Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq
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2026
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| author | Lingasamy, Prakash Godakumara, Kasun |
| author_facet | Lingasamy, Prakash Godakumara, Kasun |
| contents | <p>This dataset accompanies the manuscript:</p> <p>Lingasamy P, Saare M, Vela Moreno S, Särekannu K, Lubenets D, Sola-Leyva A, <span>Kasun G<sup> </sup></span>, Patel N, Modhukur V, Mändar R, Salumets A. "Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq." </p> <p>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.</p> <p><strong>FILE DESCRIPTIONS</strong></p> <p>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.</p> <p>OTU_table_predecontamination_41taxa.csv — Pre-decontamination raw count matrix (41 taxa × 149 samples) provided for transparency.</p> <p>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.</p> <p>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).</p> <p>Taxonomy_39taxa.csv — Full taxonomic classification (Domain to Species) for the 39 taxa in the final decontaminated dataset.</p> <p>facs_binding_events.csv — FACS-sorted bacterial event counts per immunoglobulin fraction and anatomical site for each participant.</p> <p>ReadsTable_P.csv — 16S rRNA gene sequencing read depth per sample, used for quality control reporting.</p> <p>seq_clean.csv — Quality-filtered sequence data used as input for Bayesian source tracking (SourceTracker) analysis.</p> <p>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.</p> <p>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.</p> <p>Analysis code and scripts are available at: <a href="https://github.com/Prakashbio/mflow-seq-immune-microbiome-reproductive-tract">https://github.com/Prakashbio/mflow-seq-immune-microbiome-reproductive-tract</a></p> <p>Raw sequencing data will be deposited to NCBI SRA.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19449798 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq Lingasamy, Prakash Godakumara, Kasun female reproductive tract microbiome IgA coating IgM coating IgG coating flow cytometry FACS sorting mFLOW-Seq vaginal microbiota endometrium immunoglobulin 16S rRNA sequencing mucosal immunity host–microbiome interaction <p>This dataset accompanies the manuscript:</p> <p>Lingasamy P, Saare M, Vela Moreno S, Särekannu K, Lubenets D, Sola-Leyva A, <span>Kasun G<sup> </sup></span>, Patel N, Modhukur V, Mändar R, Salumets A. "Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq." </p> <p>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.</p> <p><strong>FILE DESCRIPTIONS</strong></p> <p>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.</p> <p>OTU_table_predecontamination_41taxa.csv — Pre-decontamination raw count matrix (41 taxa × 149 samples) provided for transparency.</p> <p>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.</p> <p>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).</p> <p>Taxonomy_39taxa.csv — Full taxonomic classification (Domain to Species) for the 39 taxa in the final decontaminated dataset.</p> <p>facs_binding_events.csv — FACS-sorted bacterial event counts per immunoglobulin fraction and anatomical site for each participant.</p> <p>ReadsTable_P.csv — 16S rRNA gene sequencing read depth per sample, used for quality control reporting.</p> <p>seq_clean.csv — Quality-filtered sequence data used as input for Bayesian source tracking (SourceTracker) analysis.</p> <p>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.</p> <p>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.</p> <p>Analysis code and scripts are available at: <a href="https://github.com/Prakashbio/mflow-seq-immune-microbiome-reproductive-tract">https://github.com/Prakashbio/mflow-seq-immune-microbiome-reproductive-tract</a></p> <p>Raw sequencing data will be deposited to NCBI SRA.</p> |
| title | Immunoglobulin class–resolved engagement of membrane-intact microbiota across female reproductive tract compartments using mFLOW-Seq |
| topic | female reproductive tract microbiome IgA coating IgM coating IgG coating flow cytometry FACS sorting mFLOW-Seq vaginal microbiota endometrium immunoglobulin 16S rRNA sequencing mucosal immunity host–microbiome interaction |
| url | https://doi.org/10.5281/zenodo.19449798 |