Microbial enrichment method validated on gut/saliva samples
76 samples (saliva, stool, intestinal biopsies/scrapings) from the USA (University of Chicago, IL; Caltech, CA), used to validate a microbial-enrichment method (MEM) for reducing host DNA before shotgun metagenomic sequencing. machine-written summary
70 samples · 85 runs · US · Age unknown · 2023 · 0.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 341 sample values (collection date, country, location region, location site, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10885704 |
| ○ 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
6 of 6 people sampled more than once (61 samples; median 12, up to 12 per person).
Genera, mean relative abundance over 22 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 | 70 | 100% | 70 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 61 | 87% | 61 | |||
| collection_date | 70 | 100% | 70 | |||
| detailed_location | 70 | 100% | ||||
| location_region | 70 | 100% | 70 | |||
| location_site | 70 | 100% | 70 |
- Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples. 2023 PMID 37828152 PMC10885704 own_data
Archive description
Validation of MEM (microbial enrichment methodology) performed on human intestinal biopsies and human saliva samples. Study focused on identifying percentage of non-host reads following MEM treatment and analysis of microbial communities alteration from processing method.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool / oral cavity shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “10090”
- host study.description · “human intestinal biopsies and human saliva samples”
- body site study.description · “human intestinal biopsies”
- body site study.description · “human saliva samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36290066 | collection_date | 2021-06-09 | R1 | 0.90 | biosample.attribute:collection_date | 2021-06-09 |
| SAMN36290066 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: University of Chicago IL |
| SAMN36290066 | location_region | Illinois | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: University of Chicago IL |
| SAMN36290066 | location_site | University of Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: University of Chicago IL |
| SAMN36290066 | subject_id | CT7 | R1 | 0.70 | sample.name_rule:alias | CT7_TI1 |
Sequencing
85 runs over 70 samples · mean 5.59 Gbp per run (median 0.67 Gbp, total 474.99 Gbp; 85 runs with a base count) · layout PAIRED 85 · platform ILLUMINA 85 · models Illumina NovaSeq 6000 (85) · 40% of runs with a Sandpiper profile · first public 2023-08-25 – 2023-08-27
Authors (8)
Wu-Woods NJ first · Barlow JT · Trigodet F · Shaw DG · Romano AE · Jabri B · Eren AM · Ismagilov RF last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA991155.csv.gz (2.5 KB) · parquet (72.4 KB) — all 70 samples, every field with route and confidence · PRJNA991155_determinations.csv.gz (3.0 KB) — 341 evidence rows