Kimchi intake promotes antigen-presenting cell signaling and CD4? T cell remodeling without inducing systemic immune activation: A single-cell RNA-seq substudy of a randomized, double-blind, placebo-controlled clinical trial

This study aimed to investigate the systemic immunological effects of kimchi consumption in humans. We conducted a 12-week randomized, double-blind, placebo-controlled clinical trial involving thirteen overweight but otherwise healthy adults who consumed either placebo, spontaneously fermented kimchi (S-K), or starter kimchi fermented with Leuconostoc mesenteroides KCKM0828 (LMS-K). Peripheral blood mononuclear cells (PBMCs) were collected before and after the intervention and subjected to single-cell RNA sequencing (scRNA-seq) to profile immune responses at single-cell resolution. Overall design: Thirteen overweight but otherwise healthy adults (BMI 23–30 kg/m²) were enrolled in a 12-week randomized, double-blind, placebo-controlled trial of kimchi consumption (ClinicalTrials.gov: NCT05898802). Participants were randomized to placebo (n = 4), spontaneously fermented kimchi powder (S-K; n = 5), or starter-fermented kimchi powder prepared with Leuconostoc mesenteroides KCKM0828 (LMS-K; n = 4). Peripheral blood mononuclear cells (PBMCs) were collected at two time points per subject—baseline (pre-intervention) and post-intervention (week 12)—yielding 26 samples. Cryopreserved PBMCs were thawed, washed, and counted, then multiplexed via antibody-conjugated poly(A) DNA barcodes. Single cells were captured and barcoded on the BD Rhapsody HT Xpress system, followed by cDNA synthesis on mRNA-capture beads. Whole-transcriptome and sample-tag libraries were constructed using the BD Rhapsody WTA amplification kit and sequenced on an Illumina NovaSeq X Plus (2 × 100 bp, paired-end). Raw FASTQ files were processed with the BD Rhapsody WTA Analysis Pipeline v2.2.1 and aligned to GRCh38 for downstream single-cell analyses.