Shallow shotgun vs 16S, healthy adults, California
78 stool samples from healthy adults in California, USA, comparing shallow shotgun and 16S rRNA sequencing for technical variation and taxonomic resolution; curated design field labels the study cross-sectional. machine-written summary
78 samples · 78 runs · US · Age unknown · 2023 · 70.7 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 546 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 · PMC10175443 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 156 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
5 of 5 people sampled more than once (78 samples; median 16, up to 16 per person) · follow-up median 1 d (max 1 d) · median interval between samples 1 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “stool on day 1, day 2, day 8 and day 9 (twice daily/weekly collection cycle)” (time origin: enrolment); stated follow-up 8 d.
Each row is one person (5 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 25 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 | 78 | 100% | ||||
| country | 78 | 100% | 78 | |||
| health_condition | 78 | 100% | 78 | |||
| subject_id | 78 | 100% | 78 | |||
| collection_date | 78 | 100% | 78 | |||
| detailed_location | 78 | 100% | ||||
| health_condition_detail | 78 | 100% | 78 | |||
| latitude | 78 | 100% | 78 | |||
| location_region | 78 | 100% | 78 | |||
| longitude | 78 | 100% | 78 | |||
| timepoint_label | 78 | 100% | 78 |
- Shallow shotgun sequencing reduces technical variation in microbiome analysis. 2023 PMID 37169816 PMC10175443 own_data
Archive description
The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.description · “shallow shotgun stool microbiome sequencing”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32544719 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN32544719 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: California |
| SAMN32544719 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN32544719 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN32544719 | latitude | 37.7740 | R1 | 0.90 | biosample.attribute:lat_lon | 37.773972 N 122.431297 W |
| SAMN32544719 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California |
| SAMN32544719 | longitude | -122.4313 | R1 | 0.90 | biosample.attribute:lat_lon | 37.773972 N 122.431297 W |
| SAMN32544719 | subject_id | 1 | R1 | 0.85 | sample.attr.subject | 1 |
| SAMN32544719 | timepoint_label | 1 | R1 | 0.85 | sample.attr.week | 1 |
Sequencing
78 runs over 78 samples · mean 85.9 Mbp per run (median 70.7 Mbp, total 6.70 Gbp; 78 runs with a base count) · layout SINGLE 78 · platform ILLUMINA 78 · models NextSeq 500 (78) · 32% of runs with a Sandpiper profile · first public 2023-01-10
Authors (6)
La Reau AJ first · Strom NB · Filvaroff E · Mavrommatis K · Ward TL · Knights D last
Downloads
PRJNA917645.csv.gz (2.5 KB) · parquet (73.0 KB) — all 78 samples, every field with route and confidence · PRJNA917645_determinations.csv.gz (4.5 KB) — 702 evidence rows