16S vs shallow shotgun metagenomics, China
162 samples from China, including real fecal samples and artificial mock communities of over 60 human gut bacterial species, compared 16S rRNA amplicon sequencing against shallow and deep whole-metagenome shotgun sequencing. machine-written summary
162 samples · 162 runs · CN · Age unknown · 2021 · 1.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 471 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8361837 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
65 of 77 people sampled more than once (150 samples; median 2, up to 4 per person) · follow-up median 14 mo (max 17 mo) · median interval between samples 14 mo (time from collection dates).
Each row is one person (36 shown of 65); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 136 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 | 0 | 0% | ||||
| country | 162 | 100% | 162 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 162 | 100% | 162 | |||
| collection_date | 147 | 91% | 147 |
- Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes. 2021 PMID 34394027 PMC8361837 own_data
Archive description
Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Till now, 16S rRNA gene amplicon sequencing (16S) is the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which composed of more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data and its accuracy was not satisfactory. Contrastively, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided highly resembled outputs to WMS data at both genus and species levels and presented much higher accurate taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “human gut bacterial species”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18868321 | collection_date | 2018-05-08 | R1 | 0.90 | biosample.attribute:collection_date | 2018-05-08 |
| SAMN18868321 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN18868321 | subject_id | #1 | R1 | 0.85 | sample.attr.host_subject_id | #1 |
Sequencing
162 runs over 162 samples · mean 3.40 Gbp per run (median 1.80 Gbp, total 550.62 Gbp; 162 runs with a base count) · layout PAIRED 162 · platform ILLUMINA 162 · models Illumina NovaSeq 6000 (162) · 84% of runs with a Sandpiper profile · first public 2021-05-09 – 2021-05-13
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA725047.csv.gz (5.1 KB) · parquet (75.7 KB) — all 162 samples, every field with route and confidence · PRJNA725047_determinations.csv.gz (3.4 KB) — 471 evidence rows