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Stool samples noted a high degree of accuracy in distinguishing autism, and early diagnosis is associated with better outcomes.
By: Amy Denney
As a young mother, Lyndsy Moffatt didn’t know what autism was but brought up concerns about her son’s behavior several times with his pediatrician.
Dominic had poor eye contact, delayed speech, loss of emotional responses, obsessive behaviors, and irregular behavior and play. Symptoms eventually escalated to constipation that would last up to nine days, rashes, picky eating, and nose bleeds.
“They would say, ‘He’s fine. He looks healthy. He’ll start talking,’” Moffatt told The Epoch Times. “He started having severe meltdowns at 3 [years old] that would last an hour. He would just scream, and you didn’t even know what caused it. He stopped being able to sleep at night, and I went online and all of these things added up with autism.”
She was told it would take 10 months before Dominic could be seen for an evaluation and diagnosis. Disappointed but not deterred, Moffatt began her own research, conducted independent testing for food allergies and heavy metals, and implemented a healing diet that’s been found beneficial for those with autism spectrum disorders (ASD) called GAPS, which stands for gut and psychology syndrome.
The diet and other interventions made a big difference for Dominic, who was eventually diagnosed with ASD and is now 14. He is social, happy, well-behaved, musically gifted, kind, considerate, healthy, and excited to learn and be at school.
“I’m so grateful every day because I never knew if he would talk. He was one of the most severe cases I’ve ever seen,” said Moffatt, who went on to become an autism specialist and certified GAPS coach. “He’ll be able to overcome any challenge he has. I never worry about him.”
Starting Early
Early intervention is a key determinant for success in the treatment of ASD. However, accurate, rapid diagnosis can be complicated by many factors. In addition to long waits to see specialists, children with autism can be easily misdiagnosed due to co-morbid conditions, particularly attention deficit hyperactivity disorder (ADHD). Often, symptoms aren’t recognized until children are school-age and past the point of receiving evidence-based early interventions.
As a 2020 article in Seminars in Pediatric Neurology pointed out, while early therapeutic interventions are most effective, typical ASD symptoms “may not emerge until the disorder is well established. The article also pointed out that there’s low compliance among doctors who are recommended to screen for ASD at 18 months and 24 months.
Biomarkers could be a useful way to assist in not only diagnosing ASD but also identifying those at risk prenatally and those who may need to be screened for diagnosis. Biomarkers could also play a role in helping understand the root cause of autism and monitor treatment, according to the article.
However, the authors noted, that biomarkers alone shouldn’t replace the screening tests currently being used for ASD, which rely on clinical observation.
Recent studies are highlighting stool testing of the microbiome as a promising tool to pinpoint autism and even distinguish it from ADHD, which can be a common misdiagnosis among children with ASD, thus potentially delaying their autism diagnosis for years.
Identifying Autism Through the Gut
Published July 8 in Nature Microbiology, the latest study’s goal was to determine whether the gut microbiome—which consists of bacteria, viruses, fungi, and archaea (single-cell organisms)—could improve the diagnostic process, according to Qi Su, lead author of the study.
Su, an assistant professor at the Chinese University of Hong Kong, helped design the research, which used four independent sets of data to confirm an initial discovery of altered gut microbiota composition among children with autism. Autism currently affects one in 36 children.
Specifically, the study discovered a panel of 31 biomarkers that consistently showed superior diagnostic accuracy among 1,627 children aged 1 to 13 years.
Moffatt noted how valuable such a test could be for toddlers who aren’t hitting developmental milestones. It could help identify those most in need of early intervention. Additionally, because gut microbiota and diet are so closely related, it could show doctors which patients may benefit from diet changes, she said.
“It’s such an important evaluation time. I feel like the diagnosis right now—since it is strictly behavioral and there are no lab tests available—would be incredibly valuable, especially because there’s so many root causes, types, and symptoms of autism,” she said.
Many Pieces to the Puzzle
Some companies are already using microbiome testing to identify children at risk of autism—something that Beth Lambert, author and founder of the autism support group Epidemic Answers, says is useful among a variety of tools that can help assist the diagnosis of many childhood diseases.
“Giving children a gut microbiome test in the first years of life could help identify relative risk for developing all sorts of conditions, not just autism. You could assess risk of allergic diseases, autism, autoimmune conditions, and more. The microbiome is an incredibly important window into someone’s health,” she told The Epoch Times in an email.
However, Lambert suspects that many other children will have symptoms of autism but do not have identifying features of gut dysbiosis, or an imbalance of the microbes common in autism.
She described autism as an interruption to development that happens in infants, toddlers, and young children who are burdened by stressors on their growing bodies and brains. It’s characterized by social and communication deficits, restricted interests, and repetitive behavior.
The stressors at play could originate in the gut from toxic bacteria or fungal metabolites, for instance, or it could be heavy metals, which may also impact gut microbes, Lambert said.
“Those two scenarios [pathogenic gut issues and heavy metals] will have different gastrointestinal microbial ‘signatures’ and that microbial ‘signature’ is changing on a moment-to-moment basis depending on what the child is eating, drinking, and experiencing in his environment,” she said. “It’s extraordinarily complex.”
In either case, the body’s resources are diverted to fighting inflammation, attempting to bring a dysregulated nervous system into balance, and ridding the body of cellular toxins, she explained. This can impair or arrest development and cause symptoms affecting the sensory, motor, and behavioral systems.
Probing the Microbiome
Previous research has found those with autism have a different microbial signature, determined by stool samples. However, while most studies focus on bacteria, the recent study also noted the fungi and viruses that were either depleted or enriched in those with ASD. It also found that 14 archaea were depleted in those with ASD. There were also alterations in 51 bacteria, seven fungi, 18 viruses, 27 microbial genes, and 12 metabolic pathways.
Archaea are single-celled organisms that comprise about 1 percent of the microbiome. Little is known about them and their association with human health and disease, according to a 2024 article in Synthetic and Systems Biotechnology.
The Nature Microbiology study found children with ASD had an overall decrease in diversity of archaea, bacteria, and viruses, compared with those children considered neurotypical. Of note, those who are neurotypical hit developmental milestones at the expected ages.
Specifically, they had significantly decreased relative abundance in 80 of 90 identified microbial species, and it was most pronounced with bacteria, in which 50 species were depleted among children with autism.
Another unique component of the study was the examination of microbial pathways and genes that offer a glimpse of gut microbiota function, a technique used in the study of metagenomics, which evaluates the DNA in a sample to identify the microbial members of a microscopic community.
Su told The Epoch Times in an email that by counting genes related to pathways, researchers can estimate how active the pathways are.
A “pathway” is a biochemical process of linked reactions whereby one molecule is processed into another, or compounds are changed in a series of processes to deliver a certain substance to a certain place in the body. Two pathways were found to be reduced in children with ASD in the study—ubiquinol-7 and thiamine diphosphate.
According to the study, ubiquinol has an antioxidant role associated with improving symptoms of autism. Thiamine diphosphate impairment is associated with ASD and mental health disorders in both animal and human research.
Validated Results
The discovery cohort in the study included 709 children with ASD and a control group of 374 children considered neurotypical.
Findings were then validated with fecal samples from a hospital that included 82 children with ASD and 90 neurotypical children. Additionally, these results were compared with published datasets.
Finally, results were also compared with samples of children with ADHD and atopic dermatitis—two conditions that are also associated with alterations in gut microbiota.
“The high accuracy and validation with independent and public datasets suggest robust and generalizable biomarkers, highlighting the importance of considering the entire microbial ecosystem in understanding and diagnosing ASD. This represents a significant advancement in early and precise ASD diagnosis,” Su said.
Distinguishing ASD from ADHD
A biomarker that could distinguish between autism and ADHD would have practical applications. A 2022 case report in Cureus noted among the challenges in diagnosing ASD are overlapping behaviors with other neurological disorders, such as ADHD. These behaviors include troubles with social communication and attention.
In the case report, a boy who had a complex ADHD diagnosis exhibited overlooked social difficulties that led to a comorbid ASD diagnosis at age 14. The authors pointed out the importance of ASD screening in situations where symptoms persist despite other treatments. Comorbid conditions are one of many diagnostic difficulties.
“Considering the growing body of research surrounding the association of ADHD and ASD, children who are diagnosed with ADHD should be screened or evaluated for autism in the right clinical setting, such as evident persistence of social interaction impairment despite ADHD treatment,” the authors wrote.
The authors explained that methylphenidate and atomoxetine are commonly prescribed to treat ADHD and exhibit different degrees of effectiveness in children with co-occurring ASD and ADHD.
A 2015 study of 1,496 children ages 2 to 17 with ASD discovered that children who received an ADHD diagnosis first were 30 times more likely to have an autism diagnosis delayed until after 6 years of age.
“The findings support implications that children with ADHD before ASD may exhibit unique dimensional traits that could bias clinicians toward an ADHD diagnosis,” wrote the authors.
“Diagnostic criteria and screening measures for ASD may need to reflect the overlapping symptomatology between ASD and ADHD,” they concluded.
Little Overlap to Previous Data
For all the promise of biomarkers, there is also still concern over their reliability. Of the 31 microbial biomarkers in the new Nature Microbiology study, almost none of them overlapped with findings from a June 26 study in Nature Neuroscience, explained one of that study’s corresponding authors, Jamie Morton.
His study also validated a microbial signature that is specific to autism. One reason for the lack of overlapping data is different computation tools being used, he told The Epoch Times.
“The data is giving us a soup of information, and we’re trying to put together what could be there, but there are many ways to interpret the data,” Morton said. Importantly, there isn’t a strong consensus on how to properly identify microbes based on sequencing data.
“These genomes are pretty complex. Imagine you have a whole library of encyclopedias, and you throw it into a blender and then you try to read the shreds and piece together the encyclopedias from an entire library,” he said.
Even within species, there can be variations, and not all technologies can pick up the differences that illustrate the differences between similar bugs.
Morton gave the example of Escherichia coli (E. coli), which has many variants including one called shigella that “encodes a toxin” that’s dangerous to humans. Other strains of E.coli are harmless, and differences can sometimes come down to only one gene.
Microbial technology, Morton said, is reaching its limit, and will require validation by other means. The science is “plugging holes” rapidly, and there’s still a lot of missing information, he said.
The Epoch Times recently reported on a study published in Nature Metabolism that noted even the time of day that stool samples are collected could reveal vastly different microbial composition.
“We really need to start leveraging other data types to alleviate the ambiguity,” Morton said.
Still, he said the study is a step in the right direction. He also said that biomarker tests for autism diagnosis could be developed even without full knowledge of the mechanism of action between the microbiome and autism.
Su said he’s currently working on a study of the stool-based microbiome test on toddlers with developmental problems to provide more validation.
“The major takeaway here is this is another study that shows a microbial difference between autism and neurotypical controls across multiple studies,” Morton said.
Explanations Still Needed
Why children with autism exhibit a lack of microbial diversity remains to be elucidated. Su’s research finds that while diet plays a role in microbial makeup, differences in microbial diversity and composition “remained present after correction for dietary factors in our analysis.”
However, it’s never too soon to apply basic principles supported by research that shows how gut health impacts mental well-being by eating more healthily, Su said.
“Based on this understanding, maintaining a balanced diet consisting of high-quality food and paying attention to their [children’s] gut health can potentially support their mental health and overall wellness,” he said.
Moffatt agreed. She said almost all people—but especially those with autism who tend to be more sensitive and more likely to have food allergies—can benefit from nutritional intervention and detoxification support.
