Gut microbiota in TB patients vs healthy controls, Beijing
Shotgun sequencing of 107 gut microbiome samples from Beijing, China, comparing tuberculosis patients and healthy controls in a case-control design to characterize gut microbiota changes associated with active M. tuberculosis infection. machine-written summary
107 samples · 107 runs · CN · Adult · 2017 · 6.35 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 702 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 107 sample values (location site) · PMC11205787, PMC6456665, PMC9446638 |
| ✓ Supplementary tables | 106 sample values (health condition, health condition detail) |
| ✓ External resources | 202 sample values (age, health condition, health condition detail, sex) · from GMrepo v3, Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 96 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 | 107 | 100% | ||||
| country | 107 | 100% | 107 | |||
| health_condition | 107 | 100% | 30 | 77 | ||
| subject_id | 0 | 0% | ||||
| collection_date | 107 | 100% | 107 | |||
| detailed_location | 107 | 100% | ||||
| health_condition_detail | 107 | 100% | 30 | 77 | ||
| latitude | 107 | 100% | 107 | |||
| location_locality | 107 | 100% | 107 | |||
| location_region | 107 | 100% | 107 | |||
| location_site | 107 | 100% | 107 | |||
| longitude | 107 | 100% | 107 | |||
| age_at_collection_days | 77 | 72% | 77 | |||
| sex | 77 | 72% | 77 |
- The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients. 2019 PMID 31001490 PMC6456665 own_data
- Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. 2022 PMID 36068270 PMC9446638 unsure
- Deciphering Microbial Shifts in the Gut and Lung Microbiomes of COVID-19 Patients. 2024 PMID 38930440 PMC11205787 unsure
Archive description
Sequencing the gut microbiota to reveal the differences beween healthy controls and TB patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Human gut microbiota Raw sequence”
- body site study.description · “Sequencing the gut microbiota to reveal”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07606172 | age_at_collection_days | 9131.2 | R2 | 0.70 | external.meta2db source | host_age: 25 |
| SAMN07606172 | collection_date | 2016-05-23 | R1 | 0.90 | biosample.attribute:collection_date | 2016-05-23 |
| SAMN07606172 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Beijing |
| SAMN07606233 | health_condition | other_infection | R1 | 0.70 | sample.name_rule:sample_title | Patient_PT02 |
| SAMN07606172 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07606173 | health_condition | healthy_control | R2 | 0.80 | paper.supp.Data_Sheet_1.xlsx[Table S1!Health] | Health |
| SAMN07606233 | health_condition_detail | Patient | R1 | 0.70 | sample.name_rule:sample_title | Patient_PT02 |
| SAMN07606172 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07606173 | health_condition_detail | Health | R2 | 0.85 | paper.supp.Data_Sheet_1.xlsx[Table S1!Health] | Health |
| SAMN07606172 | latitude | 39.5600 | R1 | 0.90 | biosample.attribute:lat_lon | 39.56 N 116.24 E |
| SAMN07606172 | location_locality | Beijing | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Beijing |
| SAMN07606172 | location_region | Beijing | R1 | 0.60 | biosample.attribute:lat_lon | 39.56 N 116.24 E |
| SAMN07606172 | location_site | Beijing Chest Hospital, Capital Medical University | R3 | 0.70 | paper.fulltext.methods | approved by local ethics committees (Beijing Chest Hospital |
| SAMN07606172 | longitude | 116.2400 | R1 | 0.90 | biosample.attribute:lat_lon | 39.56 N 116.24 E |
| SAMN07606172 | sex | female | R2 | 0.70 | external.meta2db source | host_sex: female |
Sequencing
107 runs over 107 samples · mean 6.59 Gbp per run (median 6.35 Gbp, total 705.04 Gbp; 107 runs with a base count) · layout PAIRED 107 · platform ILLUMINA 107 · models Illumina HiSeq 2500 (107) · 90% of runs with a Sandpiper profile · first public 2017-09-30
Authors (43)
Hu Y first · Feng Y · Wu J · Liu F · Zhang Z · Hao Y · Liang S · Li B · Li J · Lv N · Xu Y · Zhu B · Sun Z last · Ke S first · Weiss ST · Liu YY last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Pusadkar V first · Mazumder A · Azad A · Patil D · Azad RK last · van Sinderen D
Downloads
PRJNA401385.csv.gz (4.2 KB) · parquet (76.1 KB) — all 107 samples, every field with route and confidence · PRJNA401385_determinations.csv.gz (10.6 KB) — 1,117 evidence rows