Gut microbiome and cytokine response in healthy Dutch adults
471 fecal metagenome samples from healthy adults in the Netherlands, paired with blood cytokine production measurements, in a cross-sectional study of microbiome-host immune interactions. machine-written summary
471 samples · 875 runs · NL · Adult · 2016 · 2.85 Gbp / sample · cohort Cholesterol Metabolism by Uncultured Human Gut Bac
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,413 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10154212, PMC10808065, PMC10873414, PMC11009399, PMC11423519, PMC12560166, PMC12648112, PMC12993611, PMC13059687, PMC5131922, PMC7041091, PMC7419557, PMC7435688, PMC8328510, PMC9610947, PMC9721016 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 2,334 sample values (antibiotic exposure, bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 420 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 | 471 | 100% | ||||
| country | 471 | 100% | 471 | |||
| health_condition | 471 | 100% | 471 | |||
| subject_id | 471 | 100% | 471 | |||
| antibiotic_exposure | 471 | 100% | 471 | |||
| collection_date | 471 | 100% | 471 | |||
| health_condition_detail | 471 | 100% | 471 | |||
| sex | 465 | 99% | 465 | |||
| bmi | 456 | 97% | 456 |
- Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. 2016 PMID 27814509 PMC5131922 own_data
- Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. 2020 PMID 32093654 PMC7041091 own_data
- Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. 2020 PMID 32782301 PMC7419557 own_data
- An association between chronic widespread pain and the gut microbiome. 2021 PMID 33331911 PMC8328510 own_data
- Detection of antimicrobial peptides from fecal samples of FMT donors using deep learning. 2025 PMID 41164228 PMC12560166 own_data
13 more
- The association between flagellin producers in the gut microbiota and HDL-C level in humans. 2023 PMID 41853335 PMC12993611
- Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses 2022
- Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. 2020 PMID 32544460 PMC7435688
- Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa. 2022 PMID 36296186 PMC9610947
- The microbiome's fiber degradation profile and its relationship with the host diet. 2022 PMID 36464700 PMC9721016
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Host genetic regulation of human gut microbial structural variation. 2024 PMID 38172637 PMC10808065
- Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. 2024 PMID 38366085 PMC10873414
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399
- A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies. 2024 PMID 39322959 PMC11423519
- Systematically investigating and identifying bacteriocins in the human gut microbiome. 2025 PMID 40902606 PMC12648112
- Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway. 2025 PMID 41118772 PMC13059687
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
As part of the 500 Functional Genomics (500FG) project, stool samples from 471 healthy adults were subjected to metagenomic shotgun sequencing (one time point per individual). Concurrently, blood samples were collected from each individual and the cytokine production was measured in response to bacterial and fungal stimulations. Significant inter-individual variation was observed in the gut microbial profiles as well as the immunological profiles. Subsequent association testing showed that microbiome-host interactions modulate the inflammatory cytokine production capacity in healthy individuals.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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 · “Gut microbial interactions with”
- body site study.description · “Genomics (500FG) project, stool samples from 471”
- body site study.description · “per individual). Concurrently, blood samples were collected”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “from 471 healthy adults were subjected to”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06109999 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN06109999 | bmi | 20.94 | R2 | 0.75 | external.cmd source | bmi: 20.94 |
| SAMN06109999 | collection_date | 2013/2014 | R1 | 0.90 | biosample.attribute:collection_date | 2013/2014 |
| SAMN06109999 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN06109999 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06109999 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06109999 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMN06109999 | subject_id | HV531 | R1 | 0.85 | sample.attr.host_subject_id | HV531 |
Sequencing
875 runs over 471 samples · mean 1.61 Gbp per run (median 2.10 Gbp, total 1,412.45 Gbp; 875 runs with a base count) · layout PAIRED 471, SINGLE 404 · platform ILLUMINA 875 · models Illumina HiSeq 2000 (875) · 48% of runs with a Sandpiper profile · first public 2016-12-31
Authors (87)
Levy S · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Fernández-Pato A first · Sinha T · Gacesa R · Andreu-Sánchez S · Gois MFB · Gelderloos-Arends J · Jansen DBH · Kruk M · Jaeger M · Joosten LAB · Netea MG · Weersma RK · Wijmenga C · Harmsen HJM · Fu J · Zhernakova A · Kurilshikov A last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Zhang D first · Zou Y · Shi Y · Zhang J · Liu J · Wu G · Gao Y · Chen M · Li YX last · Jacoby C first · Scorza K · Ecker L · Nol Bernardino P · Little AS · McMillin M · Ramaswamy R · Sundararajan A · Sidebottom AM · Lin H · Dufault-Thompson K · Hall B · Jiang X · Light SH last · Wei S first · Yin H · Hu X · Chi Y · Zhang L · Zhang B · Qian K · Xu W last · Yiu JHC first · Cai J · Cheung SWM · Chin KT · Chan CF · Ma ESC · Sharma R · Dorweiler B · Woo CW last
Downloads
PRJNA319574.csv.gz (14.4 KB) · parquet (90.3 KB) — all 471 samples, every field with route and confidence · PRJNA319574_determinations.csv.gz (35.7 KB) — 3,747 evidence rows