Gut microbiota in Irish Travellers, cross-sectional
118 fecal samples from members of the Irish Travelling community in Ireland (mostly healthy adults, two elderly), examined in a cross-sectional study of gut microbiota in relation to lifestyle change. machine-written summary
118 samples · 118 runs · IE · Age unknown · 2020 · 3.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 590 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10154212, PMC9469561 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 701 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 98 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 | 111 | 94% | ||||
| country | 118 | 100% | 118 | |||
| health_condition | 117 | 99% | 117 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 118 | 100% | 118 | |||
| detailed_location | 118 | 100% | ||||
| latitude | 118 | 100% | 118 | |||
| location_region | 118 | 100% | 118 | |||
| longitude | 118 | 100% | 118 | |||
| age_at_collection_days | 117 | 99% | 117 | |||
| antibiotic_exposure | 117 | 99% | 117 | |||
| health_condition_detail | 117 | 99% | 117 | |||
| sex | 117 | 99% | 117 | |||
| bmi | 116 | 98% | 116 |
- Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population. 2022 PMID 36100953 PMC9469561 unsure
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
Archive description
Modern lifestyles increase the risk of chronic diseases, in part by modifying the microbiome, but the health effects of lifestyles enforced on ethnic minorities are under-studied. The ancient lifestyle of Irish Travellers, an ethnically distinct sub-population, was abruptly changed by legislation in 2002 which effectively ended nomadism. Comparative metagenomics of gut microbiomes shows that Travellers retain a microbiota akin to that of non-industrialised societies. This microbiome is associated with health-relevant functionality but its carriage has diminished in proportion to Travellers’ adoption of new living conditions. This forewarns public health implications when ethnic minorities are intentionally or unwittingly pressured to change lifestyles.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6591428 | age_at_collection_days | 16436.25 | R2 | 0.75 | external.cmd source | age: 45; age_unit: Year; age_group: Adult |
| SAMEA6591428 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA6591428 | bmi | 34.7 | R2 | 0.75 | external.cmd source | bmi: 34.7 |
| SAMEA6591428 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA6591428 | country | IE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Ireland |
| SAMEA6591428 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA6591428 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA6591428 | latitude | 51.8980 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.8979683 -8.4706097 |
| SAMEA6591428 | location_region | Munster | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.8979683 -8.4706097 |
| SAMEA6591428 | longitude | -8.4706 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.8979683 -8.4706097 |
| SAMEA6591428 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
Sequencing
118 runs over 118 samples · mean 3.21 Gbp per run (median 3.24 Gbp, total 379.29 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models NextSeq 500 (118) · 83% of runs with a Sandpiper profile · first public 2020-04-16
Authors (52)
Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Bai X first · Sun Y · Li Y · Li M · Cao Z · Huang Z · Zhang F · Yan P · Wang L · Luo J · Wu J · Fan D · Chen H · Zhi M · Lan P · Zeng Z · Wu X · Miao Y · Zuo T last · Ghosh TS first · Shanahan F · O'Toole PW last · Li S · Ying J · Wang H · Qu Y · Niu X · 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
Downloads
PRJEB36820.csv.gz (4.5 KB) · parquet (75.9 KB) — all 118 samples, every field with route and confidence · PRJEB36820_determinations.csv.gz (12.4 KB) — 1,291 evidence rows