Host-microbe ratio prediction from multi-site swabs, Toronto
86 samples (oropharyngeal swabs, stool, rectal swabs, vaginal secretions) from Toronto, Canada, used to assess sequencing depth effects on alpha diversity and to build a qPCR-based model predicting human-to-microbe read ratios. machine-written summary
86 samples · 86 runs · CA · Age unknown · 2021 · 3.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 582 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8409737 |
| ○ 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
17 of 17 people sampled more than once (66 samples; median 4, up to 4 per person) · follow-up median 2 mo (max 6 mo) · median interval between samples 29 d (time from collection dates).
Each row is one person (17 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 75 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 | 86 | 100% | 86 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 66 | 77% | 66 | |||
| collection_date | 86 | 100% | 86 | |||
| detailed_location | 86 | 100% | ||||
| latitude | 86 | 100% | 86 | |||
| location_locality | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| longitude | 86 | 100% | 86 |
- Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing. 2021 PMID 34254823 PMC8409737 own_data
Archive description
Metagenomes were generated from DNA isolated from oropharyngeal swabs, stool samples, rectal swabs and vaginal secretions to determine effects of sequencing depth on alpha diversity and to determine the ratio of human to microbial reads seen when sequenced via shotgun sequencing.
How this project entered the registry
Classified as human gut / stool / vaginal / urogenital / oral cavity shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “oropharyngeal swabs, stool samples, rectal swabs and vaginal secretions”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18533780 | collection_date | 2017-02-17 | R1 | 0.90 | biosample.attribute:collection_date | 2017-02-17 |
| SAMN18533780 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada:Toronto |
| SAMN18533780 | latitude | 43.6500 | R1 | 0.90 | biosample.attribute:lat_lon | 43.65 N 79.38 W |
| SAMN18533780 | location_locality | Toronto | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Toronto |
| SAMN18533780 | location_region | Ontario | R1 | 0.60 | biosample.attribute:lat_lon | 43.65 N 79.38 W |
| SAMN18533780 | longitude | -79.3800 | R1 | 0.90 | biosample.attribute:lat_lon | 43.65 N 79.38 W |
| SAMN18533800 | subject_id | R01 | R1 | 0.85 | sample.attr.patient_id | R01 |
Sequencing
86 runs over 86 samples · mean 2.66 Gbp per run (median 3.27 Gbp, total 228.40 Gbp; 86 runs with a base count) · layout PAIRED 86 · platform ILLUMINA 86 · models Illumina NovaSeq 6000 (66), Illumina MiniSeq (20) · 88% of runs with a Sandpiper profile · first public 2021-04-01
Authors (10)
Cho MY first · Oliva M · Spreafico A · Chen B · Wei X · Choi Y · Kaul R · Siu LL · Coburn B · Schneeberger PHH last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA718445.csv.gz (3.2 KB) · parquet (73.7 KB) — all 86 samples, every field with route and confidence · PRJNA718445_determinations.csv.gz (4.5 KB) — 582 evidence rows