ONT metagenomics protocol in bariatric surgery stool samples
Cross-sectional study of 139 gut microbiome samples from a bariatric surgery cohort, used to validate a semi-quantitative metagenomics protocol comparing Oxford Nanopore, Illumina, and SOLiD sequencing. machine-written summary
139 samples · 160 runs · Age unknown · 2021 · 0.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8536095 |
| ○ 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 |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population obesity · Bariatric surgery cohort
“stool samples from a bariatric surgery cohort” — abstract:34680891 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 21 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 | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% |
- Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol. 2021 PMID 34680891 PMC8536095 unsure
Archive description
The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenges. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole genome semi-quantitative metagenomics studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatic protocol to analyse ONT sequences taxonomically and functionally and optimized pre-analytic protocols including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence alignment and classification. Our protocol was evaluated using simulations of metagenomic communities which reflect naturally occuring compositional variations. Next, we validated both protocols using stool samples from a bariatric surgery cohort, sequenced with ONT, Illumina and SOLiD technologies. Results revealed similar diversity and microbial composition profiles
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 study.description · “whole genome semi-quantitative metagenomics studies of human gut microbiome”
- body site study.description · “human gut microbiome with Oxford Nanopore”
Sequencing
160 runs over 139 samples · mean 1.69 Gbp per run (median 0.34 Gbp, total 270.57 Gbp; 160 runs with a base count) · layout SINGLE 139, PAIRED 21 · platform OXFORD_NANOPORE 139, ILLUMINA 21 · models MinION (139), Illumina MiSeq (21) · 13% of runs with a Sandpiper profile · first public 2021-09-17
Help complete this project
4 of the 4 core fields are below 50% coverage: age_category, country, health_condition, subject_id. Share metadata
Downloads
PRJEB47445.csv.gz (3.7 KB) · parquet (73.3 KB) — all 139 samples, every field with route and confidence · PRJEB47445_determinations.csv.gz (168 B) — 0 evidence rows