PRJEB2054 ERP000108
Human gut gene catalog, 124 samples, Denmark/Spain
A human gut microbial gene catalog established by deep metagenomic sequencing
124 gut microbiome samples from mostly adult individuals (with some elderly and one neonate) in Den machine-written summary
124 samples · 264 runs · DK, ES · Adult · 2010 · 3.30 Gbp / sample
Sources
✓Sequence archive 372✓Abstract / description 124○Full text○Supplementary tables✓External resources 246–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 372 sample values (age, country, sex) |
| ✓ Abstract / description | 124 sample values (location region) |
| ○ Full text | read; no usable statement or table · PMC10059959, PMC10794208, PMC10939037, PMC11009399, PMC11101950, PMC11237675, PMC11357004, PMC12268991, PMC3443552, PMC3542080, PMC4040986, PMC4269443, PMC4428241, PMC4460507, PMC4476132, PMC4556158, PMC4690404, PMC4936053, PMC5943621, PMC6123480, PMC6138922, PMC6394208, PMC6417177, PMC6591925, PMC6707425, PMC6736778, PMC6947943, PMC7150542, PMC7157763, PMC7298543, PMC7854710, PMC8110962, PMC8262883, PMC8913745, PMC9048649, PMC9096808, PMC9426597 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 246 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
2 countries
Age
adult110
elderly13
neonate1
Condition
healthy_control123
Sex
female69
male55
Country
DK85
ES39
Body site
primary124
Sequencing depth per sample · this project all projects
Community composition
Prevotella 9.4%Phocaeicola 7.7%Bacteroides 7.6%Roseburia 4.1%Alistipes 3.2%Faecalibacterium 3.1%Lachnospira 2.4%Acetatifactor 1.9%Ruminococcoides 1.6%Eshraghiella 1.4%Vescimonas 1.4%Parabacteroides 1.4%not assigned to a genus 19.3%other genera 35.4%
Genera, mean relative abundance over 110 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 124 | 100% | ||||
| country | 124 | 100% | 124 | |||
| health_condition | 123 | 99% | 123 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 124 | 100% | 124 | |||
| detailed_location | 124 | 100% | ||||
| location_region | 124 | 100% | 124 | |||
| sex | 124 | 100% | 124 | |||
| health_condition_detail | 123 | 99% | 123 |
Papers (38)
- Metagenomic microbial community profiling using unique clade-specific marker genes. 2012 PMID 22688413 PMC3443552 own_data
- A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. 2013 PMID 23326225 PMC3542080 own_data
- An expanded genomic representation of the phylum cyanobacteria. 2014 PMID 24709563 PMC4040986 own_data
- Inter-individual differences in the gene content of human gut bacterial species. 2015 PMID 25896518 PMC4428241 own_data
- Identifying personal microbiomes using metagenomic codes. 2015 PMID 25964341 PMC4460507 own_data
33 more
- Compact graphical representation of phylogenetic data and metadata with GraPhlAn. 2015 PMID 26157614 PMC4476132
- Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens. 2015 PMID 26713229 PMC4690404
- MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. 2018 PMID 30219103 PMC6138922
- A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer. 2019 PMID 31474963 PMC6707425
- Deconvolute individual genomes from metagenome sequences through short read clustering. 2020 PMID 32296615 PMC7150542
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review. 2024 PMID 38765606 PMC11101950
- Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes. 2014 PMID 25517115 PMC4269443
- MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. 2015 PMID 26336640 PMC4556158
- Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. 2016 PMID 27388460 PMC4936053
- Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures. 2018 PMID 29774017 PMC5943621
- GePMI: A statistical model for personal intestinal microbiome identification. 2018 PMID 30210803 PMC6123480
- The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. 2019 PMID 30698687 PMC6394208
- Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. 2019 PMID 30866812 PMC6417177
- Metagenomic analysis of bile salt biotransformation in the human gut microbiome. 2019 PMID 31234773 PMC6591925
- Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy. 2019 PMID 31474368 PMC6736778
- Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. 2020 PMID 31910889 PMC6947943
- Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. 2020 PMID 32265336 PMC7157763
- Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning. 2020 PMID 32534441 PMC7298543
- Bacterial associations in the healthy human gut microbiome across populations. 2021 PMID 33531651 PMC7854710
- Bifidobacterium response to lactulose ingestion in the gut relies on a solute-binding protein-dependent ABC transporter. 2021 PMID 33972677 PMC8110962
- Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. 2021 PMID 34061597 PMC8262883
- Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. 2022 PMID 35240043 PMC9096808
- Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. 2022 PMID 35273169 PMC8913745
- Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. 2022 PMID 35497193 PMC9048649
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- Effective binning of metagenomic contigs using contrastive multi-view representation learning. 2024 PMID 38233391 PMC10794208
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. 2024 PMID 38423015 PMC10939037
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399
- Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations. 2024 PMID 38767350 PMC11237675
- Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis? 2024 PMID 39204125 PMC11357004
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Details
Archive description
124 individuals from Denmark and Spain were studied, 577 Gb data were generated
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “human gut microbial gene catalog”
- life stage study.description · “124 individuals from Denmark and Spain”
- life stage sample.attr.age · “64 (n=26/124)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA728561 | age_at_collection_days | 11305.8 | R1 | 0.85 | sample.attr.age | 31 |
| SAMEA728561 | country | ES | R1 | 0.85 | biosample.attribute:nation | Spain |
| SAMEA728561 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA728561 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA728561 | location_region | Denmark and Spain | R4 | 0.30 | ena.study_description | 124 individuals from Denmark and Spain |
| SAMEA728561 | sex | male | R1 | 0.90 | sample.attr.gender | male |
Sequencing
264 runs over 124 samples · mean 1.52 Gbp per run (median 1.63 Gbp, total 402.17 Gbp; 264 runs with a base count) · layout PAIRED 264 · platform ILLUMINA 264 · models Illumina Genome Analyzer II (264) · 77% of runs with a Sandpiper profile · first public 2010-04-07
Authors (39)
Qin F first · Li J · Mao T · Feng S · Lai M last · Wang Z first · You R · Han H · Liu W · Sun F · Zhu S last · Fernandes C first · Miranda MCC · Roque CR · Paguada ALP · Mota CAR · Florêncio KGD · Pereira AF · Wong DVT · Oriá RB · Lima-Júnior RCP last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last · Mizrahi I first · Zorea A · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R last
Downloads
PRJEB2054.csv.gz (4.2 KB) · parquet (74.8 KB) — all 124 samples, every field with route and confidence · PRJEB2054_determinations.csv.gz (5.5 KB) — 742 evidence rows
Samples (124 · every field this project has values for · hover a cell for its source)
Loading the sample table…