Gut microbiome after antibiotics and autoFMT, USA
1 fecal sample from the USA, part of a study of healthy adults given amoxicillin-clavulanic acid followed by autologous fecal microbiota transplantation or saline enema in an intervention design. machine-written summary
7 samples · 7 runs · US · Age unknown · 2018 · 0.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 12 sample values (antibiotic exposure, subject id, timepoint) |
| ✓ Abstract / description | 6 sample values (antibiotic exposure) |
| ✓ Full text | 21 sample values (country, health condition, health condition detail) · PMC6249645 |
| ○ 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy Faecal microbiota transplantation design randomized_controlled_trial · population healthy_control · 5 days Amox-Clav then randomized autoFMT enema vs saline enema
“All received 5 days of Amox-Clav. Half were randomized to autoFMT” — abstract:30463925 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
1 of 1 people sampled more than once (7 samples; median 7, up to 7 per person). Schedule stated by the source: “stool samples pre- and post-Amox-Clav and enema and during a 90-day follow-up period” (time origin: unknown); stated follow-up 3 mo.
Genera, mean relative abundance over 1 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 | 7 | 100% | ||||
| country | 7 | 100% | 7 | |||
| health_condition | 7 | 100% | 7 | |||
| subject_id | 7 | 100% | 7 | |||
| antibiotic_exposure | 7 | 100% | 1 | 6 | ||
| health_condition_detail | 7 | 100% | 7 | |||
| timepoint_label | 4 | 57% | 4 |
- Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential. 2018 PMID 30463925 PMC6249645 own_data
Archive description
This study elucidates the effects of Amoxicillin / Clavulanic acid and of autologous Fecal Microbiota Transplantation (autoFMT) on the gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Fecal Metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR8182708 | antibiotic_exposure | yes | R1 | 0.70 | sample.name_rule:library_name | 10PA |
| SRR8181649 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | All received 5 days of Amox-Clav |
| SRR8181649 | country | US | R3 | 0.70 | paper.fulltext.methods | Washington University School of Medicine Human Research Protection Office |
| SRR8181649 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Ten healthy volunteers were recruited to participate |
| SRR8181649 | health_condition_detail | Healthy volunteers receiving Amox-Clav and autoFMT/placebo enema | R3 | 0.70 | paper.fulltext.methods | Ten healthy volunteers were recruited to participate |
| SRR8181649 | subject_id | 10 | R1 | 0.70 | sample.name_rule:library_name | 10_D30 |
| SRR8181649 | timepoint_label | day 30 postenema | R1 | 0.70 | sample.name_rule:library_name | 10_D30 |
Sequencing
7 runs over 7 samples · mean 0.56 Gbp per run (median 0.70 Gbp, total 3.94 Gbp; 7 runs with a base count) · layout SINGLE 7 · platform ILLUMINA 7 · models NextSeq 550 (7) · 86% of runs with a Sandpiper profile · first public 2018-11-14 – 2019-01-14
Authors (13)
Bulow C first · Langdon A · Hink T · Wallace M · Reske KA · Patel S · Sun X · Seiler S · Jones S · Kwon JH · Burnham CA · Dantas G · Dubberke ER last
Downloads
PRJNA446061.csv.gz (1.1 KB) · parquet (69.6 KB) — all 7 samples, every field with route and confidence · PRJNA446061_determinations.csv.gz (1.0 KB) — 39 evidence rows