Gut metagenome of healthy adults from 3 Indian regions
Cross-sectional shotgun metagenomic study of 31 fecal samples from healthy adult individuals in Khargone (Madhya Pradesh), Jaisalmer (Rajasthan), and Ladakh (Jammu and Kashmir), India. machine-written summary
31 samples · 31 runs · IN · Age unknown · 2020 · 7.91 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 167 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 124 sample values (lifestyle, shared setting id, shared setting type, subject id) · PMC7141701 |
| ✓ Supplementary tables | 30 sample values (sex) |
| ✓ External resources | 155 sample values (age, antibiotic exposure, bmi, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
sex: supplementary table and curatedMetagenomicData disagree for 1 sample (e.g. female vs male) — withheld.
The sources disagree on 1 sample. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN11418672 | sex | female (supplementary table) | male (curatedMetagenomicData) | withheld: neither value published |
communitytribe
31 adults from 3 villages (Scur Buchan, Pipliya Buzurg, Khuri) of distinct ethnic groups3 shared settings.
member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 3 shared settings. 31 people in the project overall.
Genera, mean relative abundance over 29 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 | 31 | 100% | ||||
| country | 31 | 100% | 31 | |||
| health_condition | 31 | 100% | 31 | |||
| subject_id | 31 | 100% | 31 | |||
| age_at_collection_days | 31 | 100% | 31 | |||
| antibiotic_exposure | 31 | 100% | 31 | |||
| bmi | 31 | 100% | 31 | |||
| collection_date | 31 | 100% | 31 | |||
| detailed_location | 31 | 100% | ||||
| health_condition_detail | 31 | 100% | 31 | |||
| latitude | 31 | 100% | 31 | |||
| lifestyle | 31 | 100% | 31 | |||
| location_region | 31 | 100% | 31 | |||
| longitude | 31 | 100% | 31 | |||
| shared_setting_id | 31 | 100% | 31 | |||
| shared_setting_type | 31 | 100% | 31 | |||
| sex | 30 | 97% | 30 | |||
| location_locality | 12 | 39% | 12 |
- Metagenomics analysis reveals features unique to Indian distal gut microbiota. 2020 PMID 32267865 PMC7141701 own_data
- Statistical modeling of gut microbiota for personalized health status monitoring. 2023 PMID 37596617 PMC10436630 unsure
- Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort. 2024 PMID 37781761 PMC10803823 unsure
- Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population. 2024 PMID 41853539 PMC12993557 unsure
Archive description
The aim of the study is to find, compare, and understand the gut metagenomic composition of the healthy individuals from the different regions of India.
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 |
|---|---|---|---|---|---|---|
| SAMN11418649 | age_at_collection_days | 11322.75 | R2 | 0.75 | external.cmd source | age: 31; age_unit: Year; age_group: Adult |
| SAMN11418649 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN11418649 | bmi | 19.93 | R2 | 0.75 | external.cmd source | bmi: 19.93 |
| SAMN11418649 | collection_date | 2014-11-25 | R1 | 0.90 | biosample.attribute:collection_date | 2014-11-25 |
| SAMN11418649 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India: Khargone, Madhya Pradesh |
| SAMN11418649 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN11418649 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN11418649 | latitude | 22.2267 | R1 | 0.90 | biosample.attribute:lat_lon | 22.226704 N 75.863329 E |
| SAMN11418649 | lifestyle | indigenous_community | R3 | 0.70 | paper.fulltext.abstract | healthy individuals of Indian ethnic tribes |
| SAMN11418649 | location_locality | Khargone | R1 | 0.85 | biosample.attribute:geo_loc_name | India: Khargone, Madhya Pradesh |
| SAMN11418649 | location_region | Madhya Pradesh | R1 | 0.85 | biosample.attribute:geo_loc_name | India: Khargone, Madhya Pradesh |
| SAMN11418649 | longitude | 75.8633 | R1 | 0.90 | biosample.attribute:lat_lon | 22.226704 N 75.863329 E |
| SAMN11418649 | sex | male | R2 | 0.85 | paper.supp.pone.0231197.s008.xlsx[S3 Table!Gender (M/F)] | M |
| SAMN11418649 | shared_setting_id | Pipliya Buzurg | R3 | 0.60 | paper.body.Methods[sampling sites]+biosample.attribute:TITLE | TITLE 'Khargone 1'; Pipliya Buzurg village in Khargone |
| SAMN11418649 | shared_setting_type | village_or_community | R3 | 0.60 | paper.body.Methods[sampling sites]+biosample.attribute:TITLE | sampling sites ... Scur Buchan village in Ladakh ... Khuri village in Jaisalmer |
| SAMN11418649 | subject_id | SAMN11418649 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Fecal samples were collected from thirty-one healthy subjects, in the age group of 18–58 years |
Sequencing
31 runs over 31 samples · mean 8.40 Gbp per run (median 7.91 Gbp, total 260.34 Gbp; 31 runs with a base count) · layout PAIRED 31 · platform ILLUMINA 31 · models Illumina HiSeq 2500 (22), Illumina HiSeq 1000 (9) · 94% of runs with a Sandpiper profile · first public 2020-03-25
Authors (38)
Kaur K first · Khatri I · Akhtar A · Subramanian S · Ramya TNC last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Zhu J first · Xie H · Yang Z · Chen J · Yin J · Tian P · Wang H · Zhao J · Zhang H · Lu W · Chen W last · Chandel N first · Somvanshi PR · Thakur V last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Gorremuchu JP
Downloads
PRJNA531203.csv.gz (2.2 KB) · parquet (73.3 KB) — all 31 samples, every field with route and confidence · PRJNA531203_determinations.csv.gz (5.9 KB) — 476 evidence rows