16S vs shotgun metagenomics, gut microbiome, Rome, Italy
6 gut microbiome samples from Rome, Italy (mostly adolescents), used to compare 16S rRNA amplicon sequencing and shotgun metagenomics for taxonomic profiling. machine-written summary
6 samples · 6 runs · IT · Age unknown · 2018 · 4.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 47 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11102407 |
| ○ 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 |
Genera, mean relative abundance over 5 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 | 5 | 83% | ||||
| country | 6 | 100% | 6 | |||
| health_condition | 3 | 50% | 3 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 6 | 100% | 6 | |||
| detailed_location | 6 | 100% | ||||
| latitude | 6 | 100% | 6 | |||
| location_locality | 6 | 100% | 6 | |||
| location_region | 6 | 100% | 6 | |||
| longitude | 6 | 100% | 6 | |||
| age_at_collection_days | 5 | 83% | 5 | |||
| health_condition_detail | 3 | 50% | 3 |
- MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data. 2024 PMID 38700829 PMC11102407 unsure
Archive description
We compare the performance of 16S rRNA amplicon sequencing and shotgun metagenomics to perform taxonomic analysis of gut microbiome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “metagenomics of gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07427830 | age_at_collection_days | 5844.0 | R1 | 0.70 | sample.attr.host_age | 16 |
| SAMN07427829 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN07427829 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy:Rome |
| SAMN07427829 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:gastrointest_disord | Crohn disease |
| SAMN07427829 | health_condition_detail | Crohn disease | R1 | 0.90 | sample.attr.gastrointest_disord | Crohn disease |
| SAMN07427829 | latitude | 41.9028 | R1 | 0.90 | biosample.attribute:lat_lon | 41.9028 N 12.4964 E |
| SAMN07427829 | location_locality | Rome | R1 | 0.85 | biosample.attribute:geo_loc_name | Italy:Rome |
| SAMN07427829 | location_region | Latium | R1 | 0.60 | biosample.attribute:lat_lon | 41.9028 N 12.4964 E |
| SAMN07427829 | longitude | 12.4964 | R1 | 0.90 | biosample.attribute:lat_lon | 41.9028 N 12.4964 E |
Sequencing
6 runs over 6 samples · mean 4.41 Gbp per run (median 4.38 Gbp, total 26.45 Gbp; 6 runs with a base count) · layout PAIRED 6 · platform ILLUMINA 6 · models Illumina HiSeq 2500 (6) · 83% of runs with a Sandpiper profile · first public 2018-04-20
Authors (25)
Ormaasen I first · Rudi K · Diep DB · Snipen L last · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · Jang CS first · Kim H · Kim D · Han B last
Downloads
PRJNA394849.csv.gz (1.1 KB) · parquet (70.3 KB) — all 6 samples, every field with route and confidence · PRJNA394849_determinations.csv.gz (1016 B) — 47 evidence rows