Ex vivo faecal incubation study in healthy adults, Cork
142 faecal samples from healthy adult volunteers in Cork, Ireland, collected during anaerobic ex vivo incubation of intact feces at 37°C over time to track virome and bacterial community dynamics, including Prevotella collapses and phage blooms. machine-written summary
142 samples · 142 runs · IE · Adult · 2023 · 1.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,412 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ✓ Abstract / description | 4 sample values (health condition) |
| ✓ Full text | 142 sample values (location locality) · PMC10825054 |
| ✓ Supplementary tables | 142 sample values (bmi) |
| – 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
14 of 14 people sampled more than once (142 samples; median 14, up to 15 per person).
Genera, mean relative abundance over 43 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 | 142 | 100% | ||||
| country | 142 | 100% | 142 | |||
| health_condition | 142 | 100% | 138 | 4 | ||
| subject_id | 142 | 100% | 142 | |||
| age_at_collection_days | 142 | 100% | 142 | |||
| bmi | 142 | 100% | 142 | |||
| collection_date | 142 | 100% | 142 | |||
| detailed_location | 142 | 100% | ||||
| latitude | 142 | 100% | 142 | |||
| location_locality | 142 | 100% | 142 | |||
| location_region | 142 | 100% | 142 | |||
| longitude | 142 | 100% | 142 | |||
| sex | 142 | 100% | 142 | |||
| health_condition_detail | 138 | 97% | 138 |
- Dynamic nature of viral and bacterial communities in human faeces. 2024 PMID 38292428 PMC10825054 own_data
Archive description
In this study we used freshly collected faeces from eight healthy volunteers. To simulate extended colonic retention of faeces, intact samples were aliquoted and placed into anaerobic incubator at 37C shortly after collection, without addition of any media, diluents or substrates. Aliquots were removed for analysis at different timepoints. Virome (phageome) and microbiome composition were assessed by shotgun metagenomic and 16S rRNA amplicon library sequencing. All samples showed significant and steady changes over time. There was a steady increase in virome richness and subject specific blooms and collapses of certain phage and bacterial populations. Samples collected from Prevotella-rich individuals showed a striking collapse of Prevotella populations accompanied by a decrease in specific Petitvirales and increase of specific Crassvirales phages.
How this project entered the registry
Classified as human gut / stool mixed assays of adult by sonnet_x2 with confidence 0.70. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.title · “human faeces during ex vivo incubation”
- life stage study.description · “eight healthy volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31873707 | age_at_collection_days | 14975.2 | R1 | 0.70 | sample.attr.host_age | 41 |
| SAMN31873707 | bmi | 19.92 | R2 | 0.85 | paper.supp.mmc2.xls[Table_S1!BMI] | 19.921875 |
| SAMN31873707 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN31873707 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland: Cork |
| SAMN31873707 | health_condition | healthy_control | R1 | 0.70 | biosample.name_rule:alias | Subj927_96h_1 |
| SAMN31873713 | health_condition | healthy_control | R4 | 0.50 | study.description | freshly collected faeces from eight healthy volunteers |
| SAMN31873707 | health_condition_detail | healthy volunteers (project description) | R1 | 0.70 | biosample.name_rule:alias | Subj927_96h_1 |
| SAMN31873707 | latitude | 51.8900 | R1 | 0.90 | biosample.attribute:lat_lon | 51.89 N 8.49 W |
| SAMN31873707 | location_locality | Cork | R3 | 0.70 | paper.fulltext.methods | residents of Cork, Ireland |
| SAMN31873707 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland: Cork |
| SAMN31873707 | longitude | -8.4900 | R1 | 0.90 | biosample.attribute:lat_lon | 51.89 N 8.49 W |
| SAMN31873707 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN31873707 | subject_id | APC055_927 | R1 | 0.85 | sample.attr.host_subject_id | APC055_927 |
Sequencing
142 runs over 142 samples · mean 1.15 Gbp per run (median 1.25 Gbp, total 162.94 Gbp; 142 runs with a base count) · layout PAIRED 142 · platform ILLUMINA 142 · models Illumina HiSeq 2500 (142) · 52% of runs with a Sandpiper profile · first public 2023-10-28
Authors (7)
Shkoporov AN first · O'Regan O · Smith L · Khokhlova EV · Draper LA · Ross RP · Hill C last
Downloads
PRJNA905467.csv.gz (4.1 KB) · parquet (76.0 KB) — all 142 samples, every field with route and confidence · PRJNA905467_determinations.csv.gz (11.4 KB) — 1,700 evidence rows