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Study finds no link between autism and gut microbes

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Emily Anthes
5 November 2012

Bacterial controversy: Some studies have found certain bacterial species in children with autism and not in controls, but a new study says there are no differences between the groups.

Contradicting a popular hypothesis in autism, a new study from Australia has found no connection between autism and bacteria in the gut. The analysis, published 20 September in the journal Autism Research, reports that the gastrointestinal (GI) systems of children with autism harbor the same bacteria as those of their typically developing siblings1.

“Our conclusion was there’s no single organism that we can pinpoint as being always involved in autism,” says Enzo Palombo, associate professor of microbiology at the Swinburne University of Technology in Melbourne, Australia, who is one of the investigators.

Based on 51 children with autism and 53 unaffected siblings, the study is larger than most studies of the microbiome — the collection of microbes in the body — in children with autism. Because siblings share genes and their environment, this approach reduces ‘noise’ in the data from factors unrelated to autism, the researchers say.

However, critics argue that because children in the same family tend to have similar microbiomes, comparing children who have autism with their unaffected siblings may also make it more difficult to pick out subtle abnormalities associated with autism.

For years, scientists have suspected that something is amiss in the guts of children with autism. Multiple studies have shown, for instance, that these children suffer from GI problems at rates far higher than other children do2 3 4.

Analysis of gut bacteria in children with the disorder has revealed some provocative findings. For instance, a 2005 study found that children on the autism spectrum have elevated levels of Clostridia, a class of bacteria that can produce neurotoxins, in their guts5. And in a study this year, researchers found a class of bacteria known as Sutterella in children who have both autism and GI problems, but not in typically developing controls.

Some researchers have gone so far as to suggest that these atypical microbial populations may actively contribute to autism symptoms. For example, research last year showed that the fatty acids produced by gut bacteria can alter the brain and behavior6 7.

Murky link:

That’s a controversial proposition, especially because the connection between autism and gut microbes remains murky. So far, studies have been small and their results inconsistent, implicating different kinds of bacteria.

In the new study, the researchers sequenced DNA extracted from the stool of 51 children with autism and 53 of their unaffected siblings, all between the ages of 2 and 12. The researchers then matched the sequences against a database of bacterial genomes to identify the microbes in each sample.

There are no significant differences in the types of bacteria or in their levels between children with autism and their typically developing siblings, the researchers found. Nor did they find differences between the gut microbes of children with autism who have GI symptoms and those who do not, or between children with severe forms of autism and those with mild forms of the disorder. 

“We are showing that the link between specific bacteria in the gut and autistic symptoms and behavior is not definite,” says Palombo.

Still, other researchers say it’s too early to reject the idea that intestinal bacteria play a role in autism.

“In general, I think it’s a well-run study,” says Sydney Finegold, emeritus professor of medicine at the University of California, Los Angeles. Finegold compliments the Australian researchers in particular for their large sample size, and for including children both with and without GI problems. But, he adds, “I disagree with their conclusion that there’s no relationship between intestinal bacteria and GI dysfunction and autism.”

For one thing, Finegold says, the results of the study may be confounded by antibiotic use. Palombo and his colleagues excluded children from their study who had taken antibiotics in the previous 15 days, but Finegold says he believes that that criterion is not stringent enough.

“We know that the impact of antibiotics on intestinal bacteria lasts for months, and some would say for years,” he says. He says these studies should preferably exclude children who have taken antibiotics anytime in the previous several months.

For his part, Palombo says, “I agree that a longer abstinence period would have been ideal, but we may not have had as many study participants.”

Subtle differences:

Palombo agrees that it’s too early to rule out a connection between intestinal bacteria and autism. A handful of the children with autism have various bacterial abnormalities, such as an elevated level of one species or another, he says, indicating that a subset of children with the disorder may show differences.

Some experts say comparing the gut microbes of children who have autism with those of their unaffected siblings, rather than with unrelated controls, may make it more difficult to detect subtle differences.

“Autism is a complex etiology,” says Catherine Lozupone, a postdoctoral fellow in Rob Knight’s lab at the University of Colorado at Boulder. “There’s a genetic basis to it and there’s an environmental basis to it.”

Siblings share many genes and environmental exposures, would be expected to have similar microbiomes. In fact, some research has shown that whereas the gut microbes of children with autism are significantly different from those of unrelated controls, siblings have microbial populations that fall somewhere in the middle5 8.

The Australian team next plans to look for differences in viral populations among these groups, as well as to study whether the bacteria in children with autism produce different metabolites than those in typically developing children.

Overall, the conflicting results of these studies may result from the fact that there’s not yet a single standard way to conduct this research, Lozupone says.

In addition to using different kinds of control populations, researchers can collect microbial DNA from fecal samples or, occasionally, directly biopsy the intestines. Some scientists compare the presence of specific species or genera, and others look for differences in families or classes of bacteria, which may obscure subtle differences at the finer, species level.

“It’s really hard to interpret microbiome results,” Lozupone says. “It’s a new field — we’re still trying to figure out how to analyze data.”


1: Gondalia S.V. et al. Autism Res. Epub ahead of print (2012) PubMed

2: Valicenti-McDermott M. et al. J. Dev. Behav. Pediatr. 27, S128-S136 (2006) PubMed

3: Gilger M.A. and C.A. Redel Pediatrics 124, 796-798 (2009) PubMed

4: Horvath K. and J.A. Perman Curr. Opin. Pediatr. 14, 583-587 (2002) PubMed

5: Parracho H.M. et al. J. Med. Microbiol. 54, 987-991 (2005) PubMed

6: MacFabe D.F. et al. Behav. Brain Res. 176, 149-169 (2007) PubMed

7: Shultz S.R. et al. Neuropharmacology 54, 901-911 (2008) PubMed

8: Finegold S.M. et al. Anaerobe 16, 444-453 (2010) PubMed




Name: Paul Whiteley
5 November 2012 - 4:17PM

Thanks for the overview.

I just have 2 small points:

1. You seem to have forgotten to reference the Sutterella-autism paper which comes from the very well-known Ian Lipkin (the de-discoverer of XMRV and CFS):
Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances.
Williams BL, et al.
MBio. 2012 Jan 10;3(1). doi:pii: e00261-11. 10.1128/mBio.00261-11
(It's open-access by the way).


2. The Williams Sutterella paper is slightly different from the other research in this area in that they looked at biopsy snips rather than fecal material for their sources of bacteria. (That and some interesting plasma antibodies to Sutterella also reported, potentially indicative of bacterial translocation and dare I say it, intestinal hyperpermeability...)

Name: Emily Singer
5 November 2012 - 4:20PM

Thanks for the comment. We link to SFARI.org coverage of the Lipkin paper, which is available here: https://sfari.org/news-and-opinion/in-brief/2012/clinical-research-gut-bacteria-prevalent-in-autism
When SFARI.org has covered a paper referenced in a story, we often link to the story, which has the original reference, rather than listing the reference.

Name: Paul Whiteley
5 November 2012 - 9:54PM

Many thanks.

Name: Sarah
5 November 2012 - 6:32PM

I find the title of this article misleading. A more accurate title would be read: "Conflicting Opinions among Experts on Autism link to Gut Microbes". When you read the details you find that there are strong disagreements on this conclusion from other experts in the field. This is but one study. There are others that show a distinct difference in gut microbes in children with autism- the Lipkin Sutterella study being one. I think we need to be careful not to slam the door shut based on one study. Also regardless of whether there is a link to autism- GI issues which are common in children with autism still need to be addressed.

Name: Sarah
5 November 2012 - 7:30PM

Another perspective from Gastroenterologist Tim Buie, M.D. Dr Buie treats GI issues in children with autism. Includes references to various studies.

Gastrointestinal Illness in Autism: An Interview with Tim Buie, M.D.

Name: ASD Dad
6 November 2012 - 6:53AM

A few of the papers worth rereading on this and related subjects ...

A Microbial Association with Autism


Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses.


Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances.


... and a couple of points

Williams et al. (13) report detecting Sutterella 16S rRNA gene sequences in <b> ileal mucosal biopsy specimens </b> from 12 of 23 patients diagnosed with autism and GI symptoms but in none of the specimens from 9 control children with GI symptoms.

One would expect some differences between mucosal tissue and stool samples.


Regression (loss of language and/or other skills following acquisition) is reported in 20% to 40% of individuals with autism, and some studies suggest higher rates of GI symptoms in ASD subjects with regression than those without regression [27]. Eighty-seven percent of AUT-GI subjects in our study had behavioral regression "

Name: Paul Patterson
16 November 2012 - 3:53PM

I also find the title of this piece misleading. In Fig. 4 of the article, one finds that there are indeed differences in the microbial content of the ASD samples. These are apparently the less abundant species and so they do not contribute much to the overall "weighted" analysis. However, we all know that even a single species can give us great GI discomfort on occasion!
Another point is that prior studies did not agree on the same species as being different in ASD. This could be due to the fact that these several studies did not use the same experimental methods of sample collection and data analysis.

Name: Payman
14 February 2013 - 6:39PM

Autism have several sub categories: such as PDD, PDD NOS, Regressive, Aspergers etc. The study fails completely to relate any finding to nay of listed subtypes of autism. This is very important since the biomedical pathway to world of autism may be very different in thiese subtypes of autism.

Name: GAPS Dad
6 March 2013 - 6:41PM

I did not see the work of Elaine Gottschall or Dr. Natasha Campbell-McBride mentioned anywhere in this website? According to their hypothesis, GFCS diets are not enough. To heal the gut, large amounts of beneficial microbes need to be ingested. That is, fermented foods need to be consumed on a regular basis. Western society has gotten away from fermented foods. As our food becomes more sterile with increased sugar content, candida dominates the scene, and bacteria that should reside only in the gut migrate to places that they do not belong. For example, Helicobacter Pylori in the blood stream is the cause of heart disease, yet when it exists in the stomach, and is controlled by acidity, it has its proper function.

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