For years, researchers have been exploring the complex connections between the gut and the brain. This so-called “gut-brain axis” has become a hot topic in understanding everything from mood to memory. Now, a new study dives deep into this relationship to investigate how gut microbes may influence autism — not just through digestion or discomfort, but all the way up to brain function and behavior.
Conducted by researchers at the University of Southern California and UCLA, this study is one of the first to show how certain gut-produced chemicals are linked to brain activity and autism symptom severity in children.
Your gut is more than just a place where food is digested. It’s home to trillions of microbes that help break down nutrients, support the immune system, and produce chemicals that affect your brain. These chemicals, called metabolites, can travel through the bloodstream or communicate with the brain via the vagus nerve — a superhighway of signals running between your gut and your brain.
This gut-brain conversation is particularly interesting when it comes to neurodevelopmental conditions like autism spectrum disorder (ASD). People with autism often experience gastrointestinal (GI) issues, sensory sensitivities, and social-emotional challenges. Could the gut’s chemical messages be influencing how the brain works in autism?
To find out, researchers studied 84 children between the ages of 8 and 17 — 43 of whom had autism, and 41 who were neurotypical. Each participant provided a stool sample to analyze gut metabolites and completed a functional MRI (fMRI) scan while doing tasks related to emotion, sensory input, and social processing. The kids also completed a series of behavioral assessments that measured things like sensory sensitivity and emotional responses to disgust.
The scientists focused on a group of chemicals made from tryptophan — an amino acid found in foods like turkey, eggs, and cheese. Tryptophan is known for being the precursor to serotonin, but it can also be transformed by gut microbes into other important compounds, like kynurenate and indoles. Some of these compounds are protective to the brain; others can be harmful in high amounts.
Key Finding #1: Children with Autism Had Lower Levels of Protective Gut Metabolites
One standout result was that kids with autism had significantly lower levels of kynurenate (KA), a chemical produced in the gut that has neuroprotective qualities. This difference remained strong even when accounting for things like GI symptoms and diet.
Low KA levels have been linked to other neurological and psychiatric disorders as well, such as schizophrenia and depression. This suggests that gut microbes may not be producing enough of this helpful metabolite in some children with autism, which could impact how their brains develop and function.
Key Finding #2: Brain Regions Tied to Emotion and Sensation Showed Differences
The fMRI scans revealed that specific parts of the brain known to be involved in emotional regulation and sensory processing — particularly the insula and the cingulate cortex — showed different patterns of activity in children with autism. More importantly, the activity in these regions was connected to the levels of certain gut metabolites.
For example:
Children with lower levels of indolelactate (a gut-derived chemical) showed more activity in the mid-insula when viewing disgusting foods.
Kids who had lower levels of tryptophan betaine showed more activity in the mid-cingulate cortex when processing non-emotional facial expressions.
These regions of the brain are important for processing bodily signals and emotional reactions, and they’re commonly found to be different in individuals with autism.
Key Finding #3: Gut Metabolites, Brain Activity, and Behavior Are All Connected
Perhaps the most fascinating part of the study was that brain activity appeared to act as a “middleman” between gut chemistry and behavior. In technical terms, the brain mediated the relationship between gut metabolites and autism symptoms.
For instance:
Children with lower levels of indolelactate tended to have more severe autism symptoms, and this relationship was partially explained by heightened activity in the right mid-insula.
Similarly, the connection between tryptophan betaine levels and disgust sensitivity was mediated by the mid-cingulate cortex — a part of the brain linked to emotion regulation.
This suggests that gut chemicals could be influencing how brain regions involved in emotion and sensory processing function, which in turn may affect how children with autism respond to the world.
The Bigger Picture: Behavior, Sensory Sensitivities, and Sleep
Beyond brain scans and gut samples, the researchers also looked at how gut metabolites related to everyday behaviors. They found:
- Higher levels of tryptophol (another tryptophan-related chemical) were associated with increased sensory sensitivities, especially in how kids experienced movement and touch.
- Higher levels of anthranilate, a breakdown product of tryptophan, were linked to better sleep quality.
These findings hint that improving the gut environment might one day help with common challenges in autism, like sleep disturbances and sensory overload.
How Does Diet Play Into This?
It’s easy to jump to the conclusion that picky eating or restrictive diets in children with autism could explain these gut differences. However, this study looked at diet and found no significant differences between the two groups. The researchers were careful to control for dietary habits and still found the same patterns.
While food preferences may influence the gut microbiome in some cases, this study strengthens the idea that the relationship between autism and gut chemistry is more complex than just what’s on the plate.
Study Limitations and Future Directions
As exciting as these findings are, the study was observational — meaning it can’t prove cause and effect. We don’t yet know whether changes in the gut cause differences in brain activity, or if it’s the other way around, or whether a third factor influences both.
The sample size was also relatively small, and most participants were boys, reflecting the higher prevalence of autism in males but limiting generalizability. And while the researchers controlled for things like medication use and GI symptoms, more research is needed to understand the full picture.
Still, this study is a major step forward. It builds a stronger case for the gut-brain-behavior connection in autism and sets the stage for future research into whether modifying the gut microbiome — through diet, probiotics, or other interventions — could help manage symptoms.
What This Means for Parents and Caregivers
If you’re raising a child with autism, this study might leave you with more questions than answers — and that’s okay. The takeaway here isn’t that a probiotic will “fix” autism or that diet alone is the key. Rather, this research highlights that the body and brain are deeply interconnected. It also suggests that some of the sensory or emotional challenges seen in autism may have roots not just in the brain, but in the gut.
In time, this could open the door to new treatment approaches that support both mental and physical well-being in a more holistic way. But for now, the best course is to continue supporting your child with love, structure, and care — and to stay tuned as science continues to understand the intricate puzzle of autism better.
