Fecal Transplants and Keto Diet Both Eased Autism Symptoms, Trial Finds

If your child has autism spectrum disorder (ASD) and gastrointestinal symptoms keep showing up alongside behavioral challenges, you have probably wondered whether working on the gut could help. A new clinical trial from Shandong University in China put that question to a direct test, enrolling 30 children with ASD and comparing two gut-targeted interventions head to head: fecal microbiota transplantation (FMT, transferring processed stool from a screened healthy donor to restore gut bacteria) and a ketogenic diet (KD, a high-fat, low-carbohydrate eating pattern). Both groups improved on standardized autism symptom scales, but the two approaches shifted gut bacteria in different directions, hinting that they may be working through different biological routes even though the behavioral results looked similar on paper. This is described by its authors as the first study to compare the two interventions side by side in the same trial, and while it is small and far from conclusive, it is a useful data point for families who are actively weighing gut-based options.

Key takeaways

• Both fecal microbiota transplantation (FMT) and a ketogenic diet significantly improved autism symptom scores in a 30-child trial, the first to compare the two head to head.
• The treatments shifted different gut bacteria: FMT increased several short-chain-fatty-acid producers, while the ketogenic diet reduced Veillonella species linked to propionate production.
• The trial was not randomized and the ketogenic diet arm had a 40% dropout rate, so these results show association, not proof that either intervention treats autism.
• The study's authors are explicit that larger, randomized trials measuring actual gut metabolite levels are needed before either approach can be considered established.

Fecal Transplant and Ketogenic Diet Both Improved Autism Symptom Scores

A trial comparing fecal microbiota transplantation (FMT) against a ketogenic diet (KD) in children with autism spectrum disorder found that both interventions produced significant improvements on standardized behavior scales, according to the study published in BMC Psychiatry. Researchers used two validated tools: the Childhood Autism Rating Scale (CARS) and the Autism Behavior Checklist (ABC). In the FMT group, average CARS scores fell from 34.87 to 33.53, a small but statistically significant drop. In the KD group, CARS scores fell further, from 35.13 to 33. On the ABC scale, the pattern flipped: the KD group improved significantly, from 63.07 to 42.73, while the FMT group's ABC improvement, from 79.93 to 69.33, did not reach statistical significance. In other words, each intervention looked stronger depending on which scale you read, and FMT tended to move the more clinician-scored CARS measure while KD moved the more subjective, caregiver-reported ABC measure more.

Why Families Managing Autism and Gut Symptoms Should Care

Autism spectrum disorder now affects roughly 1 in 31 children in the United States according to the CDC's most recent surveillance data, and a large share of those children also experience chronic gastrointestinal issues such as diarrhea, reflux, and constipation. That overlap has driven years of research into the gut-brain axis (the communication network linking gut bacteria, the immune system, and the nervous system), including earlier work showing that microbiota transfer therapy can produce long-lasting improvements in both gut and behavioral symptoms in children with ASD, and separate research showing a modified ketogenic diet can reshape the gut microbiome alongside inflammatory markers in autistic children. This new trial matters because it is the first attempt to put both strategies in front of the same population and compare them directly, rather than relying on separate small studies that are hard to compare against each other.

How Researchers Ran the Trial

The trial (registered as NCT06348433 and approved by the Shandong University Qilu Hospital ethics committee) enrolled 30 children with ASD, ages 19 to 97 months, diagnosed using the ADOS-2 and DSM-5 criteria. It was not randomized: children capable of swallowing capsules were assigned to the FMT group, while those who could not, or whose parents declined FMT, went into the KD group, splitting the cohort roughly 15 and 15. The FMT group underwent a 9-week protocol, including 5 weeks of orally administered FMT capsules (prepared from a single screened 11-year-old donor under anaerobic laboratory conditions) followed by a 4-week observation period. The KD group followed a 12-week Modified Atkins Diet, with meals set at roughly 60% fat, 30% protein, and 10% carbohydrate, under close medical monitoring of blood glucose and ketone levels. Researchers also collected stool samples from 12 children in each group at baseline and at the end of treatment for metagenomic sequencing, which reads the DNA of the whole bacterial community rather than culturing individual species, to track how gut bacteria composition changed alongside the behavioral scores.

What the Gut Bacteria Data Might Mean for a Reader

The sequencing results are where the two treatments diverge. Using an analysis method called LEfSe, which flags bacterial groups that shifted the most between groups, researchers identified five taxa that increased after FMT and three that changed after KD. The FMT group saw increases in Wujia chipingensis, Eubacterium sp. MSJ-33, and Butyrivibrio crossotus, all bacteria associated with producing butyrate, a short-chain fatty acid (a small molecule made when gut bacteria ferment fiber) that other research links to a stronger gut lining and reduced brain inflammation. The KD group instead saw a decrease in two Veillonella species tied to propionate production, alongside functional gene changes suggesting suppressed propionate synthesis. That distinction matters because rodent studies have shown that injecting propionic acid can trigger autism-like behaviors in animal models, so a diet that appears to dial down propionate-producing bacteria is biologically plausible as a mechanism, even though it remains unproven in humans. None of this means a parent should attempt either intervention without medical supervision: FMT requires rigorously screened donor material and clinical administration, and a ketogenic diet in a young child carries real risks of hypoglycemia and ketoacidosis that this trial's own medical team had to actively monitor for.

The Trial's Limitations Are Significant

The researchers are upfront that this is an exploratory, hypothesis-generating study, not proof that either intervention treats autism. The design was not randomized, children were sorted into groups based on their ability to swallow capsules and their parents' preference, which introduces selection bias and makes the two groups less directly comparable. Children in the KD group were also significantly younger at baseline than those in the FMT group. The ketogenic diet arm saw a steep dropout rate, with the paper reporting that 40% of participants who started the diet did not complete it, largely due to poor dietary adherence and food selectivity common in ASD, and because the efficacy analysis was not run on an intention-to-treat basis, the reported KD benefit may be inflated. The two groups were also assessed at different points, week 9 for FMT versus week 12 for KD, which further complicates any direct comparison. Perhaps most importantly, the study never directly measured short-chain fatty acid levels in stool, so while the bacterial shifts are real and statistically associated with symptom changes, the underlying metabolic mechanism remains speculative rather than demonstrated.

Where This Research Goes Next

The study authors call for larger, randomized controlled trials that directly measure metabolites such as butyrate and propionate, rather than inferring them from bacterial gene content, to confirm whether either intervention causes symptom improvement or whether both are picking up a shared, unrelated signal. They also note that a ketogenic diet may end up being most useful specifically for children who are unable to tolerate capsule-based FMT, positioning the two as potentially complementary rather than competing options once (and if) larger trials confirm their effects.

Common Questions

Does this study prove fecal transplants or a ketogenic diet can treat autism? No. This was a small, non-randomized trial with 30 children and a high dropout rate in one arm, and its authors describe the findings as preliminary evidence of association between gut bacteria changes and symptom scores, not proof that either intervention causes improvement in autism's core features.

Which treatment performed better, FMT or the ketogenic diet? Neither clearly outperformed the other. FMT produced a larger, more consistent improvement on the CARS scale, while the ketogenic diet produced a larger improvement on the ABC scale, and the two measure somewhat different things.

Is it safe for a child with autism to try a ketogenic diet at home? This trial's ketogenic diet arm required close, structured medical supervision, including three-times-daily blood glucose and ketone monitoring and weekly dietitian visits, precisely because of risks like hypoglycemia; the reported adverse events in this trial were mostly mild and gastrointestinal, but a ketogenic diet should not be started without a doctor's involvement.

What is the gut-brain axis, and why does it come up in autism research? The gut-brain axis is the two-way communication network between gut bacteria, the immune system, and the nervous system, and it is an active area of ASD research because many autistic children also have gastrointestinal symptoms and detectable differences in their gut bacteria compared to non-autistic children.

References

1. Yu Wang, Lihong Wang, Zhifeng Cai, et al. (2026). Comparison of clinical efficacy and gut microbiota characteristics in children with ASD treated with fecal microbiota transplantation and ketogenic diet. BMC Psychiatry. https://doi.org/10.1186/s12888-026-08547-3
2. Prevalence and Early Identification of Autism Spectrum Disorder Among Children Aged 4 and 8 Years, CDC MMWR. cdc.gov. https://www.cdc.gov/mmwr/volumes/74/ss/ss7402a1.htm
3. Dae-Wook Kang, James B. Adams, Devon M. Coleman, et al. (2019). Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota. Scientific Reports. https://doi.org/10.1038/s41598-019-42183-0
4. Nina P. Allan, Brennan Y. Yamamoto, Braden P. Kunihiro, et al. (2024). Ketogenic Diet Induced Shifts in the Gut Microbiome Associate with Changes to Inflammatory Cytokines and Brain-Related miRNAs in Children with Autism Spectrum Disorder. Nutrients. https://doi.org/10.3390/nu16101401
5. Jeonghyun Choi, Seunghoon Lee, Jinyoung Won, et al. (2018). Pathophysiological and neurobehavioral characteristics of a propionic acid‐mediated autism‐like rat model. The FASEB Journal. https://doi.org/10.1096/fasebj.2018.32.1_supplement.545.8