ArticleCell2026
Immune-microbiome coordination defines interferon setpoints in healthy humans.
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Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2citing papers in PubMed
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Who cites it
2 citing papers in PubMed.
- Immunotherapy resistance in colorectal cancer: therapeutic strategies and biomarker-guided approaches.Cancer cell international · 2026Review
- A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.bioRxiv : the preprint server for biology · 2026Article
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Authors and funding
24 authors.
Joel BabdorDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Systems Pharmacology and Translational Therapeutics, Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA. Electronic address: joel.babdor@pennmedicine.upenn.edu.
Ravi K PatelDivision of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA.
Brittany DavidsonUCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA.
Kelvin KoserDepartment of Systems Pharmacology and Translational Therapeutics, Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Cecilia NoeckerDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
Maha K RahimDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Jordan E BisanzDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
Iliana TenvoorenDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Diana MarquezDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Maria CalvoDivision of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Vrinda JohriUCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA.
Elizabeth E McCarthyDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Avneet ShaheedDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
Christina EkstrandUCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA.
Allison M WeakleyChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Feiqiao B YuChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Kristen KripDepartment of Systems Pharmacology and Translational Therapeutics, Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Kashif A ShaikhDepartment of Systems Pharmacology and Translational Therapeutics, Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Hajera AmatullahDepartment of Systems Pharmacology and Translational Therapeutics, Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Oliver FiehnWest Coast Metabolomics Center, University of California, Davis Genome Center, Davis, CA, USA.
Peter J TurnbaughDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Alexis J CombesUCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA.
Gabriela K FragiadakisDivision of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA. Electronic address: gabriela.fragiadakis@ucsf.edu.
Matthew H SpitzerDepartment of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Bakar ImmunoX Program, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. Electronic address: matthew.spitzer@ucsf.edu.
Funding
Research BaseP30DK063720 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GERMAN, MICHAEL S · 2003 to 2019
$21.8MPredicting and preventing drug metabolism by the human gut microbiomeR01HL122593 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Peter James Turnbaugh · 2016 to 2026
$5.7MImmune determinants of progression from Oral Epithelial Dysplasia to Oral Squamous Cell Carcinoma by precision multiplexed imagingR01DE032033 · NIDCR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Matthew Spitzer · 2022 to 2026
$3.8MMetabolism of cancer chemotherapeutics by the human gut microbiomeR01CA255116 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Peter James Turnbaugh · 2023 to 2026
$3.1MHost-microbiome interactions shape the metabolic effects of ketogenic dietsR01DK114034 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TURNBAUGH, PETER JAMES · 2020 to 2024
$2.5MQuantitatively modeling immune responses to cancerDP5OD023056 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SPITZER, MATTHEW · 2016 to 2020
$1.9MEarly identification of immunotherapy resistance through integrated multiparameter imagingR01CA290027 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Mekhail Anwar, Matthew Spitzer · 2025 to 2026
$1.4MUCSF DVS CyTOF Mass CytometerS10OD018040 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LANIER, LEWIS LEE · 2014 to 2014
$600kIllumina NovaSeq 6000 Sequencing SystemS10OD028511 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHOW, ERIC D · 2020 to 2020
$583kSystems-level analysis of the metabolism and ecology of genetically intractable gut bacteriaF32GM140808 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI NOECKER, CECILIA · 2021 to 2022
$134kNCI NIH HHS R01 CA255116NCI NIH HHS R01 CA290027NHLBI NIH HHS R01 HL122593NIDCR NIH HHS R01 DE032033NIDDK NIH HHS P30 DK063720NIDDK NIH HHS R01 DK114034NIGMS NIH HHS F32 GM140808NIH HHS DP5 OD023056NIH HHS S10 OD018040NIH HHS S10 OD028511
Abstract
Human immune systems are highly variable, with most variation attributable to non-genetic sources. The gut microbiome crucially shapes the immune system; however, its relationship with the baseline immune states of healthy humans remains incompletely understood. Therefore, we performed multi-omic profiling of 110 healthy participants through the ImmunoMicrobiome study. A factor-based integrative approach identified coordinated variation, revealing that the interferon response was amongst the most variable immune features in healthy participants. Microbiome composition, pathways, and stool metabolites varied concomitantly with interferon response pathways. Longitudinal data spanning more than a year indicated the significant stability of these parameters within individuals over time. Our study provides extensive data to examine the relationship between the immune states and microbiomes of healthy individuals at steady state, which paves the way for delineating inter-individual differences relevant for disease susceptibility and responses to therapy.
Indexed as
Gastrointestinal MicrobiomeImmune SystemInterferonsMicrobiotaAdultFecesFemaleHumansMaleMiddle AgedMultiomicsYoung AdultInterferonshuman immunologyimmune setpointimmune systeminterferonmicrobiomemulti-omic integration
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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.