PRJNA400072 SRP129027
Paired metagenomes in IBD vs controls, USA and Netherlands
Gut microbiome structure and metabolic activity in inflammatory bowel disease
Case-control study of 220 gut metagenome samples from USA (155) and Netherlands (65) subjects with Crohn's disease (88), ulcerative colitis (76), or healthy controls (56), mostly adults (191) with some elderly (29). machine-written summary
220 samples · 220 runs · US, NL · Adult · 2018 · 3.11 Gbp / sample · cohort Cholesterol Metabolism by Uncultured Human Gut Bac
Sources
✓Sequence archive 660○Abstract / description○Full text○Supplementary tables✓External resources 870–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 660 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10813293, PMC11580338, PMC12771579, PMC13445673, PMC6342642, PMC6637180, PMC7746778, PMC8177889, PMC8896604, PMC9064000, PMC9426669 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 870 sample values (age, antibiotic exposure, health condition, health condition detail) · from GMrepo v3, Meta2DB (LLNL) |
| – 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
adult191
elderly29
Condition
crohns_disease88
ulcerative_colitis76
healthy_control56
Country
US155
NL65
Body site
primary220
Collected 2009–2014
Sequencing depth per sample · this project all projects
Community composition
Blautia_A 8.1%Roseburia 5.9%Bifidobacterium 5.2%Faecalibacterium 4.8%Bacteroides 4.8%Phocaeicola 4.5%Mediterraneibacter 3.3%Alistipes 2.2%Collinsella 2.2%Anaerostipes 2.1%Streptococcus 2.0%Prevotella 2.0%not assigned to a genus 7.2%other genera 45.7%
Genera, mean relative abundance over 194 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 | 220 | 100% | ||||
| country | 220 | 100% | 220 | |||
| health_condition | 220 | 100% | 220 | |||
| subject_id | 220 | 100% | 220 | |||
| age_at_collection_days | 220 | 100% | 220 | |||
| collection_date | 220 | 100% | 220 | |||
| health_condition_detail | 220 | 100% | 220 | |||
| antibiotic_exposure | 210 | 95% | 210 |
Papers (58)
- Gut microbiome structure and metabolic activity in inflammatory bowel disease. 2019 PMID 30531976 PMC6342642 own_data
- Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. 2019 PMID 31316056 PMC6637180 own_data
- A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data. 2020 PMID 33343536 PMC7746778 own_data
- Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation. 2021 PMID 34085924 PMC8177889 own_data
- A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. 2021 PMID 34416161 PMC9064000 own_data
53 more
- MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. 2022 PMID 34999748 PMC8896604
- Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All. 2022 PMID 35150242 PMC9426669
- Emergent Functional Organization of Gut Microbiomes in Health and Diseases. 2023 PMID 38275746 PMC10813293
- A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes. 2024 PMID 39574009 PMC11580338
- Distinct classes of gut bacterial molybdenum-dependent enzymes produce urolithins. 2025 PMID 41439715 PMC12771579
- Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery. 2026 PMID 42563165 PMC13445673
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048
- Adjusting for age improves identification of gut microbiome alterations in multiple diseases. 2020 PMID 32159510 PMC7065848
- Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. 2020 PMID 32544460 PMC7435688
- Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers. 2021 PMID 33175106 PMC7664509
- Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease. 2020 PMID 33330572 PMC7729129
- Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. 2021 PMID 33430705 PMC7808391
- Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease. 2021 PMID 33653942 PMC8546988
- Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models. 2021 PMID 33947803 PMC8269207
- Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. 2021 PMID 34342541 PMC8407477
- The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. 2021 PMID 34563136 PMC8465708
- The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome. 2021 PMID 34745023 PMC8564485
- Human gut bacterial metabolism drives Th17 activation and colitis. 2022 PMID 34822777 PMC8785648
- Expanding the Colorectal Cancer Biomarkers Based on the Human Gut Phageome. 2021 PMID 34935421 PMC8693921
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn's disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets. 2022 PMID 36268225 PMC9577114
- MIDAS2: Metagenomic Intra-species Diversity Analysis System. 2023 PMID 36321886 PMC9805558
- Faecal microbiome-based machine learning for multi-class disease diagnosis. 2022 PMID 36357393 PMC9649010
- Human Gut Metagenomes Encode Diverse GH156 Sialidases. 2022 PMID 36394327 PMC9746317
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977
- Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence. 2023 PMID 37278203 PMC10246480
- Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer. 2023 PMID 37635357 PMC10464540
- Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426
- Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. 2023 PMID 37932270 PMC10628233
- Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation. 2023 PMID 38127978 PMC10756304
- Dubosiella newyorkensis modulates immune tolerance in colitis via the L-lysine-activated AhR-IDO1-Kyn pathway. 2024 PMID 38351003 PMC10864277
- Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota. 2022 PMID 38868717 PMC10989788
- Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases. 2024 PMID 38917808 PMC11239293
- Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. 2024 PMID 38942021 PMC11293350
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. 2024 PMID 39078158 PMC11334437
- Microbial assimilatory sulfate reduction-mediated H<sub>2</sub>S: an overlooked role in Crohn's disease development. 2024 PMID 39152482 PMC11328384
- An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. 2024 PMID 39278950 PMC11402979
- Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. 2024 PMID 39367251 PMC11645270
- Pangenomic analysis identifies correlations between <i>Akkermansia</i> species and subspecies and human health outcomes. 2024 PMID 39421249 PMC11480726
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. 2025 PMID 40377187 PMC12084026
- Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM). 2025 PMID 40424276 PMC12136445
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol. 2025 PMID 41233306 PMC12615640
- Protein language models uncover carbohydrate-active enzyme function in metagenomics. 2025 PMID 41299229 PMC12659350
- Gut Microbes Secretions May Trigger Mononuclear Cell Migration and Offer Comorbidity Mechanism Between Inflammatory Bowel Disease and Diabetic Retinopathy. 2025 PMID 41333916 PMC12668851
- MMETHANE: interpretable AI for predicting host status from microbial composition and metabolomics data. 2025 PMID 41361854 PMC12802134
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome. 2026 PMID 41365303 PMC12853188
- MetaFX: feature extraction from whole-genome metagenomic sequencing data. 2026 PMID 41557465 PMC12891910
- Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836
- Landscape of flavonoid metabolism in human gut microbiome and its association with health and disease. 2025 PMID 41909884 PMC12940152
- Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease. 2026 PMID 41945859 PMC13271634
- SpiR is a gut microbial enzyme that drives cholesterol conversion. 2026 PMID 41980965 PMC13079761
Details
Archive description
This project collected and profiled paired shotgun metagenomes and LC-MS metabolomes from subjects with inflammatory bowel disease (IBD) and non-IBD controls. We identified and validated differentially abundant (DA) features in the metagenomes and metabolomes of IBD subjects, and described putatively mechanistic associations between DA microbes, enzymes, and metabolites.
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 · “Gut microbiome structure and”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08049618 | age_at_collection_days | 13879.5 | R2 | 0.75 | external.gmrepo source | host_age: 38.0 |
| SAMN08049618 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN08049618 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMN08049618 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN08049618 | health_condition | crohns_disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN08049618 | health_condition_detail | Crohn Disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN08049618 | subject_id | PRISM_7122_PRISM | R1 | 0.85 | sample.attr.host_subject_id | PRISM_7122_PRISM |
Sequencing
220 runs over 220 samples · mean 4.22 Gbp per run (median 3.11 Gbp, total 927.84 Gbp; 220 runs with a base count) · layout PAIRED 220 · platform ILLUMINA 220 · models Illumina HiSeq 2000 (220) · 88% of runs with a Sandpiper profile · first public 2018-01-13 – 2018-02-03
Authors (64)
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 · Kim S first · Thapa I · Ali H last · Thurimella K first · Mohamed AMT · Li C · Vatanen T · Graham DB · Owens RM · La Rosa SL · Plichta DR · Bacallado S · Xavier RJ last · Xu B first · Wu S · Huang J · Lin M · Liu Q · Li X · Fu M · Xia Z · Yi G last · Dawkins JJ first · Gerber GK last · Ivanov A first · Popov V · Morozov M · Olekhnovich E · Ulyantsev V last · Huang L first · Tan H · Weng S · Liu Y · Song L · Cheng S · Lin Z · Chen J · Tan F · Wang J · Cai L · Chai J · Zhong C · Shi Y · Zhang W · Zhang H · Huang C last
Downloads
PRJNA400072.csv.gz (7.8 KB) · parquet (80.5 KB) — all 220 samples, every field with route and confidence · PRJNA400072_determinations.csv.gz (15.3 KB) — 1,530 evidence rows
Samples (220 · every field this project has values for · hover a cell for its source)
Loading the sample table…