DNA extraction method comparison in faecal samples, Denmark
24 faecal samples from healthy controls in Copenhagen, Denmark, used to compare MetaHIT vs. HMP DNA extraction protocols and assess effects of sample homogenization on bacterial community structure. machine-written summary
24 samples · 48 runs · DK · Age unknown · 2014 · 7.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 162 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 48 sample values (health condition, health condition detail) · PMC4063427 |
| ○ 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
3 of 3 people sampled more than once (18 samples; median 6, up to 6 per person).
Genera, mean relative abundance over 24 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 | 24 | 100% | 24 | |||
| health_condition | 24 | 100% | 24 | |||
| subject_id | 18 | 75% | 18 | |||
| collection_date | 24 | 100% | 24 | |||
| detailed_location | 24 | 100% | ||||
| health_condition_detail | 24 | 100% | 24 | |||
| latitude | 24 | 100% | 24 | |||
| location_locality | 24 | 100% | 24 | |||
| location_region | 24 | 100% | 24 | |||
| longitude | 24 | 100% | 24 |
- Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. 2014 PMID 24949196 PMC4063427 own_data
Archive description
In this study we conducted a systematic comparison of the DNA extraction methods on feacal samples used by the two major collaborative efforts: The European MetaHIT and the American Human Microbiome Project. Additionally, effects of homogenizing the samples before extraction were addressed. We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol. Whereas it is comforting that the inter-individual variation clearly exceeded the variation resulting from choice of extraction method, our data highlights the challenge of comparing data across studies applying different methodologies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site study.description · “purification of bacterial DNA from faecal material”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02711295 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMN02711295 | country | DK | R1 | 0.90 | sample.attr.geo_loc_name | Denmark: Copenhagen |
| SAMN02711295 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | processed from three healthy human volunteers within 4 hours |
| SAMN02711295 | health_condition_detail | healthy human volunteers | R3 | 0.70 | paper.fulltext.methods | processed from three healthy human volunteers within 4 hours |
| SAMN02711295 | latitude | 55.6800 | R1 | 0.90 | biosample.attribute:lat_lon | 55.68 N 12.57 E |
| SAMN02711295 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geo_loc_name | Denmark: Copenhagen |
| SAMN02711295 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:lat_lon | 55.68 N 12.57 E |
| SAMN02711295 | longitude | 12.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 55.68 N 12.57 E |
| SAMN02711295 | subject_id | A | R1 | 0.85 | biosample.attribute:test_person | A |
Sequencing
48 runs over 24 samples · mean 3.50 Gbp per run (median 3.52 Gbp, total 167.87 Gbp; 48 runs with a base count) · layout PAIRED 48 · platform ILLUMINA 48 · models Illumina HiSeq 2000 (48) · 92% of runs with a Sandpiper profile · first public 2014-08-11
Authors (7)
Wesolowska-Andersen A first · Bahl MI · Carvalho V · Kristiansen K · Sicheritz-Pontén T · Gupta R · Licht TR last
Downloads
PRJNA243036.csv.gz (1.4 KB) · parquet (70.9 KB) — all 24 samples, every field with route and confidence · PRJNA243036_determinations.csv.gz (2.1 KB) — 210 evidence rows