Gut microbiome in Cheyenne & Arapaho vs Oklahoma non-natives
37 fecal samples from Cheyenne and Arapaho and non-native individuals in Oklahoma, comparing gut microbiome diversity between type 2 diabetes (19) and healthy controls (18) in a case-control design. machine-written summary
37 samples · 37 runs · US · Age unknown · 2015 · 4.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 74 sample values (country, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11009399, PMC13059687, PMC4703035, PMC6961876, PMC8325300 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 222 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 30 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 | 34 | 92% | ||||
| country | 37 | 100% | 37 | |||
| health_condition | 37 | 100% | 37 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 37 | 100% | 37 | |||
| antibiotic_exposure | 37 | 100% | 37 | |||
| bmi | 37 | 100% | 37 | |||
| detailed_location | 37 | 100% | ||||
| health_condition_detail | 37 | 100% | 37 | |||
| location_region | 37 | 100% | 37 | |||
| sex | 37 | 100% | 37 |
- Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma. 2015 PMID 26671671 PMC4703035 own_data
- Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. 2020 PMID 31940321 PMC6961876 unsure
- HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data. 2021 PMID 34330336 PMC8325300 unsure
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399 unsure
- Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway. 2025 PMID 41118772 PMC13059687 unsure
1 more
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
Gut microbiome diversity among the Cheyenne & Arapaho of Oklahoma
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04209218 | age_at_collection_days | 20088.75 | R2 | 0.75 | external.cmd source | age: 55; age_unit: Year; age_group: Adult |
| SAMN04209218 | antibiotic_exposure | yes | R2 | 0.75 | external.cmd source | antibiotics_current_use: Yes |
| SAMN04209218 | bmi | 31.0 | R2 | 0.75 | external.cmd source | bmi: 31 |
| SAMN04209218 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Oklahoma |
| SAMN04209218 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04209218 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04209218 | location_region | Oklahoma | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Oklahoma |
| SAMN04209218 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
Sequencing
37 runs over 37 samples · mean 4.32 Gbp per run (median 4.31 Gbp, total 159.87 Gbp; 37 runs with a base count) · layout PAIRED 37 · platform ILLUMINA 37 · models Illumina HiSeq 2000 (37) · 81% of runs with a Sandpiper profile · first public 2015-12-05
Authors (71)
Sankaranarayanan K first · Ozga AT · Warinner C · Tito RY · Obregon-Tito AJ · Xu J · Gaffney PM · Jervis LL · Cox D · Stephens L · Foster M · Tallbull G · Spicer P · Lewis CM last · Honap TP first · Schnorr SL · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Levy S · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · 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 · Zorea A first · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R · Mizrahi I last · Jacoby C first · Scorza K · Ecker L · Nol Bernardino P · Little AS · McMillin M · Ramaswamy R · Sundararajan A · Sidebottom AM · Lin H · Dufault-Thompson K · Hall B · Jiang X · Light SH last
Downloads
PRJNA299502.csv.gz (2.2 KB) · parquet (71.3 KB) — all 37 samples, every field with route and confidence · PRJNA299502_determinations.csv.gz (4.1 KB) — 296 evidence rows