Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq

This dataset accompanies the manuscript: Lingasamy P, Saare M, Vela Moreno S, Särekannu K, Lubenets D, Sola-Leyva A, Kasun G , Patel N, Modhukur V, Mändar R, Salumets A. "Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq." This dataset contains processed microbiome data, FACS sorting metadata, and statistical outputs from a viability-discriminating, immunoglobulin class–resolved profiling study of the female reproductive tract (FRT) microbiome. Matched vaginal, cervical, and endometrial specimens were collected from 16 healthy reproductive-age women. Bacteria were sorted by membrane integrity (DAPI-based gating) and immunoglobulin class (IgA, IgM, IgG) using FACS, followed by near full-length 16S rRNA gene sequencing (V1–V9, Illumina HiSeq 1000, 85 bp single-end). A total of 149 samples (from 292 FACS-sorted fractions) passed quality control and are included in this dataset. FILE DESCRIPTIONS OTU_table_decontaminated_39taxa_149samples.csv — PRIMARY ANALYSIS FILE. Raw read count matrix (39 taxa × 149 samples) after contaminant removal. Burkholderia cepacia and Streptococcus pneumoniae were removed as reagent-derived contaminants. This is the file used for all analyses in the manuscript. OTU_table_predecontamination_41taxa.csv — Pre-decontamination raw count matrix (41 taxa × 149 samples) provided for transparency. Filtered_abundance_relative_predecontamination_41taxa.csv — Pre-decontamination relative abundance matrix (41 taxa × 149 samples, total-sum scaled to 100% per sample). Provided for reference. Sample_metadata_149samples.csv — Sample metadata for all 149 post-QC samples: participant ID, anatomical site (vagina/cervix/endometrium), immunoglobulin fraction (IgA/IgM/IgG/pre-sorted), clinical condition (Lactobacillus-dominant or vaginally dysbiotic), and storage method (fresh or cryopreserved). Taxonomy_39taxa.csv — Full taxonomic classification (Domain to Species) for the 39 taxa in the final decontaminated dataset. facs_binding_events.csv — FACS-sorted bacterial event counts per immunoglobulin fraction and anatomical site for each participant. ReadsTable_P.csv — 16S rRNA gene sequencing read depth per sample, used for quality control reporting. seq_clean.csv — Quality-filtered sequence data used as input for Bayesian source tracking (SourceTracker) analysis. SupplementaryTableS1_IgACoatingScores.tsv — Per-taxon IgA coating scores [IgA mean / (IgA mean + IgM mean)] for all 39 taxa. Scores range from 0 (exclusively IgM-coated) to 1 (exclusively IgA-coated). Corresponds to Supplementary Table S1 in the manuscript. anatomical_site_enrichment.csv — Taxon enrichment ratios across anatomical sites. lactobacillus_fresh_frozen.csv — Lactobacillus species relative abundances stratified by storage condition. taxa_abundance_fresh_frozen.csv — Mean taxon relative abundances stratified by storage condition and anatomical site. filtering_statistics.xlsx — Taxon counts retained under four prevalence-based filtering thresholds, used to generate Supplementary Figure S14A. Analysis code and scripts are available at: https://github.com/Prakashbio/mflow-seq-immune-microbiome-reproductive-tract Raw sequencing data will be deposited to NCBI SRA.