Evidence map›Paper›PMID 41413022›Full record

ArticleNature communications2025

Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats.

Hélène Tonnelé, Denghui Chen, Felipe Morillo, Jorge Garcia-Calleja, Apurva S Chitre, Benjamin B Johnson, Thiago Missfeldt Sanches, Riyan Cheng, Marc Jan Bonder, Antonio Gonzalez and 26 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

36 authors.

Hélène Tonnelé *Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.ORCID http://orcid.org/0000-0001-6015-0471
Denghui Chen *Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-6541-3418
Felipe MorilloCentre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
Jorge Garcia-CallejaInstitute of Evolutionary Biology (CSIC-UPF), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.ORCID http://orcid.org/0000-0002-4614-4574
Apurva S ChitreDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Benjamin B JohnsonDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Thiago Missfeldt SanchesDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Riyan ChengDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Marc Jan BonderDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.ORCID http://orcid.org/0000-0002-8431-3180
Antonio GonzalezDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Tomasz KosciolekDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Anthony M GeorgeClinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA.
Wenyan HanDepartment of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Sciences Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0003-0886-1430
Katie HollDepartment of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.ORCID http://orcid.org/0009-0007-9166-7423
Aidan HorvathDepartment of Psychology, University of Michigan, Ann Arbor, MI, USA.
Keita IshiwariClinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-6190-2249
Christopher P KingDepartment of Psychology, University at Buffalo, Buffalo, NY, USA.
Alexander C LamparelliDepartment of Psychology, University at Buffalo, Buffalo, NY, USA.
Connor D MartinClinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA.
Angel Garcia MartinezDepartment of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Sciences Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-0149-3770
Alesa H NetzleyDepartment of Psychology, University of Michigan, Ann Arbor, MI, USA.
Jordan A TripiDepartment of Psychology, University at Buffalo, Buffalo, NY, USA.
Tengfei WangDepartment of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Sciences Center, Memphis, TN, USA.
Elena BoschInstitute of Evolutionary Biology (CSIC-UPF), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.ORCID http://orcid.org/0000-0003-2848-103X
Peter A DorisCenter for Human Genetics, Institute of Molecular Medicine, McGovern Medical School, University of Texas at Houston, Houston, TX, USA.ORCID http://orcid.org/0000-0002-0565-7939
Oliver StegleGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.ORCID http://orcid.org/0000-0002-8818-7193
Hao ChenDepartment of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Sciences Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-2680-6921
Shelly B FlagelMichigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
Paul J MeyerDepartment of Psychology, University at Buffalo, Buffalo, NY, USA.ORCID http://orcid.org/0000-0001-5665-2292
Jerry B RichardsClinical and Research Institute on Addictions, University at Buffalo, Buffalo, NY, USA.
Terry E RobinsonDepartment of Psychology, University of Michigan, Ann Arbor, MI, USA.
Leah C Solberg WoodsDepartment of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston Salem, NC, USA.ORCID http://orcid.org/0000-0002-7943-798X
Oksana PolesskayaDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-0975-9019
Abraham A PalmerDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA. aap@ucsd.edu.ORCID http://orcid.org/0000-0003-3634-0747
Amelie BaudCentre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain. amelie.baud@crg.eu.ORCID http://orcid.org/0000-0003-2448-0283

Funding

Sequencing CoreP50DA037844 · NIDA · UNIVERSITY OF CHICAGO · PI MEYER, PAUL J · 2014 to 2023
$27.4M
The role of structural variants and tandem repeats in substance abuse-related behavioral traitsU01DA051234 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GYMREK, MELISSA, PALMER, ABRAHAM A · 2021 to 2025
$3.5M
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020) LCF/BQ/PI21/11830006NIDA NIH HHS P50 DA037844NIDA NIH HHS U01 DA051234NIH HHS S10 OD026929U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA) P50DA037844U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA) U01DA051234Wellcome TrustWellcome Trust (Wellcome) 105941/Z/14/Z
6 · The paper itself

Abstract

The intestinal microbiome influences health and disease. Its composition is affected by host genetics and environmental exposures. Understanding host genetic effects is critical but challenging in humans, due to the difficulty of detecting, mapping and interpreting them. To address this, we analyse host genetic effects in four cohorts of outbred laboratory rats exposed to distinct but controlled environments. We show that polygenic host genetic effects are consistent across cohort environments. We identify three replicated microbiome-associated loci, one of which involves the sialyltransferase gene St6galnac1 and Paraprevotella. We find a similar association in a human cohort, between ST6GAL1 and Paraprevotella, both of which have been linked with immune and infectious diseases. Moreover, we find indirect (i.e. social) genetic effects on microbiome phenotypes, which substantially increase the total genetic variance. Finally, we identify a novel mechanism whereby indirect genetic effects can contribute to "missing heritability".

Indexed as

Gastrointestinal MicrobiomeHost Microbial InteractionsAnimalsCohort StudiesFemaleHumansMaleMultifactorial InheritancePhenotypeRatsSialyltransferasesSialyltransferases

Identifiers

PMID41413022
PMCPMC12715198

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.