Temporal stability of human gut microbiome over 6 months
212 fecal shotgun metagenome samples collected to assess temporal stability of microbiome diversity, species, genes, and pathways over six months, used to estimate sample sizes for future case-control microbiome studies. machine-written summary
212 samples · 212 runs · CR · Age unknown · 2024 · 0.73 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 424 sample values (subject id, timepoint) |
| ✓ Abstract / description | 424 sample values (health condition, health condition detail) |
| ✓ Full text | 636 sample values (country, location region, location site) · PMC12415979 |
| – 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
50 of 122 people sampled more than once (140 samples; median 3, up to 3 per person) · follow-up median 30 d (max 30 d) · median interval between samples 30 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Two visits per subject (visit_number 1 and 2) over a six-month period to assess temporal stability.” (time origin: enrolment); stated follow-up 6 mo.
Each row is one person (36 shown of 50); 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 | 212 | 100% | 212 | |||
| health_condition | 212 | 100% | 212 | |||
| subject_id | 212 | 100% | 212 | |||
| detailed_location | 212 | 100% | ||||
| health_condition_detail | 212 | 100% | 212 | |||
| location_region | 212 | 100% | 212 | |||
| location_site | 212 | 100% | 212 | |||
| timepoint_label | 212 | 100% | 212 |
- Sample Size Estimations Based on Human Microbiome Temporal Stability Over 6 Months: A Shallow Shotgun Metagenome Sequencing Analysis. 2025 PMID 39927868 PMC12415979 cites_accession
Archive description
We evaluated the temporal stability of fecal microbial diversity, species level composition, and genes and functional pathways based on shallow shotgun metagenome sequencing from a population-based study in Costa Rica with two fecal samples separated by an interval of six months. We quantified the biological variability over six months with intraclass correlation coefficients (ICC). We then estimated the numbers of cases, assuming 1:1 or 1:3 matched case-control study, required to detect an association at significance levels of 0.05 and 0.001 with 80% power, based on the number of fecal specimens collected per participant.</p><p>To detect modest disease associations, our calculations indicate a need for a large number of cases. Using repeated prediagnostic samples and matching cases to a greater number of controls could reduce the required number of cases for detecting these associations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “temporal stability of fecal microbial diversity”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38453196 | country | CR | R3 | 0.70 | paper.fulltext.methods | conducted in the Guanacaste region of Costa Rica |
| SAMN38453196 | health_condition | healthy_control | R4 | 0.45 | study.description | population-based study in Costa Rica with two fecal samples |
| SAMN38453196 | health_condition_detail | Population-based cohort; no disease status stated for all subjects, so this statement is not supported. | R4 | 0.45 | study.description | population-based study in Costa Rica with two fecal samples |
| SAMN38453196 | location_region | Guanacaste | R3 | 0.70 | paper.fulltext.methods | conducted in the Guanacaste region of Costa Rica |
| SAMN38453196 | location_site | Proyecto Epidemiológico Guanacaste | R3 | 0.70 | paper.fulltext.methods | stored in liquid nitrogen at the Proyecto Epidemiológico Guanacaste repository |
| SAMN38453196 | subject_id | M40219 | R1 | 0.85 | biosample.attribute:sampleid2 | M40219 |
| SAMN38453196 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:visit_number | 1 |
Sequencing
212 runs over 212 samples · mean 0.87 Gbp per run (median 0.73 Gbp, total 184.37 Gbp; 212 runs with a base count) · layout PAIRED 212 · platform ILLUMINA 212 · models Illumina MiSeq (212) · 0% of runs with a Sandpiper profile · first public 2024-07-01
Authors (0)
No author record.
Downloads
PRJNA1045701.csv.gz (6.8 KB) · parquet (78.9 KB) — all 212 samples, every field with route and confidence · PRJNA1045701_determinations.csv.gz (10.3 KB) — 1,484 evidence rows