If your child has autism and also deals with stomach problems, constipation, or digestive issues, you already know how exhausting it can be to manage both at once. But here’s something that might reframe everything: those gut issues and those behavioral challenges may not be two separate problems. They might be connected.
That’s the core of what Dr. Rosa Krajmalnik-Brown, a researcher at Arizona State University, has spent years studying. And what her team has found is changing how scientists, physicians, and families think about autism.
First, What Is the Gut Microbiome? (And Why Should You Care?)
Think of your gut as a living ecosystem. Inside your intestines, there are trillions of tiny living organisms called microbes. Bacteria, fungi, and other microscopic life forms that have set up permanent residence in your digestive system. Collectively, this community is called the gut microbiome.
These microbes are not passengers. They are workers.
They help break down the food you eat. They produce vitamins your body needs. And, perhaps most surprisingly, they help produce chemicals that directly affect how you feel, think, and behave.
You’ve probably heard of serotonin, the chemical associated with mood and happiness. A significant amount of serotonin is made in the gut, and the microbes living there play a role in producing it. The same goes for dopamine, another chemical tied to focus, motivation, and reward. When your gut microbiome is off balance, the production of these chemicals can be thrown off too.
“The bacteria that live in our gut do amazing things for us,” Dr. Krajmalnik-Brown explains. “They’re our partners.”
She puts it simply: a good partnership makes you thrive while a struggling partnership can make daily life much harder.
What Does This Have to Do With Autism?
Research has consistently shown that many autistic individuals experience significant gastrointestinal problems. Constipation and diarrhea are common, and they tend to be dismissed or treated separately from autism-related symptoms. But Dr. Krajmalnik-Brown’s work suggests that dismissing them is a mistake.
When she and her team compared the gut microbiomes of autistic children with those of neurotypical children, two clear differences showed up. Autistic children had less diversity in their gut microbiomes, meaning fewer different types of microbes overall. And they were missing several beneficial microbes that play important roles in gut health and chemical production.
The question her team asked was not “what harmful bacteria do these kids have?” but rather “what good bacteria are they missing?” That shift in perspective, stemming from her background as an environmental microbiologist who had always seen microbes as allies rather than threats, turned out to matter a great deal.
The Trial That Got the World’s Attention
In a first-of-its-kind study, Dr. Krajmalnik-Brown’s team developed what they call Microbiota Transplant Therapy, or MTT. Here is what that means in plain terms:
First, participants received a short course of antibiotics to clear out the existing gut environment. Then, they underwent a bowel cleanse, similar to what you’d have before a colonoscopy. After that, they received gut microbes from a healthy donor over the course of eight weeks, essentially receiving a diverse, thriving microbial community to replace the depleted one.
The results were striking. At the end of treatment, participants’ gastrointestinal symptoms had improved by about 80%. Autism-related behaviors, measured by an independent evaluator using a standard rating scale, improved by 45%. When the research team followed up two years later, the improvements had held and in some cases continued to progress.
At the start of the study, 83% of participants were rated as having severe autism symptoms. Two years later, that number had dropped to 17%. Nearly half of participants scored below the threshold for an ASD diagnosis altogether.
Dr. Krajmalnik-Brown is careful to note that this was an early-stage study without a control group, meaning some of the effect could be a placebo response. Her team is now running a Phase 2 clinical trial to test this more rigorously. But the magnitude of what they observed was impossible to ignore.
The Stories Behind the Numbers
Because Dr. Krajmalnik-Brown works with biological samples in the lab rather than directly with families, she receives updates through study coordinators. One message she still remembers involved a child whose teacher had told his parents he would not be advancing to the next grade.
After the treatment, that same teacher called the parents back. “I don’t know what you did with your child,” she said, “but he is now socializing, talking with other kids, paying attention in class. He’s going to move on to the next grade.”
Another child, who had been featured in a local news segment, had moved from a specialized school setting into a general classroom. He was sleeping through the night and had stopped wetting the bed. In the interview, a reporter asked him what he wanted to be when he grew up. He said he wanted to be a doctor so he could take care of people.
“That was pretty amazing,” Dr. Krajmalnik-Brown says. “I was like, this is great. What we’re doing is changing lives.”
You Don’t Have to Start With a Transplant
Microbiota Transplant Therapy is the most intensive option Dr. Krajmalnik-Brown’s team has studied, and it is still in clinical trials. But there is a spectrum of ways to support gut health, from everyday choices to medical interventions.
Here is how she frames the options, from least to most intensive:
Diet is the starting point. What your child eats shapes which microbes survive and thrive in the gut. The challenge is consistency, but the impact is real.
Probiotics are supplements that introduce beneficial bacteria into the gut. They’re widely available and generally considered safe. The limitation, Dr. Krajmalnik-Brown notes, is that most commercially available probiotics are made from microbes whose natural home is dairy products, not the human gut. This is why taking them daily is important because they don’t tend to permanently change the gut environment.
Prebiotics are foods or supplements that feed the beneficial bacteria already in your gut. Think of them as fertilizer for your microbiome. They work best when the right microbes are already present to benefit from them.
Symbiotics combine probiotics and prebiotics together. Dr. Krajmalnik-Brown describes it as “sending the microbes with their lunch,” giving them a better chance of surviving and doing their job.
Antibiotics and antifungals, when prescribed by a physician, can address specific overgrowths of harmful microbes. The trade-off is that most antibiotics clear out helpful bacteria along with harmful ones, which is why some doctors recommend probiotics afterward.
Microbiota Transplant Therapy (MTT) is the most intensive option and is currently only available through clinical research. But it is the intervention that has produced the most dramatic results in Dr. Krajmalnik-Brown’s work.
Her consistent advice: start with what you can control at home, and work closely with your child’s physician before pursuing anything more involved. Every gut is different, and what helps one child may not help another.
A Note Directly to Autistic Adults
If you have dealt with stomach problems your entire life and felt like doctors did not take them seriously, Dr. Krajmalnik-Brown wants you to know you were right to notice. Gastrointestinal symptoms in autism are not incidental, and they are not minor. Constipation in particular can meaningfully disrupt the gut environment, affecting which microbes survive and which chemicals get produced.
You deserve to have those symptoms taken seriously, investigated, and addressed. If your current doctor has not engaged with your gut health in a meaningful way, it is worth asking specifically about it or seeking out a gastroenterologist.
What You Can Do Right Now
Dr. Krajmalnik-Brown’s message to families is grounded and practical. Nothing she recommends requires a clinical trial or a prescription to get started.
Watch for constipation and address it promptly. Pay attention to your child’s diet and lean toward variety where and when possible. Protect sleep and build in regular physical activity. And remember that stress affects the gut too, both for the child and for the caregiver. A calmer home environment, reasonable as that is to ask for, supports the gut-brain system in both directions.
“Try to be supportive,” she says, “because there’s also brain-gut interaction. When you’re stressed, you also affect your microbes.”
How to Get Involved
Dr. Krajmalnik-Brown’s team is actively running Phase 2 clinical trials and is always looking for families interested in participating. If you want to stay informed about new trials or apply to be considered:
Visit autism.asu.edu to learn about ongoing research and get on the notification list.
Visit gbat.com for information about Gut Brain Axis Therapeutics, the company Dr. Krajmalnik-Brown co-founded to advance clinical development and FDA approval for MTT.
If you are in the Phoenix area and want to learn more about diagnostic tools her team is developing, search for Autism Diagnostics or Analudos for information on a urine-based test that measures some of the key chemicals her research tracks.
