Metagenomes in IBD vs healthy controls, Boston, case-control
960 stool metagenome samples from Boston, USA, from adults and elderly individuals with Crohn's disease, ulcerative colitis, unspecified IBD, or healthy controls, in a case-control study of disease-associated bacterial strains. machine-written summary
960 samples · 960 runs · US · Adult · 2024 · 2.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,801 sample values (age, country, health condition, health condition detail, location locality, medication, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,920 sample values (collection date, location site) · PMC11239293 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
157 of 443 people sampled more than once (674 samples; median 3, up to 14 per person) · follow-up median 13 mo (max 10.0 y) · median interval between samples 13 mo (time from age at collection). Schedule stated by the source: “Repeated stool sampling per subject implied by multiple biosamples per subject id (up to 14 samples for some subjects); no explicit timepoint labels or fixed schedule given.”.
Each row is one person (28 shown of 157); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 822 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 | 960 | 100% | ||||
| country | 960 | 100% | 960 | |||
| health_condition | 960 | 100% | 960 | |||
| subject_id | 960 | 100% | 960 | |||
| age_at_collection_days | 960 | 100% | 960 | |||
| collection_date | 960 | 100% | 960 | |||
| detailed_location | 960 | 100% | ||||
| health_condition_detail | 960 | 100% | 960 | |||
| location_locality | 960 | 100% | 960 | |||
| location_site | 960 | 100% | 960 | |||
| sex | 960 | 100% | 960 | |||
| medication | 81 | 8% | 81 |
- Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases. 2024 PMID 38917808 PMC11239293 unsure
Archive description
Gut bacteria are implicated in inflammatory bowel diseases (IBD) but the strains driving these associations are unknown. Large-scale studies of microbiome evolution could reveal the imprint of disease on gut bacteria, thus pinpointing the strains and genes that may underlie inflammation. Here, we use stool metagenomes of thousands of IBD patients and healthy controls to reconstruct 140,000 strain genotypes across most gut species, revealing hundreds of lineages enriched in IBD. We demonstrate that these strains are ancient, taxonomically diverse, and ubiquitous in humans. Moreover, disease-associated strains outcompete their healthy counterparts during inflammation, implying long-term adaptation to disease. We show that strain genetic differences map onto known axes of inflammation, including oxidative stress, nutrient biosynthesis, and immune evasion. Lastly, the loss of health-associated strains of Eggerthella lenta was predictive of fecal calprotectin, a biomarker of disease severity. Our work identifies novel reservoirs of strain diversity that may impact inflammatory disease and can be extended to other microbiome-associated diseases.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.age · “23 (n=862/960)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38601952 | age_at_collection_days | 10957.0 | R1 | 0.85 | sample.attr.age | 30 |
| SAMN38601952 | collection_date | 2010/2018 | R3 | 0.70 | paper.fulltext.methods | These samples were collected between 2010 and 2018 |
| SAMN38601952 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Boston |
| SAMN38601952 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | CD |
| SAMN38601952 | health_condition_detail | CD | R1 | 0.90 | sample.attr.diagnosis | CD |
| SAMN38601952 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston |
| SAMN38601952 | location_site | Prospective Registry in IBD Study at MGH (PRISM) | R3 | 0.70 | paper.fulltext.methods | Prospective Registry in IBD Study at MGH (PRISM) |
| SAMN38601952 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:cohort | cohort: AntiTNF |
| SAMN38601952 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN38601952 | subject_id | pub_S437 | R1 | 0.85 | sample.attr.subject | pub_S437 |
Sequencing
960 runs over 960 samples · mean 3.13 Gbp per run (median 2.70 Gbp, total 3,005.68 Gbp; 960 runs with a base count) · layout PAIRED 960 · platform ILLUMINA 960 · models Illumina HiSeq 2500 (960) · 88% of runs with a Sandpiper profile · first public 2024-06-24
Authors (9)
Kumbhari A first · Cheng TNH · Ananthakrishnan AN · Kochar B · Burke KE · Shannon K · Lau H · Xavier RJ · Smillie CS last
Downloads
PRJNA993675.csv.gz (28.0 KB) · parquet (107.5 KB) — all 960 samples, every field with route and confidence · PRJNA993675_determinations.csv.gz (51.7 KB) — 8,721 evidence rows