Longitudinal gut metagenomes, healthy Massachusetts adults
86 longitudinal human gut metagenome samples from healthy control individuals in Massachusetts, USA, generated to study DNA inversion-mediated phase variation (invertons) in gut bacteria. machine-written summary
86 samples · 469 runs · US · Age unknown · 2019 · 1.5 Mbp / sample · cohort Invertible promoters mediate bacterial phase varia
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 602 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6543533 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 172 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 |
longitudinal
13 of 13 people sampled more than once (86 samples; median 2, up to 34 per person) · follow-up median 2 mo (max 7 mo) · median interval between samples 3 d (time from collection dates). Schedule stated by the source: “Timepoints labeled numerically (e.g. time point 0001-0061); samples per subject: 11 subjects x2, 1 subject x30, 1 subject x34”.
Each row is one person (13 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 86 | 100% | 86 | |||
| health_condition | 86 | 100% | 86 | |||
| subject_id | 86 | 100% | 86 | |||
| collection_date | 86 | 100% | 86 | |||
| detailed_location | 86 | 100% | ||||
| health_condition_detail | 86 | 100% | 86 | |||
| latitude | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| longitude | 86 | 100% | 86 | |||
| timepoint_label | 86 | 100% | 86 |
- Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. 2019 PMID 30630933 PMC6543533 unsure
Archive description
Dense longitudinal metagenomic sequencing of bacterial species with invertible promoters from healthy individuals
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Human gut metagenome raw sequence reads”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10409998 | collection_date | 2014-07-10 | R1 | 0.90 | biosample.attribute:collection_date | 2014-07-10 |
| SAMN10409998 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Massachusetts |
| SAMN10409998 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN10409998 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN10409998 | latitude | 42.3700 | R1 | 0.90 | biosample.attribute:lat_lon | 42.37 N 71.08 W |
| SAMN10409998 | location_region | Massachusetts | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Massachusetts |
| SAMN10409998 | longitude | -71.0800 | R1 | 0.90 | biosample.attribute:lat_lon | 42.37 N 71.08 W |
| SAMN10409998 | subject_id | aa | R1 | 0.70 | sample.name_rule:library_names | library_names: sub_aa0154 |
| SAMN10409998 | timepoint_label | time point 0154 | R1 | 0.70 | sample.name_rule:library_names | library_names: sub_aa0154 |
Sequencing
469 runs over 469 samples · mean 1.6 Mbp per run (median 1.5 Mbp, total 0.76 Gbp; 469 runs with a base count) · layout PAIRED 469 · platform ILLUMINA 469 · models Illumina HiSeq 2500 (469) · 0% of runs with a Sandpiper profile · first public 2019-01-02
Authors (12)
Jiang X first · Hall AB · Arthur TD · Plichta DR · Covington CT · Poyet M · Crothers J · Moses PL · Tolonen AC · Vlamakis H · Alm EJ · Xavier RJ last
Downloads
PRJNA503484.csv.gz (3.1 KB) · parquet (74.4 KB) — all 86 samples, every field with route and confidence · PRJNA503484_determinations.csv.gz (6.7 KB) — 774 evidence rows