Gut metagenomes from Shatin, Hong Kong, cross-sectional
556 gut metagenome samples from Shatin, Hong Kong, collected cross-sectionally, used to characterize gut microbial community diversity, including fusobacterial taxa, in a southern Chinese population. machine-written summary
556 samples · 556 runs · HK · Age unknown · 2020 · 7.56 Gbp / sample · cohort Variation in the metagenomic analysis of fecal mic
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,224 sample values (country, latitude, location locality, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 556 sample values (subject id) · PMC10122048, PMC10688793, PMC10798454, PMC10926697, PMC11619352, PMC13067863, PMC13106387, PMC13155725, PMC7569397, PMC9184491 |
| ✓ Supplementary tables | 300 sample values (age, bmi, sex) |
| – 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 503 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 | 100 | 18% | ||||
| country | 556 | 100% | 556 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 556 | 100% | 556 | |||
| detailed_location | 556 | 100% | ||||
| latitude | 556 | 100% | 556 | |||
| location_locality | 556 | 100% | 556 | |||
| longitude | 556 | 100% | 556 | |||
| age_at_collection_days | 100 | 18% | 100 | |||
| bmi | 100 | 18% | 100 | |||
| sex | 100 | 18% | 100 |
- Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor. 2020 PMID 32051205 PMC7569397 own_data
- ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data. 2024 PMID 38381034 PMC10926697 own_data
- Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations. 2026 PMID 41755800 PMC13067863 own_data
- Benchmarks for taxonomic classification of jingmenviruses and closely related viruses using newly identified genomic sequences. 2026 PMID 42101460 PMC13155725 own_data
- Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer. 2022 PMID 35680952 PMC9184491 unsure
5 more
- Combing fecal microbial community data to identify consistent obesity-specific microbial signatures and shared metabolic pathways. 2023 PMID 37096041 PMC10122048
- Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis. 2023 PMID 38047279 PMC10688793
- Finding Candida auris in public metagenomic repositories. 2024 PMID 38241320 PMC10798454
- Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach. 2024 PMID 39475247 PMC11619352
- A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production. 2026 PMID 42039832 PMC13106387
Archive description
The goal of this study is to characterise diversity of gut microbial communities in southern Chinese populations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Human gut metagenomes from Hong Kong populations”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13509273 | age_at_collection_days | 19358 | R2 | 0.85 | paper.supp.gutjnl-2019-319635supp001.xlsx[Table S2!age (years)] | 53 |
| SAMN13509273 | bmi | 16.8 | R2 | 0.85 | paper.supp.gutjnl-2019-319635supp001.xlsx[Table S2!BMI] | 16.8 |
| SAMN13509273 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong: Shatin |
| SAMN13509273 | latitude | 22.3800 | R1 | 0.90 | biosample.attribute:lat_lon | 22.38 N 114.20 E |
| SAMN13509273 | location_locality | Shatin | R1 | 0.85 | biosample.attribute:geo_loc_name | Hong Kong: Shatin |
| SAMN13509273 | longitude | 114.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 22.38 N 114.20 E |
| SAMN13509273 | sex | female | R2 | 0.85 | paper.supp.gutjnl-2019-319635supp001.xlsx[Table S2!gender] | female |
| SAMN13509273 | subject_id | SAMN13509273 | R3 | 0.70 | design.one_sample_per_subject:fulltext | At the time of analysis, the HKGutMicMap cohort representing the general population in Hong Kong consisted of 556 subjects with shotgun metagenome data. |
Sequencing
556 runs over 556 samples · mean 7.57 Gbp per run (median 7.56 Gbp, total 4,206.77 Gbp; 556 runs with a base count) · layout PAIRED 556 · platform ILLUMINA 556 · models Illumina NovaSeq 6000 (556) · 90% of runs with a Sandpiper profile · first public 2020-01-16
Authors (45)
Mario-Vasquez JE first · Bagal UR · Lowe E · Morgulis A · Phan J · Sexton DJ · Shiryev S · Slatkevičius R · Welsh R · Litvintseva AP · Blumberg M · Agarwala R · Chow NA last · Xu Z first · Yeoh YK · Tun HM · Fei N · Zhang J · Morrison M · Kamm MA · Yu J · Chan FKL · Ng SC last · Ding J first · Wang M · Xu X · Wang D · Chen X · Li S · Zheng X · Che Y · Deng Y · Lam TTY · Li L · Zhang T last · Sola L first · Candeliere F · Busi E · Raimondi S · Amaretti A · Rossi M last · Colmant AMG first · Parry RH · Charrel R · Coutard B last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA557323.csv.gz (14.3 KB) · parquet (94.1 KB) — all 556 samples, every field with route and confidence · PRJNA557323_determinations.csv.gz (20.6 KB) — 3,080 evidence rows