ArticleCell host & microbe2024
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.
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Article in Cell host & microbe, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers, 2 of them syntheses that pooled it.
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104citing papers in PubMed, 2 pooled it
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Who cites it
104 citing papers in PubMed, 2 syntheses or guidelines pooled it, 111 citations in OpenAlex.
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- Oral Microbiota Characteristics in Relation to Different Dietary Patterns: A Systematic Review.Nutrients · 2026Pooled it
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- Occupational exposure to Baijiu fermentation environments alters nasal microbiota composition: a comparative analysis of Strong-flavor and Sesame-flavor production systems.Microbiology spectrum · 2026Article
- Microbial Signals in Cancer: Dissecting Host-Microbiota-Tumor Interactions and Potential Therapeutic Strategy.MedComm · 2026Review
- Clinical Predictors of Nose/Throat Bacteriome and Fungal Colonization in Skilled Nursing Facility Residents.The Journal of infectious diseases · 2026Article
- Systematic evaluation of PASEF acquisition strategies in complex metaproteomes.Nature communications · 2026Article
- Microbiome and aging: Trajectories of microbiome age across human ecosystems and their systemic effects.iMeta · 2026Review
- Oral microbiome dysbiosis and oral-gut microbial network disruption in hand osteoarthritis: data from the Xiangya Osteoarthritis Study.RMD open · 2026Observational
- Multi-site microbiomes' response to chronic obstructive pulmonary disease.Microbiology spectrum · 2026Article
- Gut Microbiota Resilience and Environmental Stressors: A Hidden Key to Lifespan Optimization?Probiotics and antimicrobial proteins · 2026Review
- Extracting host-specific developmental signatures from longitudinal microbiome data.PLoS computational biology · 2026Article
- Population-based characterisation of child and adolescent oral bacterial microbiomes.Microbiome · 2026Article
- Heavy Metal-Driven Oral Dysbiosis: Salivary Toxicometallomics at the Host-Microbiome Interface Across Pathologies.Life (Basel, Switzerland) · 2026Review
- Article
- Oral Manifestations of Prediabetes: A Narrative Review of an Early Diagnostic Window for Dental Practice.Cureus · 2026Review
44 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
38 authors at 12 institutions in 5 countries.
Xin ZhouDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Xiaotao ShenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA.
Jethro S JohnsonThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK.
Daniel J SpakowiczThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA.
Melissa AgnelloMedical Affairs, uBiome, San Francisco, CA 94103, USA.
Wenyu ZhouDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA.
Monica AvinaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Alexander HonkalaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA.
Faye ChleilatDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Shirley Jingyi ChenStanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
Kexin ChaStanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
Shana LeopoldThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
Chenchen ZhuDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Lei ChenThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC.
Lin LyuShanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC.
Daniel HornburgDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Si WuDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Xinyue ZhangDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Chao JiangDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC.
Liuyiqi JiangLife Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC.
Lihua JiangDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Ruiqi JianDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Andrew W BrooksDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Meng WangDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Kévin ContrepoisDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Peng GaoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Sophia Miryam Schüssler-Fiorenza RoseDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Thi Dong Binh TranThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Hoan NguyenThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Alessandra CelliDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
Bo-Young HongThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA.
Eddy J BautistaThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia.
Yair DorsettThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA.
Paula B KavathasDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.
Yanjiao ZhouThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA.
Erica SodergrenThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
George M WeinstockThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Michael P SnyderDepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: mpsnyder@stanford.edu.
Stanford University · USJackson Laboratory · USStanford Medicine · USZhejiang University · CNShanghai Jiao Tong University · CNYale University · USColombian Corporation for Agricultural Research - AGROSAVIA · COOregon Health & Science University · USTexas Tech University · USThe Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute · USUConn Health · USUniversity of Oxford · GB
Funding
Translational Therapeutics Research Program (TT)P30CA016058 · NCI · OHIO STATE UNIVERSITY · PI Daniel G. Stover · 1985 to 2026
$132.3MStanford Center for Clinical & Translational Education and Research (Spectrum)UL1TR003142 · NCATS · STANFORD UNIVERSITY · PI O'HARA, RUTH M · 2019 to 2023
$45.0MSpectrum Stanford Center for clinical and Translational Research and EducationUL1TR001085 · NCATS · STANFORD UNIVERSITY · PI CULLEN, MARK RICHARD, GREENBERG, HARRY BERNARD · 2013 to 2017
$37.1MStanford Alzheimer's Disease Research CenterAdmin Supp: Developing iPSC models for AD and PDP30AG066515 · NIA · STANFORD UNIVERSITY · PI Lisa Goldman Rosas · 2020 to 2026
$29.0MStanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5MCenter for Personal Dynamic RegulomesRM1HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2019 to 2023
$13.8MLongitudinal Multiomics Microbial Profiling in Healthy and Disease IndividualsU54DK102556 · NIDDK · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P., WEINSTOCK, GEORGE M · 2014 to 2015
$7.7MStanford Medicine Center for Longevity and Healthy Aging Research Education CoreP30AG059307 · NIA · STANFORD UNIVERSITY · PI PERIYAKOIL, VYJEYANTHI S · 2018 to 2025
$4.9MLongitudinal Multi-Omic Profiles to Reveal Mechanisms of Obesity-Mediated Insulin ResistanceR01DK110186 · NIDDK · STANFORD UNIVERSITY · PI MCLAUGHLIN, TRACEY, SNYDER, MICHAEL P. · 2017 to 2021
$3.2MLongitudinal Multiomics Microbial Profiling in Healthy and Disease IndividualsU54DE023789 · NIDCR · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P., WEINSTOCK, GEORGE M · 2013 to 2014
$3.0MMultiomic Signatures of Microbial Metabolites Following Prebiotic Fiber Supplementation Alzheimer's supplementR01AT010232 · NCCIH · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2018 to 2021
$2.0MIntegrating the Exposome into Longitudinal Multiomics ProfilingK08ES028825 · NIEHS · STANFORD UNIVERSITY · PI ROSE, SOPHIA MIRYAM SCHÜSSLER-FIORENZA · 2018 to 2022
$1.0MNCATS NIH HHS UL1 TR001085NCATS NIH HHS UL1 TR003142NCCIH NIH HHS R01 AT010232NCI NIH HHS P30 CA016058NHGRI NIH HHS RM1 HG007735NIA NIH HHS K01 AG070310NIA NIH HHS P30 AG059307NIA NIH HHS P30 AG066515NIDCR NIH HHS U54 DE023789NIDDK NIH HHS F32 DK126287NIDDK NIH HHS P30 DK116074NIDDK NIH HHS R01 DK110186NIDDK NIH HHS U54 DK102556NIEHS NIH HHS K08 ES028825
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
Indexed as
Core StabilityMicrobiotaBiomarkersHost Microbial InteractionsHumansSkinBiomarkersinsulin resistancelongitudinal profilingmicrobiome host interactionmicrobiome stabilitynasal microbiomeoral microbiomeprecision medicineprediabetesskin microbiomestool microbiome
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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.