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Gut microbiota differences seen in people with autism may be due to dietary preferences

Cell Press

gut biome

The diversity in species found in the guts of children with autism may be due to their restricted dietary preferences associated with autism, rather than the cause of their symptoms.


This new study adds yet more evidence to what many previous research studies have already shown - which is that poor dietary habits, and particularly selective, restricted or 'picky eating', are unusually common in children on the autistic spectrum (as many parents and professionals have always known). 

Rather more controversially, despite this study being purely correlational (and the fact that 'correlation is not causation') the researchers claim to have shown that

1) 'picky eating' is the primary cause of the gut microbial differences that have also been extensively reported in connection with autism and related conditions - and

2) their data rule out the idea that gut microbial imbalances could have any effect on ASD

This conclusion seems to go well beyond what the study data actually showed.  A huge research literature now shows (pretty definitively) that gut-brain communications work in BOTH directions. 

So yes - the highly restricted diets of many individuals with ASD would be expected to affect gut microbial balance (and not in a positive way).  But in turn, an unhealthy balance of gut microbes can affect not only gut health, but also immune system regulation, and brain function. 

ASD is associated with difficulties in all these areas - and research (including some human studies) shows that dietary interventions to improve gut microbial balance may have positive effects on behaviour in children with ASD, as well as reducing both gastro-intestinal and other symptoms. For example:

A major problem for research (and practice) is that the ASD diagnosis itself is extrenely broad and purely descriptive, so individual variability within ASD is huge.  The 'causes' of this and other neurodevelopmental conditions (which all overlap) are also highly complex - involving both genetic and environmental factors, which interact constantly, and differ both between individuals, and over time. 

These are literally 'developmental' conditions, and simplistic generalisations about their causes - let alone claims to have solved the 'chicken and egg' problem - make no sense when it comes to the role of the gut-microbial-brain axis in ASD.

By attracting attention to the very poor diets consumed by many individuals with ASD, this study could have important benefits - but only if this leads parents, professionals and researchers to find better ways to help improve the nutritional quality and balance of those diets. 

For the underlying research please see:

See also:

And for further information please see:

11/11/2021 - Medical Xpress

Research suggested that autism spectrum disorder (ASD) may be at least partly caused by differences in the composition of the gut microbiota, based on the observation that certain types of microbes are more common in people with autism. But a paper appearing November 11 in the journal Cell suggests that the link may actually work the other way around: the diversity in species found in the guts of children with autism may be due to their restricted dietary preferences associated with autism, rather than the cause of their symptoms.

"There's a lot of interest surrounding the role of the gut microbiome in autism, but not a lot of hard evidence," says senior author Jacob Gratten, of Mater Research in partnership with The University of Queensland in Brisbane, Australia. "Our study, which is the largest to date, was designed to overcome some of the limitations of prior work."

Over the past decade, as next-generation sequencing of the microbial species in the gut has made analysis of the microbiome more automated and less-time consuming, a number of studies have examined the link between particular species of microbes in the gut and mental health. The gut-brain axis has been linked not only to ASD but also to anxiety, depression, and schizophrenia. The possibility of targeting the microbiota is a growing area of research for new treatments.

In the Cell study, the investigators analyzed stool samples from a total of 247 children between the ages of 2 and 17. The samples were collected from 99 children diagnosed with ASD, 51 paired undiagnosed siblings, and 97 unrelated, undiagnosed children. The subjects included in the analysis were from the Australian Autism Biobank and Queensland Twin Adolescent Brain Project.

The investigators analyzed the samples by metagenomic sequencing, which looks at the entire genome of microbial species rather than short genetic barcodes (as with 16S analysis). It also provides gene-level information rather than just species-level information, and provides a more accurate representation of microbiome composition than 16S analysis, a technique used in many of the earlier studies linking the microbiome to autism.

"We also carefully accounted for diet in all our analyses, along with age and sex," says first author Chloe Yap, an MD-Ph.D. student who works with Gratten. "The microbiome is strongly affected by the environment, which is why we designed our study with two comparison groups."

Based on their analysis, the researchers found limited evidence for a direct association of autism with the microbiome. However, they did find a highly significant association of autism with diet and that an autism diagnosis was associated with less-diverse diet and poorer dietary quality. Moreover, psychometric measures of degree of autistic traits (including restricted interests, social communication difficulties, and sensory sensitivity) and polygenic scores (representing a genetic proxy) for ASD and impulsive/compulsive/repetitive behaviors were also related to a less-diverse diet.

"Taken together, the data support a strikingly simple and intuitive model, whereby autism-related traits promote restricted dietary preferences," Yap says. "This in turn leads to lower microbiome diversity and more diarrhea-like stool."

The researchers acknowledge several limitations to the current work. One is that the design of the study can't rule out microbiome contributions prior to ASD diagnosis, nor the possibility that diet-related changes in the microbiome have a feedback effect on behavior. Another is that they could only account for the possible effect of antibiotics on the microbiome by excluding those taking these medications at the time of stool collection. Finally, no comparable datasets are currently available to confirm the findings.

"We hope that our findings encourage others in the autism research community to routinely collect metadata in "omics" studies to account for important (but often underappreciated) potential confounders such as diet," Gratten says. "Our results also put the spotlight on nutrition for children diagnosed with autism, which is a clinically important (but underrecognized) contributor to overall health and wellbeing."

The researchers plan to generate new data in a larger sample to replicate their findings.