Evidence map›Paper›PMID 31142858›Full record

ArticleNature2019

Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Wenyu Zhou, M Reza Sailani, Kévin Contrepois, Yanjiao Zhou, Sara Ahadi, Shana R Leopold, Martin J Zhang, Varsha Rao, Monika Avina, Tejaswini Mishra and 39 more

Registry-linked trialOpen access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05808101 (Role of the Gut Microbiome as Determinant of Depression in Multiple Sclerosis Subjects), which is not on this map. Cited by 344 papers, 4 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
344citing papers in PubMed, 4 pooled it
29.6field-weighted citation impact, top 1% of its field
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.

NCT05808101 terminatednot on this mapstarted 2022, after this paper: background citation

Role of the Gut Microbiome as Determinant of Depression in Multiple Sclerosis Subjects

TypeobservationalSponsorWashington University School of MedicineRan2022 to 2024Enrolled51ConditionsMultiple Sclerosis, DepressionArmsNeuro-QoL T-score determination
3 · Its place in the literature

Who cites it

344 citing papers in PubMed, 4 syntheses or guidelines pooled it, 589 citations in OpenAlex.

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284 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

49 authors at 6 institutions in 2 countries.

Wenyu Zhou *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
M Reza Sailani *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Kévin Contrepois *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Yanjiao Zhou *The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Sara Ahadi *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Shana R LeopoldThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Martin J ZhangDepartment of Electrical Engineering, Stanford University, Stanford, CA, USA.
Varsha RaoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Monika AvinaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Tejaswini MishraDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jethro JohnsonThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Brittany Lee-McMullenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Songjie ChenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Ahmed A MetwallyDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Thi Dong Binh TranThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Hoan NguyenThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Xin ZhouThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Brandon AlbrightThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Bo-Young HongThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Lauren PetersenThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Eddy BautistaThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Blake HansonThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Lei ChenThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Daniel SpakowiczThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Amir BahmaniStanford Center for Genomics and Personalized Medicine, Stanford, CA, USA.
Denis SalinsDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Benjamin LeopoldThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Melanie AshlandDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Orit Dagan-RosenfeldDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Shannon RegoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Patricia LimcaocoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Elizabeth ColbertDivision of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA.
Candice AllisterDivision of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA.
Dalia PerelmanDivision of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA.
Colleen CraigDivision of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA.
Eric WeiDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Hassan ChaibDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Daniel HornburgDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jessilyn DunnDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Liang LiangDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Sophia Miryam Schüssler-Fiorenza RoseSpinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
Kim KukurbaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Brian PieningEarle A Chiles Research Institute, Providence Cancer Center, Portland, OR, USA.
Hannes RostDonnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
David TseDepartment of Electrical Engineering, Stanford University, Stanford, CA, USA.
Tracey McLaughlinDivision of Endocrinology, Stanford University School of Medicine, Stanford, CA, USA.
Erica SodergrenThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
George M WeinstockThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. George.Weinstock@jax.org.
Michael SnyderDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA. mpsnyder@stanford.edu.
Stanford University · USJackson Laboratory · USStanford Medicine · USProvidence Portland Medical Center · USUConn Health · USUniversity of Toronto · CA

Funding

Stanford Center for Clinical & Translational Education and Research (Spectrum)UL1TR003142 · NCATS · STANFORD UNIVERSITY · PI O'HARA, RUTH M · 2019 to 2023
$45.0M
Spectrum Stanford Center for clinical and Translational Research and EducationUL1TR001085 · NCATS · STANFORD UNIVERSITY · PI CULLEN, MARK RICHARD, GREENBERG, HARRY BERNARD · 2013 to 2017
$37.1M
Stanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5M
Longitudinal Multiomics Microbial Profiling in Healthy and Disease IndividualsU54DK102556 · NIDDK · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P., WEINSTOCK, GEORGE M · 2014 to 2015
$7.7M
Longitudinal Multi-Omic Profiles to Reveal Mechanisms of Obesity-Mediated Insulin ResistanceR01DK110186 · NIDDK · STANFORD UNIVERSITY · PI MCLAUGHLIN, TRACEY, SNYDER, MICHAEL P. · 2017 to 2021
$3.2M
Algorithms and Software for Provably Accurate De Novo RNA-Seq AssemblyR01HG008164 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI KANNAN, SREERAM, PACHTER, LIOR S · 2015 to 2017
$1.4M
Stanford Career Development Program in Omics of Lung DiseasesK12HL120001 · NHLBI · STANFORD UNIVERSITY · PI NICOLLS, MARK ROBERT, RABINOVITCH, MARLENE · 2013 to 2017
$1.3M
Integrating the Exposome into Longitudinal Multiomics ProfilingK08ES028825 · NIEHS · STANFORD UNIVERSITY · PI ROSE, SOPHIA MIRYAM SCHÜSSLER-FIORENZA · 2018 to 2022
$1.0M
High-throughput sequencer for multi-scale genomic studiesS10OD020141 · OD · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2015 to 2015
$600k
NCATS NIH HHS UL1 TR001085NCATS NIH HHS UL1 TR003142NHGRI NIH HHS R01 HG008164NHLBI NIH HHS K12 HL120001NIDDK NIH HHS P30 DK116074NIDDK NIH HHS R01 DK110186NIDDK NIH HHS U54 DK102556NIEHS NIH HHS K08 ES028825NIH HHS S10 OD020141
6 · The paper itself

Abstract

Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.

Indexed as

Computational BiologyGastrointestinal MicrobiomeTranscriptomeAdultAgedAnti-Bacterial AgentsBiomarkersCohort StudiesDatasets as TopicDiabetes Mellitus, Type 2FemaleGlucoseHealthy VolunteersHost Microbial InteractionsHumansInflammationAnti-Bacterial AgentsBiomarkersGlucoseInfluenza VaccinesInsulinProteome

Identifiers

PMID31142858
PMCPMC6666404
OpenAlexW2948018512

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

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 OpenQuestion graph.