Gut Metagenomes of South Asian Immigrants in Toronto
Cross-sectional study of 96 gut metagenome samples from first- and second-generation South Asian Canadians in Toronto, examining how migration and generational time in Canada relate to gut microbial community composition. machine-written summary
96 samples · 96 runs · CA · Adult · 2021 · 4.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,151 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 96 sample values (antibiotic exposure) · PMC8023248 |
| ○ 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 |
age: two sequence archives disagree for 1 sample (e.g. 1046.0 vs 10475.4) — withheld.
The sources disagree on 1 sample. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN15470533 | age | 1046.0 (sequence archive) | 10475.4 (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 86 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 | 96 | 100% | ||||
| country | 96 | 100% | 96 | |||
| health_condition | 96 | 100% | 96 | |||
| subject_id | 96 | 100% | 96 | |||
| antibiotic_exposure | 96 | 100% | 96 | |||
| bmi | 96 | 100% | 96 | |||
| collection_date | 96 | 100% | 96 | |||
| detailed_location | 96 | 100% | ||||
| health_condition_detail | 96 | 100% | 96 | |||
| latitude | 96 | 100% | 96 | |||
| location_locality | 96 | 100% | 96 | |||
| location_region | 96 | 100% | 96 | |||
| longitude | 96 | 100% | 96 | |||
| sex | 96 | 100% | 96 | |||
| age_at_collection_days | 95 | 99% | 95 |
- The Impact of Migration on the Gut Metagenome of South Asian Canadians. 2021 PMID 33794735 PMC8023248 unsure
Archive description
The gut metagenome of first and second generation South Asian Canadians was sequenced and characterized. Following immigration from typically low-incidence countries, South Asian Canadians experience a disproportionate risk of developing certain immune-mediate inflammatory diseases (IMIDs). We sought to understand the changes that occur in the metagenome following immigration, how this transcends to descendants-of-immigrants and future generations, and how this may influence the development of IMIDs.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
- life stage sample.attr.host_age · “18.38 (n=87/96)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15470463 | age_at_collection_days | 10815.1 | R1 | 0.70 | sample.attr.host_age | 29.61 |
| SAMN15470463 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | exclusion criteria consisted of (1) use of antibiotics |
| SAMN15470463 | bmi | 20.8 | R1 | 0.90 | sample.attr.host_body_mass_index | 20.8 |
| SAMN15470463 | collection_date | 2015-10-13 | R1 | 0.90 | biosample.attribute:collection_date | 2015-10-13 |
| SAMN15470463 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Toronto |
| SAMN15470463 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:gastrointest_disord | gastrointest_disord: Healthy |
| SAMN15470463 | health_condition_detail | Healthy | R1 | 0.90 | sample.attr.gastrointest_disord | Healthy |
| SAMN15470463 | latitude | 43.6610 | R1 | 0.90 | biosample.attribute:lat_lon | 43.661000 N 79.394390 W |
| SAMN15470463 | location_locality | Toronto | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Toronto |
| SAMN15470463 | location_region | Ontario | R1 | 0.60 | biosample.attribute:lat_lon | 43.661000 N 79.394390 W |
| SAMN15470463 | longitude | -79.3944 | R1 | 0.90 | biosample.attribute:lat_lon | 43.661000 N 79.394390 W |
| SAMN15470463 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN15470463 | subject_id | 1 | R1 | 0.85 | sample.attr.host_subject_id | 1 |
Sequencing
96 runs over 96 samples · mean 5.51 Gbp per run (median 4.19 Gbp, total 528.59 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models NextSeq 550 (96) · 90% of runs with a Sandpiper profile · first public 2021-08-25
Authors (11)
Copeland JK first · Chao G · Vanderhout S · Acton E · Wang PW · Benchimol EI · El Sohami A · Croitoru K · Gommerman JL · Guttman DS · GEMINI Research Team last
Downloads
PRJNA644666.csv.gz (4.6 KB) · parquet (76.7 KB) — all 96 samples, every field with route and confidence · PRJNA644666_determinations.csv.gz (10.8 KB) — 1,247 evidence rows