Human gut microbiome time series, healthy, NYC
88 samples from healthy individuals in New York City, USA, in a longitudinal design using replicate sampling and spike-in sequencing to quantify temporal, spatial, and technical variability in gut microbiota abundances. machine-written summary
88 samples · 88 runs · US · Age unknown · 2019 · 1.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 616 sample values (collection date, country, latitude, location locality, location region, longitude, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 264 sample values (health condition, health condition detail, sex) · PMC7219825 |
| ○ 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 |
longitudinal — not resolved
Genera, mean relative abundance over 80 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 | 88 | 100% | ||||
| country | 88 | 100% | 88 | |||
| health_condition | 88 | 100% | 88 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 88 | 100% | 88 | |||
| detailed_location | 88 | 100% | ||||
| health_condition_detail | 88 | 100% | 88 | |||
| latitude | 88 | 100% | 88 | |||
| location_locality | 88 | 100% | 88 | |||
| location_region | 88 | 100% | 88 | |||
| longitude | 88 | 100% | 88 | |||
| sex | 88 | 100% | 88 | |||
| timepoint_label | 88 | 100% | 88 |
- Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. 2019 PMID 31308552 PMC7219825 own_data
Archive description
Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here we present DIVERS, a widely applicable method based on replicate sampling and spike-in sequencing. The method rigorously quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan’s Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance variance at short time scales (weeks), while temporal variability dominated at longer time scales (several months).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11572016 | collection_date | 2016-11-02 | R1 | 0.90 | biosample.attribute:collection_date | 2016-11-02 |
| SAMN11572016 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: New York City |
| SAMN11572016 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | a healthy male adult |
| SAMN11572016 | health_condition_detail | healthy adult male volunteer providing fecal time series | R3 | 0.60 | paper.fulltext.methods | a healthy male adult |
| SAMN11572016 | latitude | 40.7128 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7128 N 74.0060 W |
| SAMN11572016 | location_locality | New York City | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York City |
| SAMN11572016 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York City |
| SAMN11572016 | longitude | -74.0060 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7128 N 74.0060 W |
| SAMN11572016 | sex | male | R3 | 0.70 | paper.fulltext.methods | the subject in the study, a healthy male adult |
| SAMN11572016 | timepoint_label | 9:00AM | R1 | 0.85 | sample.attr.time | 9:00AM |
Sequencing
88 runs over 88 samples · mean 1.36 Gbp per run (median 1.39 Gbp, total 119.72 Gbp; 88 runs with a base count) · layout PAIRED 88 · platform ILLUMINA 88 · models HiSeq X Ten (88) · 91% of runs with a Sandpiper profile · first public 2019-05-08
Downloads
PRJNA541083.csv.gz (3.2 KB) · parquet (74.4 KB) — all 88 samples, every field with route and confidence · PRJNA541083_determinations.csv.gz (5.8 KB) — 880 evidence rows