Singapore gut metagenomes, healthy adults and elderly
Cross-sectional study of 45 gut metagenome samples from healthy Singaporean subjects (40 adult, 5 elderly), part of the Singapore Platinum Metagenomes Project, using Illumina, ONT and Hi-C sequencing. machine-written summary
45 samples · 218 runs · SG · Adult · 2021 · 15.12 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 225 sample values (collection date, country, health condition, health condition detail, subject id) · PMC10986321, PMC11211831, PMC11331721, PMC11836353, PMC9431525, PMC9561172 |
| ✓ Supplementary tables | 218 sample values (age, sex) |
| – 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 |
Genera, mean relative abundance over 42 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 | 45 | 100% | ||||
| country | 45 | 100% | 45 | |||
| health_condition | 45 | 100% | 45 | |||
| subject_id | 45 | 100% | 45 | |||
| age_at_collection_days | 45 | 100% | 109 | |||
| collection_date | 45 | 100% | 45 | |||
| health_condition_detail | 45 | 100% | 45 | |||
| sex | 45 | 100% | 109 |
- Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative. 2022 PMID 35699469 PMC9431525 own_data
- Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians. 2022 PMID 36229545 PMC9561172 own_data
- Comparison of <i>tet</i>(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects. 2024 PMID 38441466 PMC10986321 own_data
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes. 2024 PMID 39160564 PMC11331721 own_data
- From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia 2025 own_data
2 more
- Floria: fast and accurate strain haplotyping in metagenomes. 2024 PMID 38940183 PMC11211831
- Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo. 2025 PMID 39966439 PMC11836353
Archive description
Sequencing data for gut metagenomes of 109 Singaporean subjects from the SPMP study. The project includes read data for Illumina, ONT and Hi-C sequencing. Metagenome assembled genomes (MAG) can be found in the "Related ENA Records" section, under "Analysis".
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.description · “Sequencing data for gut metagenomes of 109”
- body site external_curation.infant_catalog · “body_site_call stool/gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA11358266 | age_at_collection_days | 20819 | R2 | 0.85 | paper.supp.41467_2022_33782_MOESM4_ESM.xlsx[Metadata!Age] | 57 |
| SAMEA11358266 | collection_date | 2018 | R3 | 0.70 | paper.fulltext.methods | were collected in 2018 using a BioCollector |
| SAMEA11358266 | country | SG | R3 | 0.70 | paper.fulltext.abstract | cohort of individuals in Singapore |
| SAMEA11358266 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.abstract | healthy cohort of individuals in Singapore |
| SAMEA11358266 | health_condition_detail | healthy cohort of individuals in Singapore | R3 | 0.70 | paper.fulltext.abstract | healthy cohort of individuals in Singapore |
| SAMEA11358266 | sex | male | R2 | 0.85 | paper.supp.41467_2022_33782_MOESM4_ESM.xlsx[Metadata!Gender] | M |
| SAMEA11358266 | subject_id | SAMEA11358266 | R3 | 0.75 | design.one_sample_per_subject:fulltext | in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore |
Sequencing
218 runs over 109 samples · mean 7.67 Gbp per run (median 7.85 Gbp, total 1,671.87 Gbp; 218 runs with a base count) · layout PAIRED 109, SINGLE 109 · platform ILLUMINA 109, OXFORD_NANOPORE 109 · models Illumina HiSeq 4000 (109), PromethION (96), GridION (10), MinION (3) · 46% of runs with a Sandpiper profile · first public 2021-12-10 – 2021-12-13
Authors (31)
Ding Y first · Er S · Tan A · Gounot JS · Saw WY · Tan LWL · Teo YY · Nagarajan N · Seedorf H last · Shaw J first · Chen H · Yu YW last · Chen X first · Yin X · Shi X · Yan W · Yang Y · Liu L · Zhang T last · Xu X · Febinia CA first · Luqman H · Kusuma P · Priliani L · Lewis J · Wihandani DM · Pinatih GNI · Sudoyo H · Almeida A · Malik SG · Jacobs GS last
Downloads
PRJEB49168.csv.gz (2.3 KB) · parquet (71.6 KB) — all 45 samples, every field with route and confidence · PRJEB49168_determinations.csv.gz (3.3 KB) — 443 evidence rows