Gut microbiome in urban and rural Central India
Cross-sectional shotgun metagenomics of 107 fecal samples from adults in urban and rural Central India, examining geography, antibiotic resistance, and acute diarrheal disease including Clostridioides difficile. machine-written summary
107 samples · 107 runs · IN · Age unknown · 2019 · 3.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 535 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC7781581 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – 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 | 107 | 100% | ||||
| country | 107 | 100% | 107 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 107 | 100% | 107 | |||
| detailed_location | 107 | 100% | ||||
| latitude | 107 | 100% | 107 | |||
| location_region | 107 | 100% | 107 | |||
| longitude | 107 | 100% | 107 |
- Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. 2020 PMID 32459982 PMC7781581 own_data
- Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. 2022 PMID 35654877 PMC9163076 unsure
- Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population. 2024 PMID 41853539 PMC12993557 unsure
Archive description
Collection of feacal samples collected from urban and rural Indian populations
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “feacal samples collected from urban and rural”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12711606 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN12711606 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India |
| SAMN12711606 | latitude | 21.1400 | R1 | 0.90 | biosample.attribute:lat_lon | 21.14 N 79.08 E |
| SAMN12711606 | location_region | Maharashtra | R1 | 0.60 | biosample.attribute:lat_lon | 21.14 N 79.08 E |
| SAMN12711606 | longitude | 79.0800 | R1 | 0.90 | biosample.attribute:lat_lon | 21.14 N 79.08 E |
Sequencing
107 runs over 107 samples · mean 3.71 Gbp per run (median 3.08 Gbp, total 396.83 Gbp; 107 runs with a base count) · layout PAIRED 107 · platform ILLUMINA 107 · models Illumina HiSeq 3000 (107) · 93% of runs with a Sandpiper profile · first public 2019-09-10
Authors (36)
Monaghan TM first · Sloan TJ · Stockdale SR · Blanchard AM · Emes RD · Wilcox M · Biswas R · Nashine R · Manke S · Gandhi J · Jain P · Bhotmange S · Ambalkar S · Satav A · Draper LA · Hill C · Kashyap RS last · Harrington RS · Shkoporov AN · Khokhlova EV · Daly KM · McDonnell SA · O'Reagan O · Nolan JA · Sheehan D · Lavelle A · Shanahan F · Ross RP · Chandel N first · Gorremuchu JP · Thakur V last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA564397.csv.gz (3.2 KB) · parquet (73.5 KB) — all 107 samples, every field with route and confidence · PRJNA564397_determinations.csv.gz (3.2 KB) — 535 evidence rows