PRJNA389280 SRP115812
Longitudinal gut metagenome in IBD patients, USA
Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)
300 stool samples from US individuals with Crohn's disease, ulcerative colitis, IBD-unspecified, or healthy controls, collected over one year as part of a longitudinal metagenome/metatranscriptome study of IBD microbiome dynamics. machine-written summary
300 samples · 300 runs · US · Age unknown · 2017 · 2.79 Gbp / sample · cohort Cholesterol Metabolism by Uncultured Human Gut Bac
Sources
✓Sequence archive 1,200✓Abstract / description 46○Full text○Supplementary tables✓External resources 1,374–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,200 sample values (collection date, country, subject id, timepoint) |
| ✓ Abstract / description | 46 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10949743, PMC11525784, PMC12993454, PMC6131705, PMC8547482, PMC9580954 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,374 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from GMrepo v3, HMP / iHMP data portal |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
1 country
Age
adult141
adolescent69
child43
unknown33
elderly14
Condition
crohns_disease143
ulcerative_colitis78
healthy_control56
ibd_unspecified23
Sex
female165
male112
Country
US300
Body site
primary300
Collected 2014–2015
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal — not resolved
Schedule stated by the source: “archive time labels: C1, C2, C4, C3, C5, C7, C6, C8”; stated follow-up 12 mo.
Community composition
Bacteroides 21.7%Phocaeicola 18.9%Faecalibacterium 8.7%Prevotella 8.6%Alistipes 4.4%Roseburia 4.3%Parabacteroides 2.4%Lachnospira 1.1%Escherichia 1.0%Dialister 1.0%Enterocloster 0.9%Sutterella 0.8%not assigned to a genus 9.1%other genera 17.2%
Genera, mean relative abundance over 276 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 | 267 | 89% | ||||
| country | 300 | 100% | 300 | |||
| health_condition | 300 | 100% | 277 | 23 | ||
| subject_id | 300 | 100% | 300 | |||
| collection_date | 300 | 100% | 300 | |||
| health_condition_detail | 300 | 100% | 277 | 23 | ||
| timepoint_label | 300 | 100% | 300 | |||
| sex | 277 | 92% | 277 | |||
| antibiotic_exposure | 276 | 92% | 276 | |||
| age_at_collection_days | 267 | 89% | 267 |
Papers (40)
- Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. 2018 PMID 29311644 PMC6131705 own_data
- GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data. 2022 PMID 36304322 PMC9580954 own_data
- Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding. 2024 PMID 38504383 PMC10949743 own_data
- Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease. 2024 PMID 39477928 PMC11525784 own_data
- ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models. 2026 PMID 41841491 PMC12993454 own_data
35 more
- 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
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048
- Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. 2019 PMID 31370880 PMC6670193
- LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics. 2019 PMID 31881904 PMC6933643
- 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
- Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models. 2021 PMID 33947803 PMC8269207
- The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. 2021 PMID 34563136 PMC8465708
- BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes. 2021 PMID 34581602 PMC8547482
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520
- The human microbiome encodes resistance to the antidiabetic drug acarbose. 2021 PMID 34819672 PMC10258454
- 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
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- 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
- Enteral nutrition promotes the remission of colitis by gut bacteria-mediated histidine biosynthesis. 2024 PMID 38215690 PMC10827402
- Dubosiella newyorkensis modulates immune tolerance in colitis via the L-lysine-activated AhR-IDO1-Kyn pathway. 2024 PMID 38351003 PMC10864277
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. 2024 PMID 38423015 PMC10939037
- <i>Anaerostipes hadrus</i>, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. 2024 PMID 38470044 PMC11036815
- Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics. 2024 PMID 38754417 PMC11176022
- Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. 2024 PMID 38942021 PMC11293350
- Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis. 2024 PMID 39633812 PMC11614764
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- Healthy microbiome-moving towards functional interpretation. 2025 PMID 40117176 PMC11927397
- Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation. 2025 PMID 40210868 PMC11985902
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. 2025 PMID 40377187 PMC12084026
- A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people. 2025 PMID 41131367 PMC12578642
- Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol. 2025 PMID 41233306 PMC12615640
- Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota. 2025 PMID 41342600 PMC12721379
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome. 2026 PMID 41365303 PMC12853188
- Microbiota-derived IPA protects against colitis by regulating intestinal HMGCS2-mediated ketogenesis to facilitate mucosal healing. 2026 PMID 41651833 PMC12988232
- A microbiota-IPA axis facilitates intestinal stem cell-mediated regeneration in colitis through a Hopx-associated program. 2026 PMID 41741429 PMC13057028
- Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease. 2026 PMID 41945859 PMC13271634
Details
Archive description
We examined the dynamics of microbiome functionality in Inflammatory bowel disease (IBD) by profiling metagenomic and metatranscriptomic sequencing of the human gut microbiome among 100 individuals sampled over a one year period. Here, we present the first results based on the functional analysis of 78 paired metagenomes/metatranscriptomes and 222 additional metagenomes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07424251 | age_at_collection_days | 10985.5 | R2 | 0.75 | external.hmp_ihmp source | consent_age: 30; week_num: 4 |
| SAMN07424251 | antibiotic_exposure | no | R2 | 0.75 | external.hmp_ihmp source | Antibiotics: No |
| SAMN07424251 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN07424251 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN07424251 | health_condition | crohns_disease | R2 | 0.75 | external.hmp_ihmp source | diagnosis: CD |
| SAMN07424527 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07424327 | health_condition | ibd_unspecified | R4 | 0.50 | study.description | Inflammatory bowel disease (IBD) |
| SAMN07424251 | health_condition_detail | Crohn's disease | R2 | 0.75 | external.hmp_ihmp source | diagnosis: CD |
| SAMN07424527 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07424327 | health_condition_detail | All 100 individuals have IBD | R4 | 0.50 | study.description | Inflammatory bowel disease (IBD) |
| SAMN07424251 | sex | male | R2 | 0.75 | external.hmp_ihmp source | sex: Male |
| SAMN07424527 | sex | female | R2 | 0.75 | external.gmrepo source | sex: Female |
| SAMN07424251 | subject_id | M2021C1_MGX | R1 | 0.85 | sample.attr.host_subject_id | M2021C1_MGX |
| SAMN07424251 | timepoint_label | C1 | R1 | 0.70 | sample.name_rule:attr:host_subject_id | M2021C1_MGX |
Sequencing
300 runs over 300 samples · mean 2.77 Gbp per run (median 2.79 Gbp, total 831.33 Gbp; 300 runs with a base count) · layout PAIRED 300 · platform ILLUMINA 300 · models Illumina HiSeq 2000 (300) · 92% of runs with a Sandpiper profile · first public 2017-11-09
Authors (31)
Bauchinger F first · Seki D · Berry D last · Zielińska K first · Udekwu KI · Rudnicki W · Frolova A · Łabaj PP last · Wu F first · Wang Y · Mai Z · Xu Z · Li S · Li Y · Yin R · Li J · Yu Z · Wu Y · Tian X · Feng X · Huo X · Wang C · Ma X last · Vidal E first · Phanthanourak AL · Gharib A · Webel H · Assis J · Ayala-Ruano S · Cunha AF · Santos A last
Downloads
PRJNA389280.csv.gz (10.8 KB) · parquet (85.6 KB) — all 300 samples, every field with route and confidence · PRJNA389280_determinations.csv.gz (36.1 KB) — 2,620 evidence rows
Samples (300 · every field this project has values for · hover a cell for its source)
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