Infant FMT longitudinal gut metagenomes, Houston, USA
5 samples from Houston, USA, spanning infant and adult subjects, including an FMT intervention cohort (pre-FMT, post-FMT, and donor samples) and a healthy control, studied longitudinally. machine-written summary
5 samples · 5 runs · US · Age unknown · 2021 · 10.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 60 sample values (age, collection date, country, health condition, health condition detail, intervention, intervention detail, latitude) |
| ✓ Abstract / description | 4 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC9249589 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention · arms resolved
2 people have samples in more than one arm.
Faecal microbiota transplantation design single_arm_before_after · Fecal microbiota transplantation; pre-FMT vs post-FMT recipient samples and donor samples
“Pre-FMT, Post-FMT subjects as well as Donors” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
2 of 3 people sampled more than once (4 samples; median 2, up to 2 per person) · follow-up median 31 d (max 31 d) · median interval between samples 31 d (time from collection dates). Schedule stated by the source: “Pre-FMT and post-FMT samples per recipient (e.g. collection.id C0/C1 pre, C2/C3 post); donor sampled once.” (time origin: FMT intervention).
Each row is one person (2 shown); dots are samples at days since that person's first sample.
1 healthy adult donor (D003) linked to 2 FMT recipients (P017, P018) sampled pre- and post-transplant..
Genera, mean relative abundance over 5 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 | 5 | 100% | ||||
| country | 5 | 100% | 5 | |||
| health_condition | 5 | 100% | 5 | |||
| subject_id | 5 | 100% | 5 | |||
| age_at_collection_days | 5 | 100% | 5 | |||
| collection_date | 5 | 100% | 5 | |||
| detailed_location | 5 | 100% | ||||
| health_condition_detail | 5 | 100% | 1 | 4 | ||
| intervention | 5 | 100% | 5 | |||
| intervention_detail | 5 | 100% | 5 | |||
| latitude | 5 | 100% | 5 | |||
| location_locality | 5 | 100% | 5 | |||
| location_region | 5 | 100% | 5 | |||
| longitude | 5 | 100% | 5 | |||
| sex | 4 | 80% | 4 |
- SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens 2023 own_data
- KOMB: K-core based de novo characterization of copy number variation in microbiomes. 2022 PMID 35832621 PMC9249589 unsure
Archive description
Contains reads from Pre-FMT, Post-FMT subjects as well as Donors.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Human FMT samples”
- body site run.scientific_name · “human feces metagenome”
- body site study.description · “Pre-FMT, Post-FMT subjects as well as Donors”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21899241 | age_at_collection_days | 1095.8 | R1 | 0.70 | sample.attr.host_age | 3 |
| SAMN21899241 | collection_date | 2016-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01-01 |
| SAMN21899241 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Houston |
| SAMN21899241 | health_condition | intervention_cohort | R1 | 0.80 | biosample_attr | PreFMT |
| SAMN21899245 | health_condition_detail | Healthy adult stool donor | R1 | 0.85 | biosample.attribute:group | HealthyAdultDonor |
| SAMN21899241 | health_condition_detail | mixed_case_control: Cohort includes Pre-FMT subjects (disease status unspecified), Post-FMT subjects, and healthy donors | R4 | 0.50 | study.description | Pre-FMT, Post-FMT subjects as well as Donors |
| SAMN21899241 | intervention | no_intervention | R1 | 0.90 | biosample.attribute:group | group: PreFMT |
| SAMN21899241 | intervention_detail | recipient sample before FMT | R1 | 0.90 | biosample.attribute:group | group: PreFMT |
| SAMN21899241 | latitude | 29.7079 | R1 | 0.90 | biosample.attribute:lat_lon | 29.7078663 N 95.4037652 W |
| SAMN21899241 | location_locality | Houston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Houston |
| SAMN21899241 | location_region | Texas | R1 | 0.60 | biosample.attribute:lat_lon | 29.7078663 N 95.4037652 W |
| SAMN21899241 | longitude | -95.4038 | R1 | 0.90 | biosample.attribute:lat_lon | 29.7078663 N 95.4037652 W |
| SAMN21899241 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN21899241 | subject_id | P017 | R1 | 0.85 | sample.attr.host_subject_id | P017 |
Sequencing
5 runs over 5 samples · mean 10.40 Gbp per run (median 10.41 Gbp, total 51.98 Gbp; 5 runs with a base count) · layout PAIRED 5 · platform ILLUMINA 5 · models Illumina HiSeq 2000 (5) · 100% of runs with a Sandpiper profile · first public 2021-10-05
Authors (15)
Balaji A first · Sapoval N · Seto C · Leo Elworth RA · Fu Y · Nute MG · Savidge T · Segarra S · Treangen TJ last · Liu Y · Hu B · Kappell A · LeSassier DS · Godbold GD · Ternus KL
Downloads
PRJNA743023.csv.gz (1.2 KB) · parquet (71.7 KB) — all 5 samples, every field with route and confidence · PRJNA743023_determinations.csv.gz (1.6 KB) — 64 evidence rows