Stool Microbiome Testing in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a highly prevalent developmental disability, affecting 1 in every 36 children in 2020 according to the CDC. Concerningly, this is a sharp increase from the 1 in 150 prevalence in the year 2000. This begs the question: what is causing recent spikes in autism diagnoses? Interestingly, the etiology of autism is still relatively unknown, although it is thought to stem from an interaction between genetics and various environmental factors. 

Impact of Autism and Treatments Available

Autism has a definite impact on individuals’ quality of life, often impairing social interaction skills, delaying language development, and causing repetitive or restricted behaviors. Luckily, there are several interventions currently available to help reduce symptoms that may interfere with patients’ daily lives. 

Among these treatment strategies are: 

• Developmental approaches, such as speech therapy, occupational therapy, sensory integration therapy, and physical therapy
• Educational approaches specific to ASD children in schools
• Social-relational approaches, which focus on social skill development
• Psychological approaches, such as cognitive behavioral therapy

Current ASD Diagnosis

The earlier in development these treatments can be implemented, the better. More time with therapy and specialized approaches can truly benefit ASD patients, improving their function and quality of life. Unfortunately, confirmed autism diagnosis currently takes 3 to 4 years, with the average diagnosis being made at the age of 6. 

It is an ongoing process that entails assessment of a child’s development through screening tools, professional behavioral observation, and medical examinations. Unfortunately, the lengthy time frame to confirm an ASD diagnosis takes away time from children with autism who could be benefiting from treatment approaches and therapeutic methods earlier on in development.

The Gut-Brain Axis

You may be wondering what autism has to do with gut health. Within the past 10 years, expanding research has shown evidence for direct connection between the gut microbiota and the brain. This connection, termed the gut-brain axis, works via neuroimmune pathways and the enteric nervous system, the part of the nervous system that innervates the gut. The newly discovered gut-brain connection may be the missing piece in several gastrointestinal diseases with previously unknown etiologies, with Irritable Bowel Syndrome (IBS) being a key example. 

This link between the gut and the brain seems to also be involved in autism spectrum disorder. According to a July 2024 study by Qi et al. in Nature Microbiology, children with autism have been found by a body of scientific evidence to have delayed gut microbiome development and a different gut flora profile than neurotypical children. More specifically, this study found that there was a decrease in diversity of all resident GI tract organisms, including bacteria, archaea, and viruses in ASD children. Differences in abundance were found in 14 archaea, 51 bacteria, 7 fungi and 18 viruses. Autism spectrum disorder was consistently “the top factor accounting for the variation in both microbiome pathways and microbial genes.”

Stool Microbiome Testing

Multikingdom markers most consistently altered in ASD were identified by Qi et al., and ultimately, their analysis revealed a group of 31 organisms that could be used in a new stool microbiome-based diagnostic test. Importantly, these organisms remained altered in subjects with autism after correcting for dietary factors that also influence gut microbiome composition. Subjects were also diverse in ethnicity, lifestyle, and geographic location to account for other confounding factors. Ultimately, the panel has a sensitivity of 91% and a specificity of 73%, meaning that it has a low false positive rate. These results indicate potential for future clinical use of this test. 

The consequences of these findings can potentially be used to change the game of the lengthy ASD diagnosis process. Qi et al. state regarding further research, “prospective studies of genetic markers in combination with microbiome panels are needed to establish whether they can further elevate the diagnostic accuracy to predict ASD earlier for disease prevention.” Evidently, this diagnostic panel is still in its infancy, but it represents a promising future in utilizing the gut-brain axis for more efficient ASD diagnosis. 

Conclusions

The gut-brain axis is a relatively new link between neurological conditions and gastrointestinal health, particularly gut microbiome composition. Autism spectrum disorder has been found to be connected to certain markers in the gut flora, even when controlling for possible confounding factors such as diet and ethnicity. With this information, Qi et al. have assembled a 31-organism panel that can potentially be used to greatly shorten the diagnostic process of ASD, which can take several years. This can enhance the quality of life for patients with autism by allowing them to pursue treatment and therapy at an earlier developmental stage. 

Summary

Autism spectrum disorder has become increasingly prevalent since the early 2000s. Autism can have a significant impact on patients’ quality of life, affecting social skills, language, and activities of daily living. Although a wide range of treatments for ASD are currently available, it can take up to 4 years to obtain a confirmed diagnosis. 

However, a new link between autism and gut microbiome composition was recently discovered, and it could drastically improve the efficiency of the ASD diagnostic process. 31 organisms most strongly tied to ASD have been assembled into a panel and studied as a diagnostic tool. They were found to have a high sensitivity, and consequently a low false positive rate. This indicates high promise for this panel’s clinical use. However, future research is needed to study the associations between genetic markers and the microbiome panel and further assess its diagnostic accuracy in various populations.