Additional file 1 of Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation
Creators: name: Berbers, Roos-Marijn
name: Paganelli, Fernanda L.
name: van Montfrans, Joris M.
name: Ellerbroek, Pauline M.
name: Viveen, Marco C.
name: Rogers, Malbert R. C.
name: Salomons, Moniek
name: Schuurmans, Jaap
name: van Stigt Thans, Martine
name: Vanmaris, Remi M. M.
name: Brosens, Lodewijk A. A.
name: van der Wal, Maria Marlot
name: Dalm, Virgil A. S. H.
name: van Hagen, P. Martin
name: van de Ven, Annick A. J. M.
name: Uh, Hae-Won
name: van Wijk, Femke
name: Willems, Rob J. L.
name: Leavis, Helen L.
Publisher: name: figshare
Year: 2025
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Supplementary Material 1: Supplementary Figure S1. Serum IgA in healthy controls (HC, n = 48), CVID with infections only (CVIDio, n = 51) and CVID with immune dysregulation (CVIDio n = 42). The horizontal line inside the box represents the median. The whiskers represent the lowest and highest values within 1.5 × interquartile range. P values boxplots: Mann–Whitney U test. * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001. Supplementary Figure S2. Bacterial load as determined using 16S rRNA qPCR in: A: HC (n = 48), CVIDio –med (n = 32), CVIDio + med (n = 19), CVIDid –med (n = 18), CVIDid + med (n = 24), XLA (n = 11). HC: healthy control, CVIDio: CVID with infections only, CVIDid: CVID with immune dysregulation, XLA: X-linked agmmaglobulinemia. Med: patients who did ( +) or did not (-) use antibiotics or immunosuppressive therapy up to 3 months prior to sampling. The horizontal line inside the box represents the median. The whiskers represent the lowest and highest values within 1.5 × interquartile range. P values boxplots: Mann–Whitney U test. * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001. Supplementary Figure S3. Alpha diversity as calculated using the inverse Simpson index. The horizontal line inside the box represents the median. The whiskers represent the lowest and highest values within 1.5 × interquartile range. P values boxplots: Mann–Whitney U test. * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001. Supplementary Figure S4. Richness as calculated using the Chao1 index. The horizontal line inside the box represents the median. The whiskers represent the lowest and highest values within 1.5 × interquartile range. P values boxplots: Mann–Whitney U test. * p &lt; 0.05, ** p &lt; 0.01, *** p &lt; 0.001. Supplementary Figure S5. Relative abundance of the most frequently detected enterococcal species determined using shotgun metagenomic sequencing in 4 HC, 4 CVIDio and 4 CVIDid. The horizontal line inside the box represents the median. The whiskers represent the lowest and highest values within 1.5 × interquartile range. Supplementary Figure S6. Presence of enterococcal DNA in stools of controls and patients without medication use. This is expressed by the log 10 of the amount of enterococcal DNA present in one colony forming unit (CFU) corrected by the total 16S rRNA abundance per fecal sample as determined using qPCR. Results below the detection limit of the qPCR assay were not displayed. HC (HC, n = 48), CVID with infections only (CVIDio, n = 32), CVID with immune dysregulation (CVIDid, n = 18), X-linked agammaglobulinemia (XLA, n = 3). Supplementary Figure S7. Cytokine production after in-vitro stimulation of monocytes from 10 HC, 10 CVIDio and 10 CVIDid with bacterial supernatants from E.coli E783, E.gallinarum E9950, E.gallinarum E.9951, E.hirae E9954 and E.hirae E9958 (pooled data). A: IL-6 production, B: IL-10 production, C: IL6/IL10 ratio. Supplementary Table S1. qPCR primer–probe sequences, ordered from IDT DNA technologies. All sequences reported from 5′-3’, all probes flanked by 6-FAM/ZEN (5’) and Iowa Black®Fluorescence Quencher2. Supplementary Table S2. Overview of all bacterial strains used in this study. Supplementary Table S3. Characteristics biopsy cohort. Supplementary Table S4. Differentially abundant bacteria identified using 16S rRNA sequencing. CVID (n = 93) vs healthy control (HC, n = 48): coefficients, standard errors (SE), p-values, FDR-adjusted p-values. Median relative abundance of non-zero counts per group. Statistics: ANCOM-BC. Supplementary Table S5. Differentially abundant bacteria identified using 16S rRNA sequencing. CVID without use of antibiotics or immunosuppressive therapy 3 months prior to sampling (CVID-med n = 50) vs healthy control (HC. n = 48): coefficients. standard errors (SE), p-values, FDR-adjusted p-values. Median relative abundance of non-zero counts per group. Statistics: ANCOM-BC. Supplementary Table S6. Differentially abundant bacteria identified using 16S rRNA sequencing. CVID with immune dysregulation (CVIDid. n = 42) versus CVID with infections only (CVIDio. n = 51): coefficients. standard errors (SE), p-values, FDR-adjusted p-values. Median relative abundance of non-zero counts per group. Statistics: ANCOM-BC. Supplementary Table S7. Differentially abundant bacteria identified using 16S rRNA sequencing. CVID with immune dysregulation without medication use (CVIDid -med. n = 18) versus CVID with infections only without medication use (CVIDio -med. n = 32). Patients did not use antibiotics or immunosuppressive therapy 3 months prior to sampling: coefficients. standard errors (SE), p-values, FDR-adjusted p-values. Median relative abundance of non-zero counts per group. Statistics: ANCOM-BC. Supplementary Table S8. Differentially abundant bacteria identified using 16S rRNA sequencing. CVID with IgA &lt; 0.1 g/L (CVID-IgA n = 40) versus CVID with IgA &gt; 0.1g/L (CVID + IgA n = 53): coefficients. standard errors (SE). p-values. FDR-adjusted p-values. Median relative abundance of non-zero counts per group. Statistics: ANCOM-BC. Supplementary Table S9. Differentially abundant bacteria identified using 16S rRNA sequencing. CVID with IgA &lt; 0.1 g/L without medication use (CVID-IgA-med n = 21) versus CVID with IgA &gt; 0.1g/L without medication use (CVID + IgA-med n = 29): coefficients. standard errors (SE). p-values. FDR-adjusted p-values. Median relative abundance of non-zero counts per group. Statistics: ANCOM-BC. Supplementary Table 10. Baseline characteristics of the matched serum-stool cohort.