Multi-omics method for gut microbiome secretions, Luxembourg
Cross-sectional study of 20 stool samples from healthy individuals in Luxembourg, developing a multi-omics method to extract and characterize extracellular nucleic acids, peptides, and metabolites secreted by the gut microbiome. machine-written summary
20 samples · 20 runs · LU · Age unknown · 2021 · 2.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 60 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 40 sample values (health condition, health condition detail) · PMC7612290 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
4 of 4 people sampled more than once (20 samples; median 5, up to 5 per person).
Genera, mean relative abundance over 14 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 | 20 | 100% | 20 | |||
| health_condition | 20 | 100% | 20 | |||
| subject_id | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| health_condition_detail | 20 | 100% | 20 |
- Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. 2021 PMID 35106519 PMC7612290 own_data
Archive description
The human gut microbiome produces a complex mixture of biomolecules which interact with human physiology and play essential roles in health and disease. The crosstalk between micro-organisms and host cells is favored by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of nucleic acids, (poly)peptide and small molecule moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-secreted extracellular complement, including nucleic acids, (poly)peptides and metabolites from flash-frozen human stool samples. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enables coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different intracellular and extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single omics data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those typically vesicle-associated, and their impact on host physiology in health and disease.
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 study.title · “human gut microbiome-secreted molecules”
- body site study.description · “flash-frozen human stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8740555 | collection_date | 2018-09 | R1 | 0.90 | biosample.attribute:collection_date | 2018-09 |
| SAMEA8740555 | country | LU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Luxembourg |
| SAMEA8740555 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.abstract | flash-frozen stool samples of healthy human individuals |
| SAMEA8740555 | health_condition_detail | healthy human individuals | R3 | 0.70 | paper.fulltext.abstract | flash-frozen stool samples of healthy human individuals |
| SAMEA8740555 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | int-DNA_individual_1 |
Sequencing
20 runs over 20 samples · mean 3.65 Gbp per run (median 2.59 Gbp, total 73.02 Gbp; 20 runs with a base count) · layout PAIRED 16, SINGLE 4 · platform ILLUMINA 20 · models NextSeq 500 (20) · 75% of runs with a Sandpiper profile · first public 2021-10-29
Authors (16)
De Saedeleer B first · Malabirade A · Ramiro-Garcia J · Habier J · Trezzi JP · Peters SL · Daujeumont A · Halder R · Jäger C · Busi SB · May P · Oertel W · Mollenhauer B · Laczny CC · Hettich RL · Wilmes P last
Downloads
PRJEB44766.csv.gz (1.3 KB) · parquet (69.7 KB) — all 20 samples, every field with route and confidence · PRJEB44766_determinations.csv.gz (1.2 KB) — 100 evidence rows