Human gut microbiota Metagenome

Dataset overview

Participants None

Samples 132

Reuse readiness 5.9/10 evidence-backed score

Immunomolecular and reactivity landscapes of gut IgA subclasses in homeostasis and inflammatory bowel disease.

Tejedor Vaquero S, Neuman H, Comerma L, Marcos-Fa X, Corral-Vazquez C, Uzzan M, Pybus M, Segura-Garzón D, et al. · The Journal of experimental medicine · 2024

Abstract

The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function, and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19- PC subsets, respectively. IgA2+ PCs were extensively clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. Of note, secretory IgA1 (SIgA1) and SIgA2 dually coated a large fraction of mucus-embedded bacteria, including Akkermansia muciniphila. Disruption of homeostasis by inflammatory bowel disease (IBD) was associated with an increase in actively proliferating IgA1+ plasmablasts, a depletion in long-lived IgA2+ PCs, and increased SIgA1+SIgA2+ gut microbiota. Such increase featured enhanced IgA1 reactivity to pathobionts, including Escherichia coli, combined with depletion of beneficial A. muciniphila. Thus, gut IgA1 and IgA2 emerge from clonally related PCs and show unique changes in both frequency and reactivity in IBD.

doi:10.1084/jem.20230079 ↗ PMID 39560666 ↗ PMC11577441 ↗

Study facts

Organism: —
Platform: Illumina MiSeq
Age group: —
Disease groups: —
Anatomical sites: —

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

Raw reads are advertised
Sample counts are documented

Limitations

Not documented: feature/otu tables are advertised
Not documented: taxonomic tables are advertised
Not documented: participant counts are documented

Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

Field	Value	Evidence
`assay.paired_end`	True	subjected to multiplexed sequencing on a MiSeq instrument (Illumina) with the 500 Cycle V2 Kit (2 × 250 bp) Section `Bacterial 16S rRNA gene analysis`, offset 103300
`assay.platform`	Illumina MiSeq from source	ENA instrument_model=Illumina MiSeq Section `ENA study report`, offset —
`assay.primers_reported`	True	PCR primers that target bacterial 16S V3 and V4 regions (Table S6) Section `Bacterial 16S rRNA gene analysis`, offset 103000
`assay.read_length`	250	Paired-end 250 nucleotide reads were filtered using dada2 Section `Bacterial 16S rRNA gene analysis`, offset 103300
`assay.sequencing_type`	amplicon_16s	16S rRNA amplicons from each of these bacterial fractions were generated and sequenced Section `study.description`, offset —
`assay.target_region`	16S V3-V4	PCR primers that target bacterial 16S V3 and V4 regions Section `Bacterial 16S rRNA gene analysis`, offset 103000

Cohort

Field Value Evidence

Field	Value	Evidence
`cohort.study_design`	cross_sectional inferred	Fecal samples were collected by the patient at home and brought to the hospital within 24 h and then stored at −80°C until processing. Section `Human fecal and mucus samples`, offset 73500

cohort.study_design

cross_sectional inferred

Fecal samples were collected by the patient at home and brought to the hospital within 24 h and then stored at −80°C until processing.

Section Human fecal and mucus samples, offset 73500

Data_Assets

Field	Value	Evidence
`data_assets.open_access`	True from source	"isOpenAccess": "Y" Section `publication metadata`, offset —
`data_assets.pipeline_or_tool_versions`	True	QIIME2 (v2019.1, [Bolyen et al., 2019]) was used to execute the whole 16S analysis. Section `Bacterial 16S rRNA gene analysis`, offset 104100
`data_assets.qc_or_negative_controls_reported`	True	sheath fluid samples were sequenced and processed to identify putative contaminant operational taxonomic units (OTUs) Section `Bacterial 16S rRNA gene analysis`, offset 103900
`data_assets.raw_reads`	True	Ig gene and 16s RNA sequencing data are publicly available at NCBI’s Sequence Read Archive, accession codes PRJNA596067 and PRJNA902959 Section `Data availability`, offset 109000

Specimens

Field Value Evidence

Field	Value	Evidence
`specimens.number_of_samples`	132 from source	ENA sample_count=132 Section `ENA study report`, offset —
`specimens.sample_type`	stool	profiling fecal bacteria from 6 healthy controls (HC) Section `study.description`, offset —

specimens.number_of_samples

132 from source

ENA sample_count=132

Section ENA study report, offset —

specimens.sample_type

stool

profiling fecal bacteria from 6 healthy controls (HC)

Section study.description, offset —