Gut microbiome before/after colon cleanout, Palo Alto
386 stool samples from 8 healthy adults in Palo Alto, CA, collected longitudinally before and after an induced bowel-preparation (colon cleanout) diarrhea perturbation, analyzed by V4 16S and shotgun metagenomic sequencing. machine-written summary
386 samples · 386 runs · US · Adult · 2017 · 1.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,293 sample values (age, bmi, collection date, country, health condition, health condition detail, intervention, latitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 386 sample values (antibiotic exposure) · PMC11085954, PMC12677068, PMC12764784, PMC13580483, PMC5576755, PMC6946648, PMC7707550, PMC9022020 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 18 sample values (health condition, health condition detail) · from HumanMetagenomeDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
7 people have samples in more than one arm.
Bowel cleansing / colonoscopy preparation design single_arm_before_after · population healthy_control · Polyethylene glycol bowel cleanout (colon cleanout) perturbation
“1-day induced iso-osmotic diarrhea (colon cleanout) perturbation” — bioproject.description (study level; per-sample arms are in the intervention column below)
subject ids shared by samples of both sexes (1 ids, 39 samples) — ids withheld.
The sources disagree on 39 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (39)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN07336600 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336601 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336602 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336603 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336604 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336605 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336606 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336607 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336608 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336609 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336610 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336611 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336612 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336613 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336614 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336615 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336616 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336617 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336618 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336619 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336620 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336621 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336622 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336623 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336624 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336625 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336626 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336627 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336628 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336629 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336630 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336631 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336632 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336633 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336634 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336635 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336636 | subject id | AAA | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336637 | subject id | AAA | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN07336638 | subject id | AAA | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
longitudinal
7 of 7 people sampled more than once (338 samples; median 41, up to 93 per person) · follow-up median 5 mo (max 11 mo) · median interval between samples 2 d (time from collection dates). Schedule stated by the source: “Daily or weekly stool sampling over ~22 weeks (range 20-55 weeks), ~10 weeks before and ~10 weeks after a 1-day induced diarrhea perturbation” (time origin: intervention_start); stated follow-up 2 mo.
Each row is one person (7 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 340 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 | 386 | 100% | ||||
| country | 386 | 100% | 386 | |||
| health_condition | 386 | 100% | 377 | 9 | ||
| subject_id | 338 | 88% | 338 | |||
| antibiotic_exposure | 386 | 100% | 386 | |||
| collection_date | 386 | 100% | 386 | |||
| detailed_location | 386 | 100% | ||||
| health_condition_detail | 386 | 100% | 377 | 9 | ||
| latitude | 386 | 100% | 386 | |||
| location_locality | 386 | 100% | 386 | |||
| location_region | 386 | 100% | 386 | |||
| longitude | 386 | 100% | 386 | |||
| age_at_collection_days | 377 | 98% | 377 | |||
| bmi | 377 | 98% | 377 | |||
| intervention | 377 | 98% | 377 | |||
| sex | 377 | 98% | 377 | |||
| timepoint_label | 377 | 98% | 377 |
- Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. 2017 PMID 28821012 PMC5576755 own_data
- The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria. 2020 PMID 31911589 PMC6946648 own_data
- Perturbation of the human gastrointestinal tract microbial ecosystem by oral drugs to treat chronic disease results in a spectrum of individual specific patterns of extinction and persistence of dominant microbial strains. 2020 PMID 33259474 PMC7707550 unsure
- Early indicators of microbial strain dysbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID-19 patients. 2022 PMID 35449389 PMC9022020 unsure
- Christensenella strain resources, genomic/metabolomic profiling, and association with host at species level. 2024 PMID 38722028 PMC11085954 unsure
3 more
- The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels. 2025 PMID 41331251 PMC12764784
- <i>Christensenella intestinihominis</i> MNO-863 improve obesity and related metabolic disorders via SCFAs-induced GLP-1 hormone secretion. 2025 PMID 41356823 PMC12677068
- Pangenome analysis reveals both niche-specific "specialists" and microbial "side hustlers" in colorectal cancer microbiomes. 2026 PMID 42740607 PMC13580483
Archive description
Eight healthy human adults provided about 40 stool samples each (range 37-128 samples/subject) at daily or weekly intervals over about 22 weeks (range 20-55 weeks) surrounding a 1-day induced iso-osmotic diarrhea (colon cleanout) perturbation. The cleanout was identical to a common bowel preparation procedure prior to colonoscopy, involving the consumption of up to 4L of a polyethylene glycol-electrolyte solution until diarrhea was clear and watery. DNA was extracted from stool samples and investigated with V4 16S amplicon sequencing and with shotgun metagenomic sequencing (both sequencing modes using the Illumina HiSeq platform).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “stool samples”
- life stage study.description · “Eight healthy human adults provided”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07336600 | age_at_collection_days | 11312.8 | R1 | 0.85 | sample.attr.host_age | 31 |
| SAMN07336600 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic use in the previous 6 months |
| SAMN07336600 | bmi | 20.0 | R1 | 0.90 | sample.attr.host_body_mass_index | 20.0 |
| SAMN07336600 | collection_date | 2014-05-19 | R1 | 0.90 | biosample.attribute:collection_date | 2014-05-19 |
| SAMN07336600 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Palo Alto, CA |
| SAMN07336600 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | healthy |
| SAMN07336977 | health_condition | healthy_control | R2 | 0.70 | external.hmgdb source | HMgDB Diagnosis=control; HMgDB Control=control |
| SAMN07336600 | health_condition_detail | healthy | R1 | 0.90 | sample.attr.host_disease | healthy |
| SAMN07336977 | health_condition_detail | control / control | R2 | 0.70 | external.hmgdb source | HMgDB Diagnosis=control; HMgDB Control=control |
| SAMN07336600 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:Colon_Cleanout_Interval | PreCC |
| SAMN07336600 | latitude | 37.4400 | R1 | 0.90 | biosample.attribute:lat_lon | 37.44 N 122.14 W |
| SAMN07336600 | location_locality | Palo Alto | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Palo Alto, CA |
| SAMN07336600 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Palo Alto, CA |
| SAMN07336600 | longitude | -122.1400 | R1 | 0.90 | biosample.attribute:lat_lon | 37.44 N 122.14 W |
| SAMN07336600 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN07336639 | subject_id | AAB | R1 | 0.85 | sample.attr.host_subject_id | AAB |
| SAMN07336600 | timepoint_label | Colon_Cleanout_Relative_Day -170 | R1 | 0.85 | biosample.attribute:Colon_Cleanout_Relative_Day | -170 |
Sequencing
386 runs over 386 samples · mean 1.86 Gbp per run (median 1.69 Gbp, total 716.20 Gbp; 386 runs with a base count) · layout PAIRED 386 · platform ILLUMINA 386 · models Illumina HiSeq 4000 (386) · 88% of runs with a Sandpiper profile · first public 2017-07-10
Authors (30)
Koo H first · Morrow CD last · Zhao Y first · Chen H · Huang J · Chistoserdova L · Yu Z last · Kong P first · Xian Y · Lao C · Huang B · Zhang D · Tai L · Pu Z · Lan Z · Zhang C · Liu Z · Xiao C · Zhao G · Zhu R · Liang Y · Lin CS · Lin JH · Sun JZ · Wang T · Liu HW · Jiang X last · Lee J first · Minot S · Dey N last
Downloads
PRJNA388263.csv.gz (11.9 KB) · parquet (87.7 KB) — all 386 samples, every field with route and confidence · PRJNA388263_determinations.csv.gz (35.5 KB) — 5,697 evidence rows