipulation could produce similar results. In 2014, a study by Dr. MacFabe found that certain biologically-produced molecules like butyric acid can act as regulators of critical genes within the cells of the GI tract. This causes behavioral changes that could mitigate the effects of PPA. However, butyric acid may also have additional benefits. MacFabe found that in vitro butyric acid exposure altered cells’ genetic regulation of a critical protein, tyrosine hydroxylase, an enzyme which is responsible for making many of the precursors to neurotransmitters implicated in ASD symptomatology like dopamine. As such, butyric acid’s impact on cells in vivo in the GI tract may mean that butyric acid supplementation could impact multiple behavioral ASD symptoms.

If butyric acid’s impact on tyrosine hydroxylase can be clarified via future research, it may be possible to identify which symptoms supplementation can most effectively target. As the research stands, butyric acid supplementation is an intriguing intervention that could provide symptom relief similar to that of more invasive MTT and FMT, making therapeutic microbiome manipulation far more accessible and comfortable.

Foundational Medicine Review is dedicated to exploring evidence-based  treatment options for addressing symptoms of Autism Spectrum Disorder and gastrointestinal disorders. Join our mailing list for monthly updates on the latest news and research.

Works Cited

Frye RE, Rose S, Slattery J, Macfabe DF. 2015. Gastrointestinal dysfunction in autism spectrum disorder: the role of the mitochondria and the enteric microbiome. Microbial Ecology in Health & Disease. 26(1).

Frye RE, Slattery J, Macfabe DF, Allen-Vercoe E, Parker W, Rodakis J, et al. 2015. Approaches to studying and manipulating the enteric microbiome to improve autism symptoms. Microbial Ecology in Health & Disease. 26(1).

Kang D-W, Adams JB, Gregory AC, Borody T, Chittick L, et al. 2017. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 5(10).

Nankova BB, Agarwal R, Macfabe DF, La Gamma EF. 2014. Enteric Bacterial Metabolites Propionic and Butyric Acid Modulate Gene Expression, Including CREB-Dependent Catecholaminergic Neurotransmission, in PC12 Cells – Possible Relevance to Autism Spectrum Disorders. PLOS ONE 9(8).

Slattery J, Macfabe DF, Frye RE. 2016. The Significance of the Enteric Microbiome on the Development of Childhood Disease: A Review of Prebiotic and Probiotic Therapies in Disorders of Childhood. Clinical Medicine Insights: Pediatrics. 10:91-107.

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