Gut microbiome in Crohn's disease: diet and genetics
Nine samples from healthy volunteers and individuals with Crohn's disease. Pilot dietary intervention study examining sulfate-reducing bacteria abundance in response to high versus low sulfur-containing amino acid diets using 16S rRNA and shotgun sequencing. machine-written summary
9 samples · 18 runs · Age unknown · 2010 · 15.4 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 16 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5927471, PMC6708278, PMC6748593 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 16 sample values (health condition, health condition detail) · from mBodyMap |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design crossover · population healthy_control · High vs low sulfur amino acid diets, 10-14 days each
“consumed two interventional diets for 10-14 days, containing high or low SAA” — abstract:30810441 (study level; per-sample arms are in the intervention column below)
longitudinal
2 of 4 people sampled more than once (6 samples; median 3, up to 4 per person) · follow-up median 4 d (max 7 d) · median interval between samples 1 d (time from timepoint labels).
Each row is one person (2 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 8 | 89% | 8 | |||
| subject_id | 8 | 89% | 8 | |||
| health_condition_detail | 8 | 89% | 8 | |||
| timepoint_label | 8 | 89% | 8 |
- Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria. 2019 PMID 30810441 PMC6748593 own_data
- Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet. 2019 PMID 31324413 PMC6708278 own_data
- Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. 2018 PMID 29668682 PMC5927471 unsure
Archive description
The bacteria present in the intestinal tract, known as the gut microbiome, probably play a role in the pathogenesis of Crohn's disease, but the mechanism remains unclear. In this study, we propose to determine the composition of the gut microbiome associated with Crohn's disease while controlling for confounding factors known to alter the gut microbiome, such as host genetics and diet. These studies will provide a clearer vision of the types of bacteria associated with Crohn's disease and provide new insights into pathogenic mechanisms and potential therapy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.title · “Gut Microbiome in Crohn's Disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN00018629 | health_condition | crohns_disease | R2 | 0.70 | external.mbodymap source | phenotype: Crohn Disease; disease: D003424 |
| SAMN00018629 | health_condition_detail | Crohn Disease [MeSH D003424] | R2 | 0.70 | external.mbodymap source | phenotype: Crohn Disease; disease: D003424 |
| SAMN00018629 | subject_id | 275639 | R1 | 0.85 | sample.attr.gap_subject_id | 275639 |
| SAMN00018629 | timepoint_label | day 2 | R1 | 0.70 | biosample.attribute:submitted sample id | submitted sample id: 2016_d2_M1 |
Sequencing
18 runs · mean 27.4 Mbp per run (median 15.4 Mbp, total 0.49 Gbp; 18 runs with a base count) · layout SINGLE 18 · platform LS454 18 · models 454 GS FLX Titanium (18) · 0% of runs with a Sandpiper profile · first public 2010-06-01
Authors (18)
Hannigan GD first · Duhaime MB · Koutra D · Schloss PD last · Dostal Webster A first · Staley C · Hamilton MJ · Huang M · Fryxell K · Erickson R · Kabage AJ · Sadowsky MJ · Khoruts A last · Bisanz JE first · Upadhyay V · Turnbaugh JA · Ly K · Turnbaugh PJ last
Downloads
PRJNA46879.csv.gz (1019 B) · parquet (69.0 KB) — all 9 samples, every field with route and confidence · PRJNA46879_determinations.csv.gz (1005 B) — 32 evidence rows