Intra-individual gut microbiota variation, Tokyo
21 stool samples from a single healthy adult in Tokyo, Japan, examined in a cross-sectional design to assess whether gut microbiota profiles within a stool sample are homogenous or heterogeneous. machine-written summary
21 samples · 21 runs · JP · Adult · 2023 · 27.22 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 84 sample values (collection date, country, location region, subject id) |
| ✓ Abstract / description | 21 sample values (health condition) |
| – Full text | no open-access full text linked |
| – 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 |
longitudinal
10 of 11 people sampled more than once (20 samples; median 2, up to 2 per person) · follow-up median 7 d (max 7 d) · median interval between samples 7 d (time from collection dates).
Each row is one person (10 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 19 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 | 21 | 100% | ||||
| country | 21 | 100% | 21 | |||
| health_condition | 21 | 100% | 21 | |||
| subject_id | 21 | 100% | 21 | |||
| collection_date | 21 | 100% | 21 | |||
| detailed_location | 21 | 100% | ||||
| location_region | 21 | 100% | 21 |
Archive description
The composition of the gut microbiome can be considered as a complex ecosystem, with variations in the microbiome affected by a number of host and environmental factors. Several studies investigate the covariates that influence its structure and function, and find potential variables including diet, lifestyle, race, medication, and disease. These novel findings elucidate gut microbiota variations between inter-populations, and disentangle multiple confounding factors shaping human gut microbiome composition. Although most of the previous reports discussed 'inter'-individual gut microbiota variations, those within 'intra'-individual are less well understood. Then, we investigated whether human gut microbiota profiles within intra-stool sample are homogenous or heterogenous.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “gut microbiota composition within”
- body site study.description · “composition of the gut microbiome can be”
- life stage study.title · “from a healthy adult”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00428802 | collection_date | 2019-06-05 | R1 | 0.90 | biosample.attribute:collection_date | 2019-06-05 |
| SAMD00428802 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan:Tokyo |
| SAMD00428802 | health_condition | healthy_control | R4 | 0.50 | study.title | healthy adult |
| SAMD00428802 | location_region | Tokyo | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Tokyo |
| SAMD00428802 | subject_id | 1 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: Feces from Healthy human_1_1 |
Sequencing
21 runs over 21 samples · mean 30.04 Gbp per run (median 27.22 Gbp, total 630.83 Gbp; 21 runs with a base count) · layout PAIRED 21 · platform ILLUMINA 21 · models Illumina NovaSeq 6000 (21) · 90% of runs with a Sandpiper profile · first public 2023-12-21
Authors (0)
No author record.
Downloads
PRJDB12607.csv.gz (1.4 KB) · parquet (69.9 KB) — all 21 samples, every field with route and confidence · PRJDB12607_determinations.csv.gz (1.3 KB) — 105 evidence rows