IHMS fecal DNA extraction protocol comparison study
323 samples from two fecal specimens, processed by 15 contributors across 12 countries using different DNA preparation protocols, in a cross-sectional study comparing extraction methods for microbiome sequencing quality and comparability. machine-written summary
323 samples · 372 runs · Age unknown · 2017 · 5.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 318 sample values (subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6739870 |
| ○ 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 — not resolved
8 of 302 people sampled more than once (24 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 288 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 | 318 | 98% | 318 |
- Consistent and correctable bias in metagenomic sequencing experiments. 2019 PMID 31502536 PMC6739870 own_data
- Assessment of fecal DNA extraction protocols for metagenomic studies. 2020 PMID 32657325 PMC7355182 unsure
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression. 2023 PMID 37894218 PMC10609127 unsure
Archive description
A detailed understanding of human-microbe symbiosis requires a precise characterization of human-associated microorganisms, the human microbiome. To progress towards this ambitious goal it is of utmost importance that the data generated in each of many large projects involved in human metagenome research be optimally comparable. The International Human Microbiome Standards (IHMS) project coordinated the development of standard operating procedures designed to optimize data quality and comparability in the human microbiome field. Overall, IHMS focused on all key aspects of from human sample identification, collection and processing to DNA sequence generation and analysis. We herein outline IHMS contribution concerning sample identification, collection and processing. Consideration was given to the requirement for high throughput treatment of large sample sets. A suite of sample collection procedures were compared allowing the management of different conditions and delivery-time for appropriately identified samples. The 8 partners of IHMS and 15 contributors across 12 different countries further participated in a study designed to identify the critical features and optimal protocols for DNA preparation. Contributors were offered to treat aliquots of two fecal samples using their own lab procedures. Stringent selection criteria were applied for DNA yield and quality. Full metagenomic sequencing and analysis allowed to assess the recovery of diversity and specific bacterial taxa. An initial subset of 3 satisfactory protocols was selected and analysed with respect to sequencing and data analysis standards. A final set of 14 SOPs, covering all stages of the process, have been produced. It must be kept in mind that the specific area of nucleic acids preparation does see constant evolutions and improvements, such that IHMS protocols may not be regarded as optimal in the long run. Yet they will highlight critically key feature, may serve as benchmark and help move towards automation. Supported by the European Commission under the 7th Framework Programme, IHMS Project organizes public access to downloadable SOPs and enables exchanges between users and providers of the standards For mode details, see : http://www.microbiome-standards.org/
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 study.description · “human sample identification, collection and processing”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104057378 | subject_id | Conan | R1 | 0.70 | sample.name_rule:alias | sample_BYQ_2_1_Conan_Q |
| SAMEA4347455 | subject_id | B1-033 | R1 | 0.50 | sample.attr.anonymized_name | B1-033 |
Sequencing
372 runs over 323 samples · mean 4.85 Gbp per run (median 4.87 Gbp, total 1,805.37 Gbp; 372 runs with a base count) · layout PAIRED 343, SINGLE 29 · platform ILLUMINA 372 · models Illumina HiSeq 2000 (343), Illumina HiSeq 2500 (29) · 83% of runs with a Sandpiper profile · first public 2017-06-21
Authors (22)
McLaren MR first · Willis AD · Callahan BJ last · Yang F first · Sun J · Luo H · Ren H · Zhou H · Lin Y · Han M · Chen B · Liao H · Brix S · Li J · Yang H · Kristiansen K · Zhong H last · Wang L first · Ding R · He S · Wang Q · Zhou Y last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJEB14847.csv.gz (9.1 KB) · parquet (81.4 KB) — all 323 samples, every field with route and confidence · PRJEB14847_determinations.csv.gz (4.2 KB) — 318 evidence rows