Fecal metagenomes and irinotecan metabolism, New York adults
Cross-sectional study of 20 fecal metagenome samples from adults in New York (17 healthy control, 3 obesity), examining gut microbiota β-glucuronidase activity and inter-individual variability in reactivating irinotecan's inactive metabolite. machine-written summary
20 samples · 20 runs · US · Age unknown · 2017 · 3.62 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 100 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 81 sample values (antibiotic exposure, health condition, location locality, location site, subject id) · PMC5665930 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 79 sample values (age, health condition, health condition detail, sex) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 15 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 | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 20 | 100% | 19 | 1 | ||
| subject_id | 20 | 100% | 20 | |||
| age_at_collection_days | 20 | 100% | 20 | |||
| antibiotic_exposure | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| detailed_location | 20 | 100% | ||||
| health_condition_detail | 20 | 100% | 20 | |||
| latitude | 20 | 100% | 20 | |||
| location_locality | 20 | 100% | 20 | |||
| location_region | 20 | 100% | 20 | |||
| location_site | 20 | 100% | 20 | |||
| longitude | 20 | 100% | 20 | |||
| sex | 20 | 100% | 20 |
- Human microbiome signatures of differential colorectal cancer drug metabolism. 2017 PMID 29104759 PMC5665930 own_data
Archive description
It is well appreciated that metabolism of irinotecan by the gut microbiota can influence efficacy and potentially produce patient-specific adverse drug responses. However, a direct connection between irinotecan metabollism and the composition of an individual’s gut microbiota has not previously been made. Here, we report the first quantitative evidence of inter-individual variability in microbiome metabolism of the inactive metabolite of irinotecan, a first-line chemotherapeutic for metastatic colorectal cancer, to its active form. We identify a high turnover microbiota metabotype with potentially elevated risk for irinotecan-dependent adverse drug responses. We link the high turnover metabotype to previously unreported microbial β-glucuronidases and suggest that inhibiting these enzymes therapeutically may decrease irinotecan-dependent adverse drug responses in targeted subsets of patients. In total, this study demonstrates that metagenomic mining of the microbiome, when combined with metabolomics, defines a non-invasive approach to develop biomarkers for colorectal cancer treatment outcomes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- host study.title · “Healthy human fecal metagenomes”
- body site study.title · “human fecal metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06220509 | age_at_collection_days | 9131.25 | R2 | 0.75 | external.gmrepo source | host_age: 25.0 |
| SAMN06220509 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | had not used antibiotics within the prior 6 months |
| SAMN06220509 | collection_date | 2015-07-07 | R1 | 0.90 | biosample.attribute:collection_date | 2015-07-07 |
| SAMN06220509 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: New York |
| SAMN06220509 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07534319 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 20 healthy individuals were recruited |
| SAMN06220509 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN06220509 | latitude | 40.7128 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7128 N 74.0059 W |
| SAMN06220509 | location_locality | Bronx | R3 | 0.70 | paper.fulltext.methods | Subjects were recruited via flyers posted at Albert Einstein College of Medicine |
| SAMN06220509 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York |
| SAMN06220509 | location_site | Albert Einstein College of Medicine | R3 | 0.70 | paper.fulltext.methods | Subjects were recruited via flyers posted at Albert Einstein College of Medicine |
| SAMN06220509 | longitude | -74.0059 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7128 N 74.0059 W |
| SAMN06220509 | sex | female | R2 | 0.75 | external.gmrepo source | sex: Female |
| SAMN06220509 | subject_id | SAMN06220509 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Fecal samples were collected from 20 healthy individuals; details of the cohort are provided in Table S1 |
Sequencing
20 runs over 20 samples · mean 3.59 Gbp per run (median 3.62 Gbp, total 71.86 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models Illumina HiSeq 2500 (20) · 75% of runs with a Sandpiper profile · first public 2017-11-09
Authors (21)
Guthrie L first · Gupta S · Daily J · Kelly L 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
Downloads
PRJNA373879.csv.gz (1.7 KB) · parquet (72.2 KB) — all 20 samples, every field with route and confidence · PRJNA373879_determinations.csv.gz (3.4 KB) — 260 evidence rows