Simulated gut microbiome benchmark, Austria/France/Germany
1029 simulated samples generated with CAMISIM from real human gut microbiota data (Austria, France, Germany), designed to benchmark microbiome taxonomic profiling pipelines against GTDB and UHGG references. machine-written summary
1,029 samples · 1,029 runs · AT, FR, DE · Age unknown · 2024 · 2.99 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 8,502 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region) |
| ○ Abstract / description | read; no usable statement |
| – 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 |
longitudinal — not resolved
343 of 344 people sampled more than once (1,028 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 943 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 | 562 | 55% | ||||
| country | 1,029 | 100% | 1,029 | |||
| health_condition | 562 | 55% | 562 | |||
| subject_id | 1,029 | 100% | 1,029 | |||
| collection_date | 1,029 | 100% | 1,029 | |||
| latitude | 1,029 | 100% | 1,029 | |||
| longitude | 1,029 | 100% | 1,029 | |||
| age_at_collection_days | 562 | 55% | 562 | |||
| detailed_location | 562 | 55% | ||||
| health_condition_detail | 562 | 55% | 562 | |||
| location_region | 562 | 55% | 562 | |||
| sex | 562 | 55% | 562 | |||
| bmi | 547 | 53% | 547 |
- Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines. 2025 PMID 39804694 PMC11728698 unsure
Archive description
This study proposes some reference Human Gut Microbiota simulated samples with known species distribution, based upon real samples from PRJEB6070 and PRJEB7774, simulated with CAMISIM whose purpose is to benchmark microbiome pipelines.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “reference Human Gut Microbiota simulated samples”
- life stage sample.attr.age · “63.0 (n=292/1029)”
- life stage sample.attr.age · “66.0 (n=255/1029)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN35995419 | age_at_collection_days | 18993.0 | R1 | 0.70 | sample.attr.age | 52.0 |
| SAMN35995419 | bmi | 20.0 | R1 | 0.90 | sample.attr.body_mass_index | 20.0 |
| SAMN35995263 | collection_date | 2013 | R1 | 0.90 | biosample.attribute:collection_date | 2013 |
| SAMN35995263 | country | AT | R1 | 0.90 | sample.attr.geo_loc_name | Austria |
| SAMN35995419 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Normal |
| SAMN35995419 | health_condition_detail | Normal | R1 | 0.90 | sample.attr.diagnosis | Normal |
| SAMN35995263 | latitude | 47.8000 | R1 | 0.90 | biosample.attribute:lat_lon | 47.80 N 13.04 E |
| SAMN35995419 | location_region | Ile-de-France | R1 | 0.60 | biosample.attribute:lat_lon | 48.86 N 2.35 E |
| SAMN35995263 | longitude | 13.0400 | R1 | 0.90 | biosample.attribute:lat_lon | 47.80 N 13.04 E |
| SAMN35995419 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN35995263 | subject_id | 31766 | R1 | 0.70 | sample.name_rule:TITLE | 31766 |
| SAMN35995419 | subject_id | FR-001 | R1 | 0.85 | sample.attr.host_subject_id | FR-001 |
Sequencing
1,029 runs over 1,029 samples · mean 2.99 Gbp per run (median 2.99 Gbp, total 3,076.65 Gbp; 1,029 runs with a base count) · layout PAIRED 1,029 · platform ILLUMINA 1,029 · models Illumina MiSeq (1,029) · 92% of runs with a Sandpiper profile · first public 2024-01-11 – 2024-07-29
Authors (4)
Puller V first · Plaza Oñate F · Prifti E · de Lahondès R last
Downloads
PRJNA987980.csv.gz (22.1 KB) · parquet (107.1 KB) — all 1,029 samples, every field with route and confidence · PRJNA987980_determinations.csv.gz (60.9 KB) — 8,502 evidence rows