Stool microbiome in TB/H. pylori breath-test study, Mali
Shotgun metagenomic analysis of stool from 10 samples collected in Mali as part of a study comparing oral urease breath test results with tuberculosis and Helicobacter pylori status. machine-written summary
10 samples · 10 runs · ML · Age unknown · 2017 · 18.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 10 sample values (country) |
| ✓ Abstract / description | 10 sample values (location region) |
| ✓ Full text | 50 sample values (collection date, health condition, health condition detail, location locality, location site) · PMC5046223 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 10 | 100% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 10 | 100% | 10 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| health_condition_detail | 10 | 100% | 10 | |||
| location_locality | 10 | 100% | 10 | |||
| location_region | 10 | 100% | 10 | |||
| location_site | 10 | 100% | 10 |
- Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali. 2016 PMID 27532494 PMC5046223 own_data
Archive description
Genome sequencing of M.tb
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.50. Assay shotgun_dna.
- host runs.scientific_name · “human gut metagenome (10)”
- host runs.isolation_source · “feces (10)”
- body site runs.scientific_name · “human gut metagenome (10)”
- body site runs.isolation_source · “feces (10)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07740643 | collection_date | 2011-06/2012-12 | R3 | 0.70 | paper.fulltext.methods | From June of 2011 to December 2012 |
| SAMN07740643 | country | ML | R1 | 0.90 | sample.attr.geo_loc_name | Mali |
| SAMN07740643 | health_condition | healthy_control | R3 | 0.60 | paper.fulltext.results | healthy control participants with no clinical or laboratory evidence |
| SAMN07740643 | health_condition_detail | TB- and H. pylori- healthy controls with positive oral UBT, stool sequenced | R3 | 0.60 | paper.fulltext.results | healthy control participants with no clinical or laboratory evidence |
| SAMN07740643 | location_locality | Bamako | R3 | 0.70 | paper.fulltext.methods | six referring health centers of Bamako and Point-G Hospital of Bamako |
| SAMN07740643 | location_region | Bamako | R4 | 0.50 | paper.abstract | healthy subjects in Bamako, Mali and performed |
| SAMN07740643 | location_site | Point-G Hospital of Bamako | R3 | 0.70 | paper.fulltext.methods | Point-G Hospital of Bamako, Mali |
Sequencing
10 runs over 10 samples · mean 17.08 Gbp per run (median 18.06 Gbp, total 170.79 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina HiSeq 2000 (10) · 80% of runs with a Sandpiper profile · first public 2017-10-11 – 2017-10-17
Authors (23)
Maiga M first · Cohen K · Baya B · Srikrishna G · Siddiqui S · Sanogo M · Somboro AM · Diarra B · Diallo MH · Mazumdar V · Yoder C · Orsega S · Belson M · Kassambara H · Goita D · Murphy RL · Dao S · Polis M · Diallo S · Timmins GS · Dodd L · Earl AM · Bishai WR last
Downloads
PRJNA413356.csv.gz (1.2 KB) · parquet (70.4 KB) — all 10 samples, every field with route and confidence · PRJNA413356_determinations.csv.gz (1.1 KB) — 70 evidence rows