Healthy adult gut microbiome-immune study, San Francisco

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. Overall design: PBMC samples were collected from healthy individuals and surface protein and gene expression were analyzed using CITE-seq. The dataset contains PBMC samples collected at two timepoints from the ImmunoMicrobiome cohort (110 healthy donors): baseline dataset (pool1 - pool7) and follow-up dataset (pool8 - pool14). The follow-up dataset was generated for a subset of the cohort, with their corresponding baseline samples repeated to reduce technical biases. The 10X 5' NEXT GEM, v1.1 kits were used for baseline dataset and 5' NEXT GEM, v2 for follow-up dataset. The WMS dataset contains stool samples collected from participants in the ImmunoMicrobiome cohort at two timepoints. Baseline samples are denoted by the suffix "BLE", while follow-up samples are denoted by "AAE6" or "ABE4." The follow-up dataset was generated for a subset of participants, with their corresponding samples repeated to reduce technical bias (denoted by suffix "BLE2"). WMS libraries were prepared from DNA extracted from human stool samples using standard chemical and mechanical lysis methods. Libraries were generated using the Nextera XT kit (Illumina) and sequenced as paired-end reads on an Illumina NovaSeq S4 flow cell.

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.

• host run.host_tax_id · “9606”
• body site run.scientific_name · “human gut metagenome”
• life stage study.description · “110 healthy participants through the ImmunoMicrobiome study”

267 runs over 267 samples · mean 9.64 Gbp per run (median 9.19 Gbp, total 2,574.41 Gbp; 267 runs with a base count) · layout PAIRED 267 · platform ILLUMINA 267 · models Illumina NovaSeq 6000 (267) · 0% of runs with a Sandpiper profile · first public 2026-03-22

Babdor J first · Patel RK · Davidson B · Koser K · Noecker C · Rahim MK · Bisanz JE · Tenvooren I · Marquez D · Calvo M · Johri V · McCarthy EE · Shaheed A · Ekstrand C · Weakley AM · Yu FB · Krip K · Shaikh KA · Amatullah H · Fiehn O · Turnbaugh PJ · Combes AJ · Fragiadakis GK · Spitzer MH last

PRJNA1390888.csv.gz (8.3 KB) · parquet (81.5 KB) — all 267 samples, every field with route and confidence · PRJNA1390888_determinations.csv.gz (22.7 KB) — 3,202 evidence rows