Healthy Indian Gut Microbiome, Kasaragod & Bhopal
110 samples from healthy Indian subjects in Kasaragod and Bhopal, India, studied by 16S rRNA, shotgun metagenomic and metabolomic analysis; cross-sectional design. machine-written summary
110 samples · 110 runs · IN · Adult · 2018 · 1.12 Gbp / sample · cohort Destination shapes antibiotic resistance gene acqu
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 919 sample values (age, collection date, country, diet, diet detail, latitude, location locality, location region) |
| ✓ Abstract / description | 110 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC10234815, PMC10556866, PMC10673094, PMC10803823, PMC10904984, PMC11264842, PMC11418011, PMC11685674, PMC12089645, PMC12199706, PMC12283368, PMC12390848, PMC12504321, PMC12710343, PMC12940152, PMC12993557, PMC13035836, PMC13059687, PMC13381771, PMC13387006, PMC6394208, PMC7407896, PMC7854710, PMC8023248, PMC8182900, PMC8394144, PMC8497558, PMC9454621, PMC9721016, PMC9903723 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 547 sample values (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 |
age: sequence archive and curatedMetagenomicData disagree for 1 sample (e.g. 87.0 vs 730.5) — 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 |
|---|---|---|---|---|
| SAMN07449004 | age | 87.0 (sequence archive) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
Genera, mean relative abundance over 104 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 | 110 | 100% | ||||
| country | 110 | 100% | 110 | |||
| health_condition | 110 | 100% | 110 | |||
| subject_id | 110 | 100% | 110 | |||
| antibiotic_exposure | 110 | 100% | 110 | |||
| collection_date | 110 | 100% | 110 | |||
| detailed_location | 110 | 100% | ||||
| health_condition_detail | 110 | 100% | 110 | |||
| latitude | 110 | 100% | 110 | |||
| location_locality | 110 | 100% | 110 | |||
| location_region | 110 | 100% | 110 | |||
| longitude | 110 | 100% | 110 | |||
| sex | 110 | 100% | 110 | |||
| age_at_collection_days | 109 | 99% | 109 | |||
| bmi | 107 | 97% | 107 | |||
| diet | 75 | 68% | 75 | |||
| diet_detail | 75 | 68% | 75 |
- The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. 2019 PMID 30698687 PMC6394208 unsure
- Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India. 2019 PMID 31719139 PMC7407896 unsure
- Bacterial associations in the healthy human gut microbiome across populations. 2021 PMID 33531651 PMC7854710 unsure
- The Impact of Migration on the Gut Metagenome of South Asian Canadians. 2021 PMID 33794735 PMC8023248 unsure
- Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers. 2021 PMID 34092249 PMC8182900 unsure
25 more
- Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. 2021 PMID 34446072 PMC8394144
- Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis. 2021 PMID 34620880 PMC8497558
- Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes. 2022 PMID 36077748 PMC9454621
- The microbiome's fiber degradation profile and its relationship with the host diet. 2022 PMID 36464700 PMC9721016
- Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. 2022 PMID 36778050 PMC9903723
- Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. 2023 PMID 37188815 PMC10234815
- Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort. 2024 PMID 37781761 PMC10803823
- Machine learning approaches in microbiome research: challenges and best practices. 2023 PMID 37808286 PMC10556866
- The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures. 2023 PMID 38004753 PMC10673094
- The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. 2024 PMID 38433907 PMC10904984
- Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity. 2024 PMID 39030520 PMC11264842
- The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. 2024 PMID 39122003 PMC11418011
- DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction. 2024 PMID 39738309 PMC11685674
- PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2. 2025 PMID 40293718 PMC12089645
- Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer. 2025 PMID 40461820 PMC12283368
- Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp. 2025 PMID 40569694 PMC12199706
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models. 2025 PMID 41070134 PMC12504321
- Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway. 2025 PMID 41118772 PMC13059687
- Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification. 2025 PMID 41283667 PMC12710343
- Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836
- Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population. 2024 PMID 41853539 PMC12993557
- Landscape of flavonoid metabolism in human gut microbiome and its association with health and disease. 2025 PMID 41909884 PMC12940152
- Instance-based transfer learning enables cross-cohort early detection of colorectal cancer. 2026 PMID 42106361 PMC13381771
- Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data. 2026 PMID 42262136 PMC13387006
Archive description
Through Next Generation Sequencing we delineated the composition and functional detail of gut microbiota in various world populations. The relationship of the gut microbiota to health and disease is one of the primary goals of human microbiome studies. The microbiota of the Indian population is of particular interest to researchers because India encompasses a unique diversity in environmental conditions, diet and ethnic geographical population. In this study, we conduct 16s rRNA sequencing, shotgun metagenomic and metabolomics analysis of 110 healthy Indian subjects, which reveals novel gut microbial community structures
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and child 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 · “Indian Human Gut Microbiome”
- body site study.description · “functional detail of gut microbiota in various”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “10 (n=12/110)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07448968 | age_at_collection_days | 9496.5 | R1 | 0.85 | sample.attr.host_age | 26 |
| SAMN07448968 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN07448968 | bmi | 22.72 | R2 | 0.75 | external.cmd source | bmi: 22.72 |
| SAMN07448968 | collection_date | 2016-07-20 | R1 | 0.90 | biosample.attribute:collection_date | 2016-07-20 |
| SAMN07448968 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India: Bhopal |
| SAMN07448968 | diet | omnivore | R1 | 0.90 | biosample.attribute:host_diet | Non_veg |
| SAMN07448968 | diet_detail | Non_veg | R1 | 0.90 | biosample.attribute:host_diet | Non_veg |
| SAMN07448968 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN07448968 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN07448968 | latitude | 23.2600 | R1 | 0.90 | biosample.attribute:lat_lon | 23.26 N 77.41 E |
| SAMN07448968 | location_locality | Bhopal | R1 | 0.85 | biosample.attribute:geo_loc_name | India: Bhopal |
| SAMN07448968 | location_region | Madhya Pradesh | R1 | 0.60 | biosample.attribute:lat_lon | 23.26 N 77.41 E |
| SAMN07448968 | longitude | 77.4100 | R1 | 0.90 | biosample.attribute:lat_lon | 23.26 N 77.41 E |
| SAMN07448968 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMN07448968 | subject_id | SAMN07448968 | R4 | 0.60 | design.one_sample_per_subject:description | shotgun metagenomic and metabolomics analysis of 110 healthy Indian subjects |
Sequencing
110 runs over 110 samples · mean 1.19 Gbp per run (median 1.12 Gbp, total 130.95 Gbp; 110 runs with a base count) · layout PAIRED 110 · platform ILLUMINA 110 · models NextSeq 500 (110) · 95% of runs with a Sandpiper profile · first public 2018-10-14
Authors (63)
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 · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · Joo M first · Nam S last · Wright RJ first · Langille MGI 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 · Zhang J first · Meng F · Sun Y · Xu W · Wu S · Su X last · Iacovacci J first · Cannon N · McCulloch JA · Rancati T · Trinchieri G last
Downloads
PRJNA397112.csv.gz (4.7 KB) · parquet (77.7 KB) — all 110 samples, every field with route and confidence · PRJNA397112_determinations.csv.gz (15.1 KB) — 1,576 evidence rows