Journal article
Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders
Nature communications, Vol.15(1), 9743
11/11/2024
DOI: 10.1038/s41467-024-53934-7
PMCID: PMC11555315
PMID: 39528484
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.
Here, Manghi et al. identify potential salivary microbial biomarkers for autism through a large-scale metagenomic analysis of 2,000 families, revealing shifts in neurotransmitter-related pathways
Details
- Title: Subtitle
- Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders
- Creators
- Paolo Manghi - Fondazione Edmund MachMichele Filosi - Institute for BiomedicineMoreno Zolfo - University of TrentoLucas G. Casten - University of IowaAlbert Garcia-Valiente - University of TrentoStefania Mattevi - University of TrentoVitor Heidrich - University of TrentoDavide Golzato - University of TrentoSamuel Perini - University of TrentoAndrew M. Thomas - University of TrentoSimone Montalbano - University of TrentoSamuele Cancellieri - University of TrentoLevi Waldron - The Graduate Center, CUNYJacob B. Hall - Simons FoundationSimon Xu - Simons FoundationNatalia Volfovsky - Simons FoundationLeeAnne Green Snyder - Boston Children's HospitalJacob J. Michaelson - University of IowaPamela Feliciano - Simons FoundationNicola Segata - University of TrentoFrancesco Asnicar - University of TrentoEnrico Domenici - University of TrentoMireia Valles-Colomer - Universitat Pompeu Fabra
- Resource Type
- Journal article
- Publication Details
- Nature communications, Vol.15(1), 9743
- DOI
- 10.1038/s41467-024-53934-7
- PMID
- 39528484
- PMCID
- PMC11555315
- NLM abbreviation
- Nat Commun
- ISSN
- 2041-1723
- eISSN
- 2041-1723
- Publisher
- Nature Publishing Group UK
- Grant note
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020): 648614 SFARI: MetaPG-716575, MicroTOUCH-101045015 European Research Council (ERC-STG project): ONCOBIOME-825410, MASTER-818368 European H2020 program: 1U01CA230551 National Cancer Institute of the National Institutes of Health
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.
- Language
- English
- Date published
- 11/11/2024
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Communication Sciences and Disorders; Psychiatry; Iowa Neuroscience Institute
- Record Identifier
- 9984747819902771
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