Scientists Identify Connections Between Autism and the Gut Biome

After reanalyzing existing data, a multidisciplinary research team was able to identify a microbial signature in the gut microbiome that distinguishes autistic from neurotypical individuals.

Despite the volumes of existing research, there are still many unanswered questions about what causes autism spectrum disorder (ASD). While genetic factors and environmental triggers are thought to play a role in the development of ASD, scientists have also found associations between autism and disrupted communication between the gut and the central nervous system, known as the gut–brain axis (GBA). However, study results haven't been consistent.

Now, in a study initiated by the Simons Foundation's Autism Research Initiative (SFARI), a team of 46 computational biology, engineering, medicine, autism, and microbiome researchers from four continents have clarified the connection between the gut microbiome and autism.


"We wanted to address the constantly evolving question of how the microbiome is associated with autism, and thought, 'Let's go back to existing datasets and see how much information we may be able to get out of them,'" says co-corresponding author Gaspar Taroncher-Oldenburg, director of Therapeutics Alliances at New York University, in a press release.

To do this, the research team developed an algorithm and reanalyzed 25 previously published datasets. The data included information on the microbiome, diet, gene expression, and immune system responses of autistic and neurotypical participants. In addition, the algorithm matched pairs of autistic and neurotypical individuals by age and sex.

The team found that by using this computational approach, they were able to identify specific microbes that differ in abundance between participants with ASD and those without the disorder.

What's more, the team identified metabolic pathways associated with certain human gut microbes specific to autism. The scientists also observed these pathways in brain-associated gene expression profiles and the diets of autistic participants.

Moreover, the autism-specific microbes identified overlapped with those found in a 2019 study examining the benefits of microbiota transfer therapy for autistic people. The study authors say they have not previously observed this clear overlap between gut microbial and human metabolic pathways in autism.

"We were able to harmonize seemingly disparate data from different studies and find a common language with which to unite them. With this, we were able to identify a microbial signature that distinguishes autistic from neurotypical individuals across many studies," says study author Jamie Morton. "But the bigger point is that going forward, we need robust long-term studies that look at as many datasets as possible and understand how they change when there is a [therapeutic] intervention."

Study co-author Rob Knight, director of the Center for Microbiome Innovation at the University of California San Diego, adds, "Before this, we had smoke indicating the microbiome was involved in autism, and now we have fire. We can apply this approach to many other areas, from depression to Parkinson's to cancer, where we think the microbiome plays a role, but where we don't yet know exactly what the role is."

Still, while this study appears to show that microbiomes and metabolic pathways differ significantly between autistic and non-autistic individuals, the reasons why they are different remain unclear.


Some research suggests that picky eating habits associated with autism may impact gut microbiota. While contrasting studies say that diet is not related to gut biome differences in autistic people. Moreover, some scientists believe other factors, such as antibiotic use, may play a role in the differences.

In addition, a 2022 systematic review of research suggests that genetics, stress, specific medications, or other environmental factors may trigger changes in an autistic person's gut biome.


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