Find a therapist to help with autism

A recent article challenges the validity of gut-autism research.

It can be hard to pin down causality in the gut-brain axis, but it may not even be necessary.

Microbes may not cause autism, but they can affect mood and anxiety.

Studies show that it is possible to lower anxiety levels in autistic kids with diet and supplements.

“When you have exhausted all possibilities, remember this: you haven’t.” — Thomas A. Edison

“When you have exhausted all possibilities, remember this: you haven’t.” — Thomas A. Edison

As a writer and a scientist, I have to say: writing is a lot easier than sciencing. In science, if you recommend a drug that doesn’t work, people may die. In writing, the worst that can happen is that people die of boredom. Fortunately, they usually revive.

For such a nerdy field, science can be surprisingly cutthroat. Witness a recent article that says gut-autism research is so bad they might as well just throw in the towel.

The article from the journal Neuron argues that the gut-autism axis is a house of cards built on lousy studies with inconsistent data. They assert that the studies are contradictory and that too much emphasis is placed on dubious mouse models.

They may have a point.

It is notoriously challenging to nail down microbial causes of disease—it is hard enough to simply identify a normal microbiome. Moreover, many of these studies were done with mice, and what exactly is an autistic mouse?

One of their strongest critiques is that the studies have causality backward: Instead of microbes causing autism, they posit that people with autism have strange diets that compromise their microbiome.

But this may be a straw man argument. Microbiome studies are particularly prone to this criticism because there is some inherent circularity in the gut-brain axis. Your diet will clearly alter your microbiome, but your microbes can cause cravings that alter your diet. The take-home is that when you change either your diet or your microbes, you can convert a vicious cycle into a virtuous one. It isn’t necessary to pin down causality in order to make an improvement.

More importantly, none of this research asserts that microbes cause autism. Rather, they find that changes in the microbiome can ameliorate certain symptoms. That seems uncontroversial and extremely useful. Let’s look at some of the studies.

The microbial connection

One study found an interesting connection between autism and microbes in the mouth. According to Kathy Kar-man Shum at the University of Hong Kong, there is a microbial signature of autism in the mouth microbiome. Simply by looking at oral microbes, the researchers can predict if a child will develop autism with 80 percent accuracy. That’s important for early identification and intervention, when therapy is most effective.

John Cryan and Ted Dinan of University College Cork in Ireland have published widely on a mouse model of autism and have found specific populations of gut bacteria that are associated with the syndrome. They have also found microbes that ameliorate social symptoms of autism, including Blautia stercoris. (Full disclosure, I wrote a book with Cryan and Dinan called The Psychobiotic Revolution from National Geographic.) Cryan says, “There seems to be something about the social brain in particular that makes it sensitive to signals from the microbiome.”

It’s not just rodents. There is a gut microbe signature of autism in humans as well. Autistic children have lower levels of Prevotella, Coprococcus, and Veillonella. These microbes can produce GABA and serotonin, two neurotransmitters that may reduce agitation in people with autism.

Despite the circular nature of the gut-brain axis, studies by Sarkis Mazmanian and colleagues at Caltech provide some strong evidence for causality. They collected fecal samples from autistic and non-autistic people and transferred them to mice. The mice that received the autistic poop avoided socializing and engaged in repetitive behaviors, while the control mice acted normally. The autistic behavior was transferred by fecal microbes. That is as close to showing causality as biology can come right now.

Autistic kids often adhere to an idiosyncratic diet, whether it is healthy or not. In fact, their abnormal gut microbes may affect their cravings, making it difficult to alter their diet, but probiotics may help. A study by Rosa Krajmalnik-Brown and colleagues at Arizona State University showed that probiotic supplements reduced gastric distress and lowered autism scores by almost 50 percent. That’s a remarkable result and points to future therapies.

Find a therapist to help with autism

These studies are still too small, but that is to be expected from a new field of research. And we need to move beyond mice, but that’s expensive, and in America, research funding is drying up. Still, there is no reason to abandon this research, just as it is producing tangible results that are improving life for thousands of autistic kids and their parents.

There is a lot to be learned about autism, but like many other brain disruptions, there is a surprising link to the gut. Further studies will improve our understanding. Science is hard, but despite the naysayers, now is not the time to throw in the towel.

Mitchell, Kevin J., Darren L. Dahly, and Dorothy V. M. Bishop. “Conceptual and Methodological Flaws Undermine Claims of a Link between the Gut Microbiome and Autism.” Neuron 114, no. 2 (2026): 196–211.

Tang, Jacqueline Wai-yan, Charles Cheuk-fung Hau, Wai-man Tong, Rory Munro Watt, Cynthia Kar Yung Yiu, and Kathy Kar-man Shum. “Alterations of Oral Microbiota in Young Children with Autism: Unraveling Potential Biomarkers for Early Detection.” Journal of Dentistry 152 (January 1, 2025): 105486.

Sen, Paromita, Eoin Sherwin, Kiran Sandhu, et al. “The Live Biotherapeutic Blautia Stercoris MRx0006 Attenuates Social Deficits, Repetitive Behaviour, and Anxiety-like Behaviour in a Mouse Model Relevant to Autism.” Brain, Behavior, and Immunity 106 (November 2022): 115–26.

Aziz-Zadeh, Lisa, Sofronia M. Ringold, Aditya Jayashankar, Emily Kilroy, Christiana Butera, Jonathan P. Jacobs, Skylar Tanartkit, et al. “Relationships between Brain Activity, Tryptophan-Related Gut Metabolites, and Autism Symptomatology.” Nature Communications 16, no. 1 (April 14, 2025): 3465.

Srinivasjois, Ravisha, Shripada Rao, and Sanjay Patole. “Probiotic Supplementation in Children with Autism Spectrum Disorder.” Archives of Disease in Childhood 100, no. 5 (May 1, 2015): 505–506.

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