Gut microbiome, obesity and bacterial richness in Danish adults
Case-control study of 292 gut metagenome samples from Danish adults, comparing non-obese and obese individuals to examine links between gut microbial richness, biosynthetic gene clusters, and obesity-related metabolic markers. machine-written summary
292 samples · 595 runs · DK · Adult · 2013 · 4.89 Gbp / sample · cohort Conjugated C-6 hydroxylated bile acids in serum re
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,460 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 292 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC10839664, PMC4299606, PMC4747322, PMC6594340, PMC6977071, PMC7861615, PMC8225906, PMC9665866 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,163 sample values (antibiotic exposure, bmi, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3), GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 258 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 | 292 | 100% | ||||
| country | 292 | 100% | 292 | |||
| health_condition | 292 | 100% | 292 | |||
| subject_id | 292 | 100% | 292 | |||
| bmi | 292 | 100% | 292 | |||
| collection_date | 292 | 100% | 292 | |||
| detailed_location | 292 | 100% | ||||
| health_condition_detail | 292 | 100% | 292 | |||
| latitude | 292 | 100% | 292 | |||
| location_region | 292 | 100% | 292 | |||
| longitude | 292 | 100% | 292 | |||
| antibiotic_exposure | 287 | 98% | 287 |
- Richness of human gut microbiome correlates with metabolic markers. 2013 PMID 23985870 own_data
- A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans. 2019 PMID 31309109 PMC6594340 own_data
- Potential of fecal microbiota for early-stage detection of colorectal cancer. 2014 PMID 25432777 PMC4299606 unsure
- Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. 2015 PMID 26633628 PMC4681099 unsure
- Value, but high costs in post-deposition data curation. 2016 PMID 26861660 PMC4747322 unsure
35 more
- Subspecies in the global human gut microbiome. 2017 PMID 29242367 PMC5740502
- Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy. 2019 PMID 31474368 PMC6736778
- Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. 2020 PMID 31940321 PMC6961876
- MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota. 2020 PMID 31964767 PMC6977071
- 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
- Assessment of fecal DNA extraction protocols for metagenomic studies. 2020 PMID 32657325 PMC7355182
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. 2020 PMID 33372654 PMC7861615
- Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. 2021 PMID 33769280 PMC8062136
- Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. 2021 PMID 34061597 PMC8262883
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803
- Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species. 2021 PMID 34168163 PMC8225906
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520
- Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. 2022 PMID 35240043 PMC9096808
- Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders. 2022 PMID 35754734 PMC9213702
- Gut microbiota insights into human adaption to high-plateau diet. 2022 PMID 35989883 PMC9387673
- Integrating phylogenetic and functional data in microbiome studies. 2022 PMID 36179077 PMC9665866
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977
- Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population. 2022 PMID 36564713 PMC9789565
- Gene-based microbiome representation enhances host phenotype classification. 2023 PMID 37404032 PMC10469787
- Four functional profiles for fibre and mucin metabolism in the human gut microbiome. 2023 PMID 37858269 PMC10588041
- Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs. 2024 PMID 38199973 PMC10839664
- 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
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. 2024 PMID 39078158 PMC11334437
- The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. 2024 PMID 39122003 PMC11418011
- Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis? 2024 PMID 39204125 PMC11357004
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. 2025 PMID 40377187 PMC12084026
- Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria. 2025 PMID 40624564 PMC12235815
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- Systematically investigating and identifying bacteriocins in the human gut microbiome. 2025 PMID 40902606 PMC12648112
- The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels. 2025 PMID 41331251 PMC12764784
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They harbour known and previously unknown bacterial species at different proportions individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the former also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.
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.title · “Richness of human gut microbiome correlates with”
- body site study.description · “report the human gut microbial composition in”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “the general white adult population who may”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA1964270 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA1964270 | bmi | 33.2 | R2 | 0.75 | external.cmd source | bmi: 33.2 |
| SAMEA2143941 | bmi | 25.6 | R2 | 0.75 | external.gmrepo source | BMI: 25.6 |
| SAMEA1964270 | collection_date | 2008/2010 | R1 | 0.90 | biosample.attribute:collection_date | 2008/2010 |
| SAMEA1964270 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | Denmark |
| SAMEA1964270 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA2143941 | health_condition | obesity | R2 | 0.75 | external.gmrepo source | phenotype: Overweight |
| SAMEA1964270 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA2143941 | health_condition_detail | Overweight | R2 | 0.75 | external.gmrepo source | phenotype: Overweight |
| SAMEA1964270 | latitude | 55.6761 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.676097 12.568337 |
| SAMEA1964270 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.676097 12.568337 |
| SAMEA1964270 | longitude | 12.5683 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.676097 12.568337 |
| SAMEA1964270 | subject_id | SAMEA1964270 | R4 | 0.60 | design.one_sample_per_subject:abstract | population sample of 123 non-obese and 169 obese Danish individuals |
Sequencing
595 runs over 292 samples · mean 2.76 Gbp per run (median 1.66 Gbp, total 1,641.29 Gbp; 595 runs with a base count) · layout PAIRED 595 · platform ILLUMINA 595 · models Illumina Genome Analyzer IIx (288), Illumina Genome Analyzer II (186), Illumina HiSeq 2000 (121) · 55% of runs with a Sandpiper profile · first public 2013-09-11
Authors (86)
Le Chatelier E first · Nielsen T · Qin J · Prifti E · Hildebrand F · Falony G · Almeida M · Arumugam M · Batto JM · Kennedy S · Leonard P · Li J · Burgdorf K · Grarup N · Jørgensen T · Brandslund I · Nielsen HB · Juncker AS · Bertalan M · Levenez F · Pons N · Rasmussen S · Sunagawa S · Tap J · Tims S · Zoetendal EG · Brunak S · Clément K · Doré J · Kleerebezem M · Kristiansen K · Renault P · Sicheritz-Ponten T · de Vos WM · Zucker JD · Raes J · Hansen T · MetaHIT consortium · Bork P · Wang J · Ehrlich SD · Pedersen O last · Van Syoc E first · Nixon MP · Silverman JD · Luo Y · Gonzalez FJ · Elbere I · Klovins J · Patterson AD · Rogers CJ · Ganda E last · Fernandes C first · Miranda MCC · Roque CR · Paguada ALP · Mota CAR · Florêncio KGD · Pereira AF · Wong DVT · Oriá RB · Lima-Júnior RCP last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Zhu J first · Jiang MZ · Chen X · Li M · Wang YL · Liu C · Liu SJ · Chen WH last · Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last
Downloads
PRJEB4336.csv.gz (9.8 KB) · parquet (85.8 KB) — all 292 samples, every field with route and confidence · PRJEB4336_determinations.csv.gz (30.2 KB) — 2,915 evidence rows