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PRJNA588513 SRP237559

Human gut metagenome from Yunnan and Hong Kong, China

human gut metagenome Metagenome

942 human fecal metagenome samples collected from China (Yunnan: 881, Hong Kong: 61); no health conditions, interventions, or age data specified in available sources. machine-written summary

942 samples · 942 runs · CN · Infant / toddler · 2021 · 13.46 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 883○Abstract / description○Full text✓Supplementary tables 1,735–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive883 sample values (country, timepoint)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC11019788, PMC11494892, PMC9512645
✓ Supplementary tables1,735 sample values (sex, timepoint)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
unknown942
Sex
female515
male286
Country
CN881
Body site
primary942
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 3 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 46 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 893 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 13.46 Gbp per sample0130Gbp
! Self-contradictory metadata

country: two sequence archives disagree for 61 samples (e.g. CN vs HK) — withheld.

The sources disagree on 61 samples. 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 (40 of 61)
samplefieldvalueother valuehandling
SAMN13247058countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247059countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247060countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247061countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247062countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247063countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247064countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247065countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247066countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247067countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247068countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247069countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247070countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247071countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247072countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247073countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247074countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247075countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247076countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247077countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247078countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247079countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247080countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247081countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247082countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247083countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247084countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247085countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247086countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247087countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247088countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247089countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247090countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247091countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247092countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247093countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247094countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247095countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247096countryCN (sequence archive)HK (sequence archive)withheld: neither value published
SAMN13247097countryCN (sequence archive)HK (sequence archive)withheld: neither value published
Community composition
Roseburia 10.6%Prevotella 8.4%Blautia_A 7.1%Mediterraneibacter 3.5%Faecalibacterium 3.5%Bifidobacterium 3.1%Gemmiger 3.0%Ruminococcoides 3.0%Megamonas 3.0%Lachnospira 2.8%Phocaeicola 2.0%Anaerostipes 1.9%not assigned to a genus 2.9%other genera 45.2%

Genera, mean relative abundance over 852 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country881 94%881
health_condition0 0%
subject_id0 0%
timepoint_label936 99%2934
sex801 85%801
Papers (3)
  • Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
  • Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788 curated
  • Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
Details
Archive description

human fecal metagenome

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.50. Assay shotgun_dna.

  • host run.scientific_name · “human gut metagenome”
  • body site study.description · “human fecal metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN13246177countryCNR10.90biosample_attrChina: Yunnan
SAMN13246177sexfemaleR20.75paper.supp.tableSex=F
SAMN13247117timepoint_labelD4R10.70sample.titleD4
SAMN13246177timepoint_labelFR20.75paper.supp.tablecol3=F
Sequencing

942 runs over 942 samples · mean 13.60 Gbp per run (median 13.46 Gbp, total 12,809.46 Gbp; 942 runs with a base count) · layout PAIRED 942 · platform ILLUMINA 942 · models Illumina NovaSeq 6000 (942) · 90% of runs with a Sandpiper profile · first public 2021-01-04

Authors (18)

Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D

Help complete this project

3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata

Downloads

PRJNA588513.csv.gz (22.7 KB) · parquet (108.5 KB) — all 942 samples, every field with route and confidence · PRJNA588513_determinations.csv.gz (14.1 KB) — 2,618 evidence rows

Samples (942 · every field this project has values for · hover a cell for its source)
Loading the sample table…