In vitro gut microbial colonization experiments, China
3,563 samples from healthy controls in China, using an intervention design to study colonization outcomes of exogenous species in human stool-derived in vitro microbial communities. machine-written summary
3,564 samples · 3,994 runs · CN · Age unknown · 2023 · 0.34 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 7,127 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 7,128 sample values (health condition, health condition detail) · PMC10944475 |
| ✓ Supplementary tables | 3,117 sample values (subject id) |
| – 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
40 of 40 people sampled more than once (3,117 samples; median 105, up to 173 per person).
Genera, mean relative abundance over 83 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 | 3,564 | 100% | 3,564 | |||
| health_condition | 3,564 | 100% | 3,564 | |||
| subject_id | 3,117 | 87% | 3,117 | |||
| health_condition_detail | 3,564 | 100% | 3,564 | |||
| collection_date | 3,563 | 100% | 3,563 |
- Data-driven prediction of colonization outcomes for complex microbial communities. 2024 PMID 38493186 PMC10944475 own_data
Archive description
Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they of pathogenic or nonpathogenic in nature. Predicting the colonization outcome of exogenous species from the baseline compositions of complex communities remains a fundamental challenge in microbial ecology, largely due to our limited knowledge of the diverse physical, biochemical and ecological processes governing the microbial dynamics. Here, we proposed a purely data-driven approach that is independent of any dynamics model to predict colonization outcomes of exogenous species for complex microbial communities. We systematically validated this approach using synthetic data, finding that it can predict not only the binary outcome but also the final abundance of the invading species. Then we conducted in vitro colonization experiments of two commensal human gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that our approach can successfully predict the colonization outcomes. The presented results suggest that the data-driven approach could be a powerful tool to inform the management of complex microbial communities.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “human stool-derived in vitro microbial communities”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112732795 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA112732795 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA112732795 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Stool samples were collected from healthy human donors |
| SAMEA112732795 | health_condition_detail | healthy human donors | R3 | 0.70 | paper.fulltext.methods | Stool samples were collected from healthy human donors |
| SAMEA112732795 | subject_id | S01 | R2 | 0.85 | paper.supp.41467_2024_46766_MOESM4_ESM.xlsx[metadata for COP!Subject] | S01 |
Sequencing
3,994 runs over 3,564 samples · mean 0.43 Gbp per run (median 0.32 Gbp, total 1,734.23 Gbp; 3,994 runs with a base count) · layout PAIRED 3,994 · platform ILLUMINA 3,994 · models Illumina NovaSeq 6000 (3,994) · 2% of runs with a Sandpiper profile · first public 2023-11-30
Downloads
PRJEB60398.csv.gz (65.3 KB) · parquet (175.4 KB) — all 3,564 samples, every field with route and confidence · PRJEB60398_determinations.csv.gz (84.1 KB) — 17,372 evidence rows