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Microbiome signatures correlate with diet-mediated ADHD symptom reduction.

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Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Shell · 13 lines · 418 B · MIT

  1. #!/usr/bin/env bash
  3. # Customise the terminal command prompt
  4. echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
  5. echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
  6. export PROMPT_DIRTRIM=2
  7. export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
  9. # Update Nextflow
  10. nextflow self-update
  12. # Update welcome message
  13. echo "Welcome to the nf-core/rnaseq devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

setup.sh, under MIT · at the source

Overview

Authors: Saartje Hontelez1, Martin Guthrie1, Tim Stobernack1, Peter van Baarlen1, Céline Rousseau2, Marco P Boks2, Rob Rodrigues Pereira3, Jos Boekhorst1, Michiel Kleerebezem1
ORCID iDs: Peter van Baarlen, Michiel Kleerebezem
  1. Department of Animal Sciences, Host-Microbe Interactomics, Wageningen University and Research, Wageningen, The Netherlands
  2. Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
  3. Medical Centre Kinderplein, Rotterdam, The Netherlands
Institutions: Wageningen University & Research (Netherlands); Utrecht University (Netherlands); University Medical Center Utrecht (Netherlands)
Journal: Gut microbes, volume 18, issue 1, article 2659400
Dates: received 23 October 2025; accepted 9 April 2026; published online 16 April 2026; in print December 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1080/19490976.2026.2659400 · PMID 41989380 · PMCID PMC13089928 · OpenAlex W7154598358
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), ADHD (population), clinical / translational (subfield)
Methods: Statistics, Preprocessing, Connectivity
Keywords: Gut microbiome, attention deficit hyperactivity disorder (ADHD), few foods diet (FFD), multi-omics
MeSH: Attention Deficit Disorder with Hyperactivity*, Bacteria*, Gastrointestinal Microbiome*, Child, Diet, Feces, Female, Humans, Male, Multiomics (* major topic)
Topic: Attention Deficit Hyperactivity Disorder (Psychiatry and Mental health, Medicine), according to OpenAlex
Funding: Porticus Foundation
Citations: not cited yet (Europe PMC); 52 references in the paper

Abstract

Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8–10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut–brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above.

Zenodo 1400710

License: MIT
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the text, “Sample collection and processing”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: DESeq2 (1 file), ggplot2 (1 file), Nextflow (1 file), pheatmap (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
  • 29 September 2026: the link answers (HTTP 200)
15 files
At the source: doi.org/10.5281/zenodo.1400710

nf-core/rnaseq

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: a1fcdddd3b826fe46eb46f0479f2ff8a7815af05, 23 September 2026
Languages: Python (6), R (4), Shell (2), Perl (1)
Size: 851 files, 13 scripts
Software Heritage: archived
Found in: the Zenodo archive record
Holds: README, license file, environment (.devcontainer/devcontainer.json, .devcontainer/setup.sh, modules/local/deseq2_qc/environment.yml, modules/local/preprocess_transcripts_fasta_gencode/environment.yml, modules/local/star_genomeparams_upgrade/environment.yml, modules/nf-core/dupradar/environment.yml, modules/nf-core/fastp/environment.yml, modules/nf-core/fastqc/environment.yml, modules/nf-core/gffread/environment.yml, modules/nf-core/gunzip/environment.yml, modules/nf-core/multiqc/environment.yml, modules/nf-core/ribodetector/environment.gpu.yml), continuous integration, documentation
Not found: CITATION.cff, tests
Tools: DESeq2 (1 file), ggplot2 (1 file), Nextflow (1 file), pheatmap (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
15 files
At the source: github.com/nf-core/rnaseq/tree/3.27.0

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 26 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability statement

The individual behavior scores per participant are provided in Supplementary Table ST1, as well as through supplementary datafile SDF1, and the Data Archiving and Networked Services (DANS) of the Netherlands Science Foundation (NWO); doi: 10.17026/dans-z56-fz75. The blood and urine metabolite data are available in supplementary datafile SDF2, and at DANS; doi: 10.17026/dans-xuc-jsux. The PBMC RNAseq transcriptome data are available in supplementary datafile SDF3. The sequence files underlying the 16S rRNA microbiota composition profiling are available through the European Nucleotide Archive (ENA) repository; project code PRJEB96501. The functional MRI data sets used in this study were previously published10 and are available at DANS; doi: 10.17026/dans-xzf-wh36. Since the remaining datasets include potential participant-traceability information, they are considered privacy-sensitive, therefore access to Shotgun metagenome, SNP profiling, and DNA-methylation data can be requested via the communicating author.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 4 keywords, 10 MeSH terms, 1 funder, 50 references.

Cite

This paper

Hontelez, S., Guthrie, M., Stobernack, T., van Baarlen, P., Rousseau, C., Boks, M. P., Pereira, R. R., Boekhorst, J., & Kleerebezem, M. (2026). Microbiome signatures correlate with diet-mediated ADHD symptom reduction. Gut microbes, 18(1), 2659400. https://doi.org/10.1080/19490976.2026.2659400

BibTeX

@article{hontelez2026microbiome,
author = {Hontelez, Saartje and Guthrie, Martin and Stobernack, Tim and van Baarlen, Peter and Rousseau, Céline and Boks, Marco P and Pereira, Rob Rodrigues and Boekhorst, Jos and Kleerebezem, Michiel},
title = {{Microbiome signatures correlate with diet-mediated ADHD symptom reduction}},
journal = {Gut microbes},
year = {2026},
month = apr,
volume = {18},
number = {1},
pages = {2659400},
publisher = {Taylor \& Francis},
issn = {1949-0976},
doi = {10.1080/19490976.2026.2659400},
url = {https://doi.org/10.1080/19490976.2026.2659400},
pmid = {41989380},
pmcid = {PMC13089928}
}

RIS

TY - JOUR
AU - Hontelez, Saartje
AU - Guthrie, Martin
AU - Stobernack, Tim
AU - van Baarlen, Peter
AU - Rousseau, Céline
AU - Boks, Marco P
AU - Pereira, Rob Rodrigues
AU - Boekhorst, Jos
AU - Kleerebezem, Michiel
TI - Microbiome signatures correlate with diet-mediated ADHD symptom reduction
T2 - Gut microbes
J2 - Gut Microbes
PY - 2026
DA - 2026/04/16
VL - 18
IS - 1
SP - 2659400
SN - 1949-0976
PB - Taylor & Francis
DO - 10.1080/19490976.2026.2659400
UR - https://doi.org/10.1080/19490976.2026.2659400
LA - en
ER -

CSL-JSON

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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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