Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders

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  • dc.contributor.author Manghi, Paolo
  • dc.contributor.author Vallès Colomer, Mireia
  • dc.contributor.author Domenici, Enrico
  • dc.date.accessioned 2025-01-14T13:56:59Z
  • dc.date.available 2025-01-14T13:56:59Z
  • dc.date.issued 2024
  • dc.description.abstract The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005). The relative abundance of these species is highly correlated with cognitive impairment as measured by Full-Scale Intelligence Quotient (IQ). ASD children with IQ < 70 also exhibit lower microbiome strain sharing with parents (p < 10-6) with respect to NTs. A two-pronged functional enrichment analysis suggests the contribution of enzymes from the serotonin, GABA, and dopamine degradation pathways to the distinct microbial community compositions observed between ASD and NT samples. Although measures of restrictive eating diet and proxies of oral hygiene show relatively minor effects on the microbiome composition, the observed associations with ASD and IQ may still represent unaccounted-for underlying differences in lifestyle among groups. While causal relationships could not be established, our study provides substantial support to the investigation of oral microbiome biomarkers in ASD.
  • dc.description.sponsorship This work was supported by a grant from SFARI (Award 648614, E.D. and N.S.); by the European Research Council (ERC-STG project MetaPG-716575 and ERC-CoG project MicroTOUCH-101045015) to N.S.; by the European H2020 program (ONCOBIOME-825410 project and MASTER-818368 project) to N.S.; by the National Cancer Institute of the National Institutes of Health (1U01CA230551) to N.S.; by the Premio Internazionale Lombardia e Ricerca 2019 to N.S. We are grateful in particular to all of the families in SPARK, the SPARK clinical sites and SPARK staff. We appreciate obtaining access to the metagenomic raw data, the genetic data and the associated samples metadata on SFARI Base. The authors would like to thank Michael Whalen for his inspiring suggestion, which provided the starting point for this research. Approved researchers can obtain the SPARK population dataset described in this study (SFARI_SPARK_iWGS_v1.1) by applying at https://base.sfari.org.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Manghi P, Filosi M, Zolfo M, Casten LG, Garcia-Valiente A, Mattevi S, et al. Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders. Nat Commun. 2024 Nov 11;15(1):9743. DOI: 10.1038/s41467-024-53934-7
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-024-53934-7
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/69122
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2024 Nov 11;15(1):9743
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/716575
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101045015
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825410
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/818368
  • dc.rights © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
  • dc.subject.keyword Autism spectrum disorders
  • dc.subject.keyword Metagenomics
  • dc.title Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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