Gut microbiome in Lynch syndrome, longitudinal
87 stool/mucosal metagenome samples from Lynch syndrome patients, studied longitudinally to assess gut microbiome changes preceding colorectal neoplasia. machine-written summary
87 samples · 87 runs · US · Age unknown · 2020 · 3.00 Gbp / sample · cohort Structure of the Mucosal and Stool Microbiome in L
One study deposited as 2 BioProjects (218 catalog samples together): PRJNA526861 · PRJNA699934 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 87 sample values (collection date) |
| ✓ Abstract / description | 87 sample values (health condition detail) |
| ✓ Full text | 87 sample values (country) · PMC11324910, PMC7453618 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 80 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 | 87 | 100% | ||||
| country | 87 | 100% | 87 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 87 | 100% | 87 | |||
| health_condition_detail | 87 | 100% | 87 |
- Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. 2020 PMID 32240601 PMC7453618 own_data
- Metatranscriptomic analysis indicates prebiotic effect of isomalto/malto-polysaccharides on human colonic microbiota in-vitro. 2024 PMID 39143192 PMC11324910 unsure
Archive description
Changes in the gut microbiota have been associated with colorectal cancer (CRC), but it is not yet clear which potentially causal microbiome changes precede or follow CRC development. Lynch syndrome is the most common hereditary form of CRC, and its patients’ high risk of CRC development provides a setting in which microbiome changes linked to CRC can be assessed prospectively.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “mucosal and stool microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11117505 | collection_date | 2013-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2013-01-01 |
| SAMN11117505 | country | US | R3 | 0.70 | paper.fulltext.methods | Massachusetts General Hospital (MGH) or the Clinical Genetics |
| SAMN11117505 | health_condition_detail | mixed_case_control: Lynch syndrome patients; some with colectomy and CRC history | R4 | 0.50 | paper.abstract | Lynch syndrome patients using 16S rRNA |
Sequencing
87 runs over 87 samples · mean 2.98 Gbp per run (median 3.00 Gbp, total 259.13 Gbp; 87 runs with a base count) · layout SINGLE 87 · platform ILLUMINA 87 · models Illumina HiSeq 2500 (87) · 92% of runs with a Sandpiper profile · first public 2020-04-14
Authors (26)
Yan Y first · Drew DA · Markowitz A · Lloyd-Price J · Abu-Ali G · Nguyen LH · Tran C · Chung DC · Gilpin KK · Meixell D · Parziale M · Schuck M · Patel Z · Richter JM · Kelsey PB · Garrett WS · Chan AT · Stadler ZK · Huttenhower C last · Borewicz K first · Hornung B · Gu F · van der Zaal PH · Schols HA · Schaap PJ · Smidt H last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA526861.csv.gz (3.0 KB) · parquet (72.6 KB) — all 87 samples, every field with route and confidence · PRJNA526861_determinations.csv.gz (1.9 KB) — 261 evidence rows