DNA extraction protocols for gut microbiota in C. difficile
Fifty-six stool samples from nine healthy volunteers and nine C. difficile patients in Lyon, France. Cross-sectional comparison of four DNA extraction methods for 16S rRNA and metagenomic sequencing, evaluating protocol efficiency and microbiota recovery. machine-written summary
56 samples · 56 runs · FR · Adult · 2022 · 11.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 480 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10290636 |
| ○ 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
7 of 7 people sampled more than once (56 samples; median 8, up to 8 per person).
Genera, mean relative abundance over 51 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 | 56 | 100% | ||||
| country | 56 | 100% | 56 | |||
| health_condition | 48 | 86% | 48 | |||
| subject_id | 56 | 100% | 56 | |||
| detailed_location | 56 | 100% | ||||
| latitude | 56 | 100% | 56 | |||
| location_locality | 56 | 100% | 56 | |||
| location_region | 56 | 100% | 56 | |||
| longitude | 56 | 100% | 56 | |||
| collection_date | 48 | 86% | 48 | |||
| health_condition_detail | 48 | 86% | 48 |
- Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome. 2023 PMID 37355726 PMC10290636 own_data
Archive description
The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to select a unique and best performing DNA extraction protocol for both metagenomic sequencing methods. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Stand-alone versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMerieux) in order to facilitate DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium Difficile infection were extracted with all protocols and sequenced with both metagenomic methods. Protocols were ranked using wet- and dry-lab criteria, including quality control of extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “DNA extraction protocols from stool samples”
- life stage study.description · “nine healthy volunteers and nine patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15638185 | collection_date | 2017-01-04 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-04 |
| SAMN15638185 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France: Lyon |
| SAMN15638185 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | CDI positive |
| SAMN15638185 | health_condition_detail | CDI positive | R1 | 0.90 | sample.attr.host_disease | CDI positive |
| SAMN15638185 | latitude | 45.4300 | R1 | 0.90 | biosample.attribute:lat_lon | 45.43 N 4.49 E |
| SAMN15638185 | location_locality | Lyon | R1 | 0.85 | biosample.attribute:geo_loc_name | France: Lyon |
| SAMN15638185 | location_region | Rhone-Alpes | R1 | 0.60 | biosample.attribute:lat_lon | 45.43 N 4.49 E |
| SAMN15638185 | longitude | 4.4900 | R1 | 0.90 | biosample.attribute:lat_lon | 45.43 N 4.49 E |
| SAMN15638185 | subject_id | 2 | R1 | 0.70 | sample.name_rule:sample_alias | S-MN-2-1 |
Sequencing
56 runs over 56 samples · mean 12.07 Gbp per run (median 11.88 Gbp, total 675.67 Gbp; 56 runs with a base count) · layout PAIRED 56 · platform ILLUMINA 56 · models NextSeq 500 (56) · 91% of runs with a Sandpiper profile · first public 2022-10-20 – 2022-10-21
Authors (13)
Elie C first · Perret M · Hage H · Sentausa E · Hesketh A · Louis K · Fritah-Lafont A · Leissner P · Vachon C · Rostaing H · Reynier F · Gervasi G · Saliou A last
Downloads
PRJNA648321.csv.gz (2.3 KB) · parquet (71.8 KB) — all 56 samples, every field with route and confidence · PRJNA648321_determinations.csv.gz (4.1 KB) — 480 evidence rows