Gut microbiome sequencing method comparison, Taizhou, China
Cross-sectional study of 47 gut microbiome samples from Taizhou, China, comparing sampling sites, sequencers (HiSeq2500, X10, NovaSeq), and 16S vs. whole-metagenome shotgun library preparation protocols. machine-written summary
47 samples · 47 runs · CN · Age unknown · 2019 · 2.35 Gbp / sample
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what each source gave
| ✓ Sequence archive | 282 sample values (collection date, country, latitude, location locality, longitude, subject id) |
| – Abstract / description | no abstract or project description |
| – 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
4 of 4 people sampled more than once (47 samples; median 12, up to 12 per person) · follow-up median 5 mo (max 5 mo) · median interval between samples 5 mo (time from collection dates).
Each row is one person (1 shown of 4); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 37 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 | 47 | 100% | 47 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 47 | 100% | 47 | |||
| collection_date | 47 | 100% | 47 | |||
| detailed_location | 47 | 100% | ||||
| latitude | 47 | 100% | 47 | |||
| location_locality | 47 | 100% | 47 | |||
| longitude | 47 | 100% | 47 |
Archive description
The gut microbiome sequencing has made highly diverse microbiota profiling possible and push the frontiers of Omics studies in human biology. However, there are thorny issues in the microbiome sequencing quality control aspect. How the sampling site affects sequencing results and the extent of variations between sequencers with respect to whole-metagenome shotgun (WMS) library preparation protocols remains a neglected area of research. It is also unknown whether sequencing results from WMS protocols are comparable with those from the 16s amplicon protocol.</p><p>In the current study, we compared biological replicates from different sampling sites, evaluated three widely adopted sequencers (HiSeq2500, X10 and NovSeq) with the WMS protocol, and further compared the 16s data with the WMS library protocol. Finally, several algorithms were employed and compared to improve the population-wide comparability between the 16s and WMS protocols. We found heterogeneity between two sampling sites, comparable sequencing results generated by three sequencers, and major taxonomic profiling differences between the 16s protocol and WMS protocol. Additionally, our approach provides an effective tool to enhance the population-wide comparability between 16s and WMS data. Our orthogonal study not only the irreproducibility behind sampling sites, sequencer, and library preparation protocol, but also provided an effective way to reduce the biased readout of the datasets. We hope this work future can constitute a fundamental reference for WMS sequencer choice, sample preparation, and integrated analysis across 16s and WMS datasets.
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 study.description · “gut microbiome sequencing has made highly diverse”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10144967 | collection_date | 2017-04-14 | R1 | 0.90 | biosample.attribute:collection_date | 2017-04-14 |
| SAMN10144967 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Taizhou |
| SAMN10144967 | latitude | 32.3900 | R1 | 0.90 | biosample.attribute:lat_lon | 32.39 N 119.90 E |
| SAMN10144967 | location_locality | Taizhou | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Taizhou |
| SAMN10144967 | longitude | 119.9000 | R1 | 0.90 | biosample.attribute:lat_lon | 32.39 N 119.90 E |
| SAMN10144967 | subject_id | A | R1 | 0.70 | sample.name_rule:sample_alias | A1-T1-WMS-X10 |
Sequencing
47 runs over 47 samples · mean 6.91 Gbp per run (median 2.35 Gbp, total 325.00 Gbp; 47 runs with a base count) · layout PAIRED 47 · platform ILLUMINA 47 · models Illumina HiSeq 2500 (16), Illumina NovaSeq 6000 (16), HiSeq X Ten (15) · 79% of runs with a Sandpiper profile · first public 2019-04-02
Authors (0)
No author record.
Downloads
PRJNA493884.csv.gz (1.9 KB) · parquet (70.9 KB) — all 47 samples, every field with route and confidence · PRJNA493884_determinations.csv.gz (2.4 KB) — 282 evidence rows