Gut microbiota in CVID and immune dysregulation (case-control)
24 stool samples from a case-control study comparing gut microbiota in common variable immunodeficiency (CVID), X-linked agammaglobulinemia, and healthy controls, investigating links between dysbiosis and immune dysregulation. machine-written summary
24 samples · 24 runs · NL · Age unknown · 2022 · 3.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11740714 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 24 sample values (country) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
households — not resolved
Healthy controls are household members of CVID patients; patient–control household pairing not published.
Genera, mean relative abundance over 19 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 24 | 100% | 24 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% |
- Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation. 2025 PMID 39819634 PMC11740714 own_data
Archive description
Common Variable Immunodeficiency (CVID) is a primary antibody deficiency characterised by hypogammaglobulinemia and recurrent infections. Most morbidity and mortality is caused by immune dysregulation complications (CVIDid), which affect around one-third of CVID patients and are of poorly understood etiology. Here, we investigate the hypothesis that gut microbial dysbiosis contributes to the inflammation underlying CVIDid. In this cross-sectional multicentre study, bacterial localization and crypt architecture were analyzed in gut biopsies of 15 CVID patients, 3 patients with X-linked agammaglobulinemia (XLA), and 9 healthy controls (HC). Next, bacterial load and microbiota composition were characterized using 16S rRNA-targeted qPCR and next-generation sequencing in stool samples of 42 CVIDid patients, 51 CVID patients with infections only (CVIDio), 48 HC and 11 XLA patients. The CVID gut microbiota was characterized by expansion of Enterobacteriaceae and bacterial invasion of colonic crypts in CVID and XLA colon biopsies. Increased fecal bacterial load, decreased alpha diversity were observed in CVIDid compared to HC, as well as a distinct beta diversity in CVIDid. Metagenomic shotgun sequencing followed by selective culturing and qPCR revealed a higher prevalence of Enterococcus gallinarum in CVIDid relative to CVIDio. Presence of E. gallinarum in stool correlated with increased serum IL-17A, IL-10, LILRB4 and Flt3L. When exposed to E. gallinarum supernatants, CVID and HC monocytes showed increased production of IL-6 and IL-6/IL-10 ratio.This study further supports the hypothesis that a dysregulated gut microbiota contributes to systemic inflammation in primary antibody deficiency, and introduces E.gallinarum as a potential pathobiont in CVID with immune dysregulation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “stool samples of 42 CVIDid patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110188191 | country | NL | R2 | 0.60 | external.bugsigdb source | Location of subjects: Netherlands |
Sequencing
24 runs over 24 samples · mean 5.28 Gbp per run (median 3.69 Gbp, total 126.82 Gbp; 24 runs with a base count) · layout PAIRED 24 · platform ILLUMINA 24 · models NextSeq 500 (24) · 79% of runs with a Sandpiper profile · first public 2022-06-27 – 2022-06-28
Authors (19)
Berbers RM first · Paganelli FL · van Montfrans JM · Ellerbroek PM · Viveen MC · Rogers MRC · Salomons M · Schuurmans J · van Stigt Thans M · Vanmaris RMM · Brosens LAA · van der Wal MM · Dalm VASH · van Hagen PM · van de Ven AAJM · Uh HW · van Wijk F · Willems RJL · Leavis HL last
Downloads
PRJEB44275.csv.gz (1.4 KB) · parquet (68.9 KB) — all 24 samples, every field with route and confidence · PRJEB44275_determinations.csv.gz (567 B) — 24 evidence rows