Pre-diabetic FMT gut microbiome study in Minneapolis, MN
25 gut microbiome samples from type 2 diabetes patients in Minneapolis, MN, in an intervention study of fecal microbiota transplantation (FMT). machine-written summary
25 samples · 25 runs · US · Age unknown · 2017 · 8.35 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 223 sample values (collection date, country, intervention, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 50 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
12 people have samples in more than one arm.
Faecal microbiota transplantation design single_arm_before_after · population type2_diabetes · Faecal microbiota transplantation in pre-diabetic patients
“pre-diabetic patients treated with FMT” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
12 of 13 people sampled more than once (24 samples; median 2, up to 2 per person) · follow-up median 2 mo (max 3 mo) · median interval between samples 2 mo (time from collection dates). Schedule stated by the source: “pre; post; donor” (time origin: intervention_start).
Each row is one person (12 shown); dots are samples at days since that person's first sample.
Pre-diabetic FMT: 1 sampled donor (Donor006) and 12 recipients pre/post; donor-recipient links not stated.
Genera, mean relative abundance over 24 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 | 25 | 100% | 25 | |||
| health_condition | 25 | 100% | 25 | |||
| subject_id | 25 | 100% | 25 | |||
| detailed_location | 25 | 100% | ||||
| health_condition_detail | 25 | 100% | 25 | |||
| latitude | 25 | 100% | 25 | |||
| location_locality | 25 | 100% | 25 | |||
| location_region | 25 | 100% | 25 | |||
| longitude | 25 | 100% | 25 | |||
| timepoint_label | 25 | 100% | 25 | |||
| collection_date | 24 | 96% | 24 | |||
| intervention | 24 | 96% | 24 |
Archive description
Characterization of gut bacterial communities in pre-diabetic patients treated with FMT
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “pre-diabetic patients treated with FMT”
- body site study.description · “gut bacterial communities”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07607958 | collection_date | 2016-09-13 | R1 | 0.90 | biosample.attribute:collection_date | 2016-09-13 |
| SAMN07607958 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Minneapolis, MN |
| SAMN07607958 | health_condition | type2_diabetes | R2 | 0.75 | external.gmrepo source | phenotype: Prediabetic State |
| SAMN07607958 | health_condition_detail | Prediabetic State | R2 | 0.75 | external.gmrepo source | phenotype: Prediabetic State |
| SAMN07607958 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:time_point | time_point: pre |
| SAMN07607958 | latitude | 44.9847 | R1 | 0.90 | biosample.attribute:lat_lon | 44.9847 N 93.1819 W |
| SAMN07607958 | location_locality | Minneapolis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Minneapolis, MN |
| SAMN07607958 | location_region | Minnesota | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Minneapolis, MN |
| SAMN07607958 | longitude | -93.1819 | R1 | 0.90 | biosample.attribute:lat_lon | 44.9847 N 93.1819 W |
| SAMN07607958 | subject_id | MND03 | R1 | 0.85 | sample.attr.subject | MND03 |
| SAMN07607958 | timepoint_label | pre | R1 | 0.85 | sample.attr.time_point | pre |
Sequencing
25 runs over 25 samples · mean 8.25 Gbp per run (median 8.35 Gbp, total 206.30 Gbp; 25 runs with a base count) · layout PAIRED 25 · platform ILLUMINA 25 · models Illumina HiSeq 4000 (25) · 96% of runs with a Sandpiper profile · first public 2017-11-09
Authors (0)
No author record.
Downloads
PRJNA386502.csv.gz (1.7 KB) · parquet (71.7 KB) — all 25 samples, every field with route and confidence · PRJNA386502_determinations.csv.gz (2.8 KB) — 273 evidence rows