Triangulation test for inhomogeneity in stool metagenomes
9 samples from Germany: three biological replicates taken from different locations in one human stool sample, each split into three technical replicates, used to test microbial homogeneity with MEGAN. machine-written summary
9 samples · 9 runs · DE · Age unknown · 2016 · 1.09 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 45 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 18 sample values (health condition detail, subject id) |
| – 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 |
Genera, mean relative abundance over 7 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 | 9 | 100% | 9 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 9 | 100% | 9 | |||
| collection_date | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| latitude | 9 | 100% | 9 | |||
| location_region | 9 | 100% | 9 | |||
| longitude | 9 | 100% | 9 |
- A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples. 2017 PMID 27984120 own_data
Archive description
In this study, we provide a non-parametric statistical "triangulation test" for the detection of inhomogeneity in metagenomic samples. The test requires biological replicates from one sample and additionally multiple technical replicates from each biological replicate. The test is based on a three-way computational comparisons of samples. We collected three biological replicates from different locations of a human stool sample (A, B, and C) to illustrate the application of the test. Each biological replicate is furthermore represented by three technical replicates (A1, A2, A3, B1, B2, B3, C1, C2, and C3). The triangulation test indicates that the microbial composition of human stool is not homogenous on the centimeter scale in our sample. The test is implemented in MEGAN6.
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 · “different locations of a human stool sample”
- body site study.description · “human stool sample (A, B, and C)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA3719559 | collection_date | 2015-11-09 | R1 | 0.90 | biosample.attribute:collection_date | 2015-11-09 |
| SAMEA3719559 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA3719559 | health_condition_detail | mixed_case_control: Single donor; health status not stated. Study is methodological, not a disease cohort. | R4 | 0.30 | paper.abstract | one piece of human stool |
| SAMEA3719559 | latitude | 48.5200 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.52 9.05 |
| SAMEA3719559 | location_region | Baden-Wuerttemberg | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.52 9.05 |
| SAMEA3719559 | longitude | 9.0500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.52 9.05 |
| SAMEA3719559 | subject_id | PRJEB12272_subject1 | R4 | 0.65 | design.single_subject:description | We collected three biological replicates from different locations of a human stool sample |
Sequencing
9 runs over 9 samples · mean 1.09 Gbp per run (median 1.09 Gbp, total 9.79 Gbp; 9 runs with a base count) · layout PAIRED 9 · platform ILLUMINA 9 · models Illumina MiSeq (9) · 78% of runs with a Sandpiper profile · first public 2016-10-25
Authors (6)
Huson DH first · Steel M · El-Hadidi M · Mitra S · Peter S · Willmann M last
Downloads
PRJEB12272.csv.gz (1.1 KB) · parquet (70.5 KB) — all 9 samples, every field with route and confidence · PRJEB12272_determinations.csv.gz (1.2 KB) — 63 evidence rows