Fecal microbiome, cardiometabolic risk, Torres Strait
100 stool samples, 50 each from Mer and Waiben Islands (Torres Strait, Australia), cross-sectional study of fecal microbiome traits linked to cardiometabolic disease markers in Indigenous island residents. machine-written summary
100 samples · 100 runs · AU · Adult · 2020 · 2.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 750 sample values (age, collection date, country, latitude, location region, location site, longitude, sex) |
| ✓ Abstract / description | 350 sample values (health condition detail, lifestyle, lifestyle detail, location region) |
| ✓ Full text | 100 sample values (subject id) · PMC7572126 |
| ○ 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 90 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 | 100 | 100% | ||||
| country | 100 | 100% | 100 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 100 | 100% | 100 | |||
| age_at_collection_days | 100 | 100% | 100 | |||
| collection_date | 100 | 100% | 100 | |||
| detailed_location | 100 | 100% | ||||
| health_condition_detail | 100 | 100% | 100 | |||
| latitude | 100 | 100% | 100 | |||
| lifestyle | 100 | 100% | 100 | |||
| lifestyle_detail | 100 | 100% | 100 | |||
| location_region | 100 | 100% | 50 | 50 | ||
| location_site | 100 | 100% | 100 | |||
| longitude | 100 | 100% | 100 | |||
| sex | 100 | 100% | 100 |
- Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities. 2020 PMID 33074097 PMC7572126 own_data
Archive description
This study was conducted in two Torres Straight Islands (TSI), Waiben (Thursday) and Murray (Mer) islands. Waiben island is a ~3.5 km2 island of the TSI archipelago located approximately 39 km north of Cape York Peninsula in the Torres Strait, Queensland, Australia. Besides local diet, residents of Waiben island have access to a versatile fast-food industry and ease of movement. Murray Island, on the other hand, is a ~4.3 km2 remote island of volcanic origin, the most easterly inhabited island of the TSI archipelago, just north of the Great Barrier Reef. Locals of Murray Island have a high intake of local fish (Sardine) and garden produce. Samples used in this study were collected as part of Torres Strait Islands Health Surveys in the Zenadth-Kes Health Partnership of 2016. A cohort of 100 volunteers, 50 from each island provided stool samples for metagenomic sequencing and that guided the inclusion criteria for this study.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “provided stool samples for metagenomic sequencing”
- life stage study.description · “A cohort of 100 volunteers”
- life stage sample.attr.age · “69 (n=16/100)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10383104 | age_at_collection_days | 23010.8 | R1 | 0.70 | sample.attr.age | 63 |
| SAMN10383104 | collection_date | 2016-09-26 | R1 | 0.90 | biosample.attribute:collection_date | 2016-09-26 |
| SAMN10383104 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia: Waiben (Thursday Isand) |
| SAMN10383104 | health_condition_detail | mixed_case_control: Mer (remote island, traditional diet) and Waiben (accessible island, takeaway food access) represent | R4 | 0.50 | paper.abstract | two Indigenous communities in the Torres Strait Islands |
| SAMN10383104 | latitude | -10.5799 | R1 | 0.90 | biosample.attribute:lat_lon | 10.5799 S 142.2194 E |
| SAMN10383104 | lifestyle | indigenous_community | R4 | 0.50 | paper.abstract | two Indigenous communities in the Torres Strait Islands |
| SAMN10383104 | lifestyle_detail | Indigenous Torres Strait Islander communities | R4 | 0.50 | paper.abstract | two Indigenous communities in the Torres Strait Islands |
| SAMN10383104 | location_region | Queensland | R1 | 0.60 | biosample.attribute:lat_lon | 10.5799 S 142.2194 E |
| SAMN10383154 | location_region | Queensland | R4 | 0.45 | ena.study_description | Torres Strait, Queensland, Australia |
| SAMN10383104 | location_site | Waiben (Thursday Isand) | R1 | 0.85 | biosample.attribute:geo_loc_name | Australia: Waiben (Thursday Isand) |
| SAMN10383104 | longitude | 142.2194 | R1 | 0.90 | biosample.attribute:lat_lon | 10.5799 S 142.2194 E |
| SAMN10383104 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN10383104 | subject_id | SAMN10383104 | R3 | 0.70 | design.one_sample_per_subject:fulltext | stool samples for metagenomic sequencing (total n = 100; 50 participants from each site) |
Sequencing
100 runs over 100 samples · mean 2.48 Gbp per run (median 2.39 Gbp, total 248.32 Gbp; 100 runs with a base count) · layout PAIRED 100 · platform ILLUMINA 100 · models Illumina HiSeq 2500 (100) · 90% of runs with a Sandpiper profile · first public 2020-08-21
Authors (35)
Mobegi FM first · Leong LE · Thompson F · Taylor SM · Harriss LR · Choo JM · Taylor SL · Wesselingh SL · McDermott R · Ivey KL · Rogers GB last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R
Downloads
PRJNA503909.csv.gz (4.3 KB) · parquet (77.0 KB) — all 100 samples, every field with route and confidence · PRJNA503909_determinations.csv.gz (8.9 KB) — 1,200 evidence rows