Toni Gabaldón
ICREA research professor and head of the Comparative Genomics group at the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center (BSC-CNS).
The study uses appropriate methodology and quality data. Of note is the high number of samples and their good characterisation in terms of diet and lifestyle factors, which are factors that strongly influence the gut microbiome. They also make the effort to recruit complementary cohorts and reanalyse public data to see the robustness of their results.
That children on the autism spectrum have a different gut microbiota has long been known, but most studies are based on analysis of the bacterial component and at the level of taxonomic composition. Using shotgun methodologies, where the entire DNA of the sample is sequenced and not just marker genes, this study gives a more complete picture, looking at changes in archaea, fungi and viruses, and providing insight into potential metabolic changes associated with changes in microbiota. It also has a particular focus on biomarker discovery and proposes a panel of 31 species that discriminate quite well.
As always, it should be remembered that correlational studies need to be confirmed by more targeted studies to determine whether any cause-effect relationship can be established. The study finds some metabolic pathways involved in neurotransmitter synthesis, which establishes an interesting hypothesis about a possible functional relationship, which should be established in future studies. Computational predictors trained on data need to be tested in other situations and with new data sets, as they tend to work very well in contexts similar to those in which they were trained, but may fail in other situations.
Current diagnosis is made on the basis of behavioural patterns that appear over time; adopting early biomarkers that could help detect autism earlier could facilitate earlier initiation of therapies. If there are metabolic changes that influence the progression of symptoms and could be compensated by diet or use of probiotics, modulation of the microbiota would open a door for new treatments to improve some aspects.